From b7dc96e400672dbdd834d1d2d68f470a747c2992 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 30 Aug 2022 19:02:38 -0700
Subject: [PATCH 01/51] use jq for basic transformer

---
 src/transformers/opentarget_transformer.ts | 20 +++++++++++---------
 src/transformers/transformer.ts            |  2 +-
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/transformers/opentarget_transformer.ts b/src/transformers/opentarget_transformer.ts
index 85ed578..c230a56 100644
--- a/src/transformers/opentarget_transformer.ts
+++ b/src/transformers/opentarget_transformer.ts
@@ -1,14 +1,16 @@
 import BaseTransformer from "./transformer";
-
+import jq from "node-jq";
 
 export default class OpenTargetTransformer extends BaseTransformer {
-    wrap(res) {
-        res.data = res.data.map(item => {
-            if ('drug' in item && "id" in item.drug && typeof item.drug.id === "string" && item.drug.id.includes("CHEMBL")) {
-                item.drug.id = item.drug.id.split('/').slice(-1)[0];
-            }
-            return item;
-        });
-        return res;
+    async wrap(res) {
+//         res.data = res.data.map(item => {
+//             if ('drug' in item && "id" in item.drug && typeof item.drug.id === "string" && item.drug.id.includes("CHEMBL")) {
+//                 item.drug.id = item.drug.id.split('/').slice(-1)[0];
+//             }
+//             return item;
+//         });
+//         return res;
+        const filterString = '.data = [(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id |= (split("/") | last))] + [(.data | .[] | select(.drug.id == null))] + [(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL") | not))]';
+        return await jq.run(filterString, res);
     }
 }
\ No newline at end of file
diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts
index 1d845b9..8c3d59c 100644
--- a/src/transformers/transformer.ts
+++ b/src/transformers/transformer.ts
@@ -169,7 +169,7 @@ export default class BaseTransformer {
         await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
             if (Array.isArray(curieResponses) && curieResponses.length > 0) {
                 await async.eachSeries(curieResponses, async response => {
-                    const predicateResponse = this.jsonTransform(this.wrap(response));
+                    const predicateResponse = this.jsonTransform(await this.wrap(response));
                     await async.eachSeries(Object.entries(predicateResponse), async ([predicate, mappedResponses]) => {
                         if (Array.isArray(mappedResponses) && mappedResponses.length > 0) {
                             await async.eachSeries(mappedResponses, async (mappedResponse: any[]) => {

From fb67caec7b7271c930d4fd7c3407c09de21f762d Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 1 Sep 2022 17:09:18 -0700
Subject: [PATCH 02/51] simplify opentarget transformer

---
 src/transformers/opentarget_transformer.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/transformers/opentarget_transformer.ts b/src/transformers/opentarget_transformer.ts
index c230a56..d5011d8 100644
--- a/src/transformers/opentarget_transformer.ts
+++ b/src/transformers/opentarget_transformer.ts
@@ -10,7 +10,7 @@ export default class OpenTargetTransformer extends BaseTransformer {
 //             return item;
 //         });
 //         return res;
-        const filterString = '.data = [(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id |= (split("/") | last))] + [(.data | .[] | select(.drug.id == null))] + [(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL") | not))]';
+        const filterString = '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)';
         return await jq.run(filterString, res);
     }
 }
\ No newline at end of file

From 5739889e334919a6ae1ca4bc5e9061713fb5137b Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 20 Sep 2022 17:45:00 -0700
Subject: [PATCH 03/51] Create JQ Transfomer for BioLink

---
 src/index.ts                      |  4 +++-
 src/transformers/jq_transfomer.ts | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)
 create mode 100644 src/transformers/jq_transfomer.ts

diff --git a/src/index.ts b/src/index.ts
index 94ea60c..6baa25c 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -7,6 +7,7 @@ import OpenTargetTransformer from "./transformers/opentarget_transformer";
 import BaseTransformer from "./transformers/transformer";
 import TRAPITransformer from './transformers/trapi_transformer';
 import EBIProteinTransformer from './transformers/ebi_protein_transformer'
+import JQTransformer from "./transformers/jq_transfomer";
 import { BTEQueryObject } from "./types";
 const debug = require("debug")("bte:api-response-transform:index");
 export { Record } from "./record";
@@ -31,7 +32,8 @@ export class Transformer {
         } else if (api.startsWith('SEMMED')) {
             this.tf = new SemmedTransformer(this.data, this.config);
         } else if (api === 'BioLink API') {
-            this.tf = new BiolinkTransformer(this.data, this.config);
+            // this.tf = new BiolinkTransformer(this.data, this.config);
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" })
         } else if (api === 'EBI Proteins API') {
             this.tf = new EBIProteinTransformer(this.data, this.config)
         } else if (tags.includes("biothings")) {
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
new file mode 100644
index 0000000..1d6d4b1
--- /dev/null
+++ b/src/transformers/jq_transfomer.ts
@@ -0,0 +1,18 @@
+import BaseTransformer from "./transformer";
+
+const jq = require('node-jq');
+
+const filterStrings = {
+  'ebi': '(select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")',
+  'ctd': '((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}',
+  'opentarget': '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)',
+  'biolink': '[del(.associations), {associations: [select(.associations != null) | .associations | .[] | select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) | .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] ]}] | add'
+}
+
+export default class JQTransformer extends BaseTransformer {
+  async wrap (res) {
+    res = JSON.parse(await jq.run(filterStrings[this.config.type], res, { input: 'json' }));
+    console.log("THIS IS WHAT WILL BE RETURNED", res.associations[1] )
+    return res;
+  }
+}
\ No newline at end of file

From 809d73e305a49c4d4f41f109911c0f8c393017dc Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 10 Oct 2022 18:07:51 -0700
Subject: [PATCH 04/51] add comments for transfomers

---
 src/transformers/jq_transfomer.ts | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 1d6d4b1..dfd48ab 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -3,9 +3,10 @@ import BaseTransformer from "./transformer";
 const jq = require('node-jq');
 
 const filterStrings = {
-  'ebi': '(select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")',
-  'ctd': '((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}',
-  'opentarget': '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)',
+  'ebi': '(select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")', //only take comments where dbReferences type is Rhea
+  'ctd': '((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}', //Split pubMedIDs by |, take last element of disease ids after spliting by :
+  'opentarget': '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)', // split drug IDs with CHEMBL by /
+  // biolink: two steps - 1. split association object ids & take last (only for CHEMBL, REACT, HGNC), 2. take publications with PMID & for IDs take last element after splitting by :
   'biolink': '[del(.associations), {associations: [select(.associations != null) | .associations | .[] | select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) | .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] ]}] | add'
 }
 
@@ -15,4 +16,4 @@ export default class JQTransformer extends BaseTransformer {
     console.log("THIS IS WHAT WILL BE RETURNED", res.associations[1] )
     return res;
   }
-}
\ No newline at end of file
+}

From 63f2cf6c5aedd9e430dce5a4d81d344e14f8d147 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 19 Oct 2022 18:13:52 -0700
Subject: [PATCH 05/51] remove extra console log

---
 src/transformers/jq_transfomer.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 1d6d4b1..91132e7 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -12,7 +12,6 @@ const filterStrings = {
 export default class JQTransformer extends BaseTransformer {
   async wrap (res) {
     res = JSON.parse(await jq.run(filterStrings[this.config.type], res, { input: 'json' }));
-    console.log("THIS IS WHAT WILL BE RETURNED", res.associations[1] )
     return res;
   }
 }
\ No newline at end of file

From c881db057648831ca04374f70ff11442b50e3132 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 20 Oct 2022 17:17:55 -0700
Subject: [PATCH 06/51] use ebi api

---
 src/index.ts | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/index.ts b/src/index.ts
index 6baa25c..37a2d7d 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -35,7 +35,8 @@ export class Transformer {
             // this.tf = new BiolinkTransformer(this.data, this.config);
             this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" })
         } else if (api === 'EBI Proteins API') {
-            this.tf = new EBIProteinTransformer(this.data, this.config)
+            // this.tf = new EBIProteinTransformer(this.data, this.config)
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" })
         } else if (tags.includes("biothings")) {
             this.tf = new BioThingsTransformer(this.data, this.config);
         } else if (tags.includes("ctd")) {

From 452b97a15eb6f6f2bc1f52e02cabeba08f40e140 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 21 Oct 2022 17:57:06 -0700
Subject: [PATCH 07/51] Refactor JQ for cleaner filter strings & functions

---
 src/transformers/jq_transfomer.ts | 35 +++++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index b965aac..7d97b43 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -2,17 +2,40 @@ import BaseTransformer from "./transformer";
 
 const jq = require('node-jq');
 
+const functions = `
+# add JQ functions to be used globally here
+`
+
 const filterStrings = {
-  'ebi': '(select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")', //only take comments where dbReferences type is Rhea
-  'ctd': '((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}', //Split pubMedIDs by |, take last element of disease ids after spliting by :
-  'opentarget': '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)', // split drug IDs with CHEMBL by /
-  // biolink: two steps - 1. split association object ids & take last (only for CHEMBL, REACT, HGNC), 2. take publications with PMID & for IDs take last element after splitting by :
-  'biolink': '[del(.associations), {associations: [select(.associations != null) | .associations | .[] | select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) | .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] ]}] | add'
+  ebi: `
+  # only take comments where dbReferences type is Rhea
+  (select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")
+  `,
+  ctd: `
+  # Split pubMedIDs by |
+  ((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | 
+  # take last element of disease ids after spliting by :
+  ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}
+  `,
+  opentarget: `
+  # split drug IDs with CHEMBL by /
+  (.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)
+  `,
+  biolink: `
+  .associations = [
+      # take associations that aren't null
+      select(.associations != null) | .associations | .[] | 
+      # split association object ids & take last (only for CHEMBL, REACT, HGNC)
+      select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
+      # take publications with PMID & for IDs take last element after splitting by :
+      .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] 
+  ]
+  `
 }
 
 export default class JQTransformer extends BaseTransformer {
   async wrap (res) {
-    res = JSON.parse(await jq.run(filterStrings[this.config.type], res, { input: 'json' }));
+    res = JSON.parse(await jq.run(functions+"\n"+filterStrings[this.config.type], res, { input: 'json' }));
     return res;
   }
 }

From e32efd5680628b901371a549686880aa5b5ddaba Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 27 Oct 2022 18:17:53 -0700
Subject: [PATCH 08/51] Fix biolink & add tests for other transformers

---
 __test__/biolink_transformers.test.js   | 38 ++++++++++++-------------
 __test__/ctd_transformer.test.js        | 20 ++++++-------
 __test__/opentarget_transformer.test.js | 14 ++++-----
 src/jq_utils.ts                         |  7 +++++
 src/transformers/jq_transfomer.ts       | 34 ++++++++++++++--------
 5 files changed, 65 insertions(+), 48 deletions(-)
 create mode 100644 src/jq_utils.ts

diff --git a/__test__/biolink_transformers.test.js b/__test__/biolink_transformers.test.js
index 95e45e1..3eb5e26 100644
--- a/__test__/biolink_transformers.test.js
+++ b/__test__/biolink_transformers.test.js
@@ -2,7 +2,7 @@
  * @jest-environment node
  */
 
-const biolink_tf = require("../built/transformers/biolink_transformer");
+const jq_tf = require("../built/transformers/jq_transfomer");
 const fs = require("fs");
 const path = require("path");
 
@@ -22,24 +22,24 @@ describe("test biolink transformer", () => {
         }
     })
 
-    test("test biolink wrapper", () => {
-        let tf = new biolink_tf.default(input);
-        let res = tf.wrap(response);
+    test("test biolink wrapper", async () => {
+        let tf = new jq_tf.default(input, { type: "biolink" });
+        let res = await tf.wrap(response);
         expect(res.associations[0].object.HGNC).toBe("10956");
         expect(res.associations[0].publications[0].id).toBe("21685912");
         expect(res.associations[1]).not.toHaveProperty("publications");
         expect(res.associations[1]).not.toHaveProperty("provided_by");
     });
 
-    test("test biolink wrapper if no association field as root key", () => {
-        let tf = new biolink_tf.default(input);
-        let res = tf.wrap({ "data": [] });
+    test("test biolink wrapper if no association field as root key", async () => {
+        let tf = new jq_tf.default(input, { type: "biolink" });
+        let res = await tf.wrap({ "data": [] });
         expect(res).toEqual({ "data": [] })
     });
 
-    test("test biolink wrapper if no object id should be prefixed", () => {
-        const tf = new biolink_tf.default(input);
-        const res = tf.wrap(
+    test("test biolink wrapper if no object id should be prefixed", async () => {
+        const tf = new jq_tf.default(input, { type: "biolink" });
+        const res = await tf.wrap(
             {
                 associations: [
                     {
@@ -52,8 +52,8 @@ describe("test biolink transformer", () => {
         expect(res.associations[0].object.MONDO).toEqual("MONDO:12345")
     });
 
-    test("test biolink wrapper if no object field present", () => {
-        const tf = new biolink_tf.default(input);
+    test("test biolink wrapper if no object field present", async () => {
+        const tf = new jq_tf.default(input, { type: "biolink" });
         const fake_response = {
             associations: [
                 {
@@ -63,12 +63,12 @@ describe("test biolink transformer", () => {
                 }
             ]
         }
-        const res = tf.wrap(fake_response);
+        const res = await tf.wrap(fake_response);
         expect(res).toEqual(fake_response)
     });
 
-    test("test biolink wrapper if no object.id field present", () => {
-        const tf = new biolink_tf.default(input);
+    test("test biolink wrapper if no object.id field present", async () => {
+        const tf = new jq_tf.default(input, { type: "biolink" });
         const fake_response = {
             associations: [
                 {
@@ -78,13 +78,13 @@ describe("test biolink transformer", () => {
                 }
             ]
         }
-        const res = tf.wrap(fake_response);
+        const res = await tf.wrap(fake_response);
         expect(res).toEqual(fake_response)
     });
 
-    test("test biolink jsonTransform function", () => {
-        let tf = new biolink_tf.default(input);
-        const wrapped_response = tf.wrap(response);
+    test("test biolink jsonTransform function", async () => {
+        let tf = new jq_tf.default(input, { type: "biolink" });
+        const wrapped_response = await tf.wrap(response);
         let res = tf.jsonTransform(wrapped_response);
         expect(res).toHaveProperty("related_to");
         expect(res.related_to[0].HGNC).toEqual("10956");
diff --git a/__test__/ctd_transformer.test.js b/__test__/ctd_transformer.test.js
index d66a418..f599d15 100644
--- a/__test__/ctd_transformer.test.js
+++ b/__test__/ctd_transformer.test.js
@@ -2,7 +2,7 @@
  * @jest-environment node
  */
 
-const ctd_tf = require("../built/transformers/ctd_transformer");
+const jq_tf = require("../built/transformers/jq_transfomer");
 const fs = require("fs");
 const path = require("path");
 
@@ -22,36 +22,36 @@ describe("test ctd transformer", () => {
         }
     })
 
-    test("test ctd wrapper", () => {
-        let tf = new ctd_tf.default(input);
-        let res = tf.wrap(response);
+    test("test ctd wrapper", async () => {
+        let tf = new jq_tf.default(input, { type: "ctd" });
+        let res = await tf.wrap(response);
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(2);
         expect(res.data[0].PubMedIDs).toEqual(["21559390"]);
         expect(res.data[0].DiseaseID).toEqual("D008545");
     })
 
-    test("test ctd wrapper if pubmed id field is not string", () => {
-        const tf = new ctd_tf.default(input);
+    test("test ctd wrapper if pubmed id field is not string", async () => {
+        const tf = new jq_tf.default(input, { type: "ctd" });
         const fake = [
             {
                 DiseaseID: "MESH:D008545"
             }
         ]
-        const res = tf.wrap(fake);
+        const res = await tf.wrap(fake);
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(1);
         expect(res.data[0].PubMedIDs).toBeUndefined;
     })
 
-    test("test ctd wrapper if disease id field is not string", () => {
-        const tf = new ctd_tf.default(input);
+    test("test ctd wrapper if disease id field is not string", async () => {
+        const tf = new jq_tf.default(input, { type: "ctd" });
         const fake = [
             {
                 PubMedID: "12345"
             }
         ]
-        const res = tf.wrap(fake);
+        const res = await tf.wrap(fake);
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(1);
         expect(res.data[0].DiseaseIDs).toBeUndefined;
diff --git a/__test__/opentarget_transformer.test.js b/__test__/opentarget_transformer.test.js
index ade966e..591907f 100644
--- a/__test__/opentarget_transformer.test.js
+++ b/__test__/opentarget_transformer.test.js
@@ -2,7 +2,7 @@
  * @jest-environment node
  */
 
-const opentarget_tf = require("../built/transformers/opentarget_transformer");
+const jq_tf = require("../built/transformers/jq_transfomer");
 const fs = require("fs");
 const path = require("path");
 
@@ -23,15 +23,15 @@ describe("test opentarget transformer", () => {
     })
 
 // skip these tests since we're not ingesting opentargets right now
-    test.skip("test opentarget wrapper", () => {
-        let tf = new opentarget_tf.default(input);
-        let res = tf.wrap(response);
+    test.skip("test opentarget wrapper", async () => {
+        let tf = new jq_tf.default(input, { type: "opentarget" });
+        let res = await tf.wrap(response);
         expect(res).toHaveProperty("data");
         expect(res.data[0].drug.id).toEqual("CHEMBL220492");
     })
 
-    test.skip("test opentarget wrapper if id field is not chembl", () => {
-        let tf = new opentarget_tf.default(input);
+    test.skip("test opentarget wrapper if id field is not chembl", async () => {
+        let tf = new jq_tf.default(input, { type: "opentarget" });
         const fake = {
             data: [
                 {
@@ -41,7 +41,7 @@ describe("test opentarget transformer", () => {
                 }
             ]
         }
-        let res = tf.wrap(fake);
+        let res = await tf.wrap(fake);
         expect(res).toHaveProperty("data");
         expect(res.data[0].drug.id).toEqual("http://identifiers.org/drugbank/DB0001");
     })
diff --git a/src/jq_utils.ts b/src/jq_utils.ts
new file mode 100644
index 0000000..0a5c5f1
--- /dev/null
+++ b/src/jq_utils.ts
@@ -0,0 +1,7 @@
+export const functions = `
+# example increment function
+def increment: . + 1;
+
+# deletes key if empty array
+def delifempty(k): (if k == [] then del(k) | . else . end);
+`
\ No newline at end of file
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 7d97b43..905ecce 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -1,11 +1,8 @@
 import BaseTransformer from "./transformer";
+import { functions } from "../jq_utils";
 
 const jq = require('node-jq');
 
-const functions = `
-# add JQ functions to be used globally here
-`
-
 const filterStrings = {
   ebi: `
   # only take comments where dbReferences type is Rhea
@@ -22,14 +19,27 @@ const filterStrings = {
   (.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)
   `,
   biolink: `
-  .associations = [
-      # take associations that aren't null
-      select(.associations != null) | .associations | .[] | 
-      # split association object ids & take last (only for CHEMBL, REACT, HGNC)
-      select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
-      # take publications with PMID & for IDs take last element after splitting by :
-      .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)] 
-  ]
+  [
+    del(.associations),
+    {
+      associations: (
+        [
+          # take associations that aren't null
+          (select(.associations != null) | .associations | .[] | 
+          # split association object ids & take last (only for CHEMBL, REACT, HGNC)
+          select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
+          # take publications with PMID & for IDs take last element after splitting by :
+          .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)])
+          # delete publications if empty array
+          | delifempty(.publications)
+        ] +
+        # include associations with null object ids
+        [select(.associations != null) | .associations | .[] | select(.object.id == null)]
+      )
+    }
+  ] | add
+  # delete association if empty array
+  | delifempty(.associations)
   `
 }
 

From c6d23d401738936a32430f23f9d2fa9bc6d517d2 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 28 Oct 2022 17:30:45 -0700
Subject: [PATCH 09/51] Fix EBI Transfomer

---
 __test__/ebi_protein_transformer.test.js | 8 ++++----
 src/transformers/jq_transfomer.ts        | 9 ++++++++-
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/__test__/ebi_protein_transformer.test.js b/__test__/ebi_protein_transformer.test.js
index 84b2c26..31421ab 100644
--- a/__test__/ebi_protein_transformer.test.js
+++ b/__test__/ebi_protein_transformer.test.js
@@ -2,7 +2,7 @@
  * @jest-environment node
  */
 
-const ebi_tf = require("../built/transformers/ebi_protein_transformer");
+const jq_tf = require("../built/transformers/jq_transfomer");
 const fs = require("fs");
 const path = require("path");
 
@@ -22,9 +22,9 @@ describe("test EBI Protein transformer", () => {
         }
     })
 
-    test("test ebi wrapper", () => {
-        let tf = new ebi_tf.default(input);
-        let res = tf.wrap(response);
+    test("test ebi wrapper", async () => {
+        let tf = new jq_tf.default(input, { type: "ebi" });
+        let res = await tf.wrap(response);
         expect(res.comments[0].reaction.dbReferences).toHaveLength(1);
     })
 })
\ No newline at end of file
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 905ecce..ce2bd50 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -6,7 +6,14 @@ const jq = require('node-jq');
 const filterStrings = {
   ebi: `
   # only take comments where dbReferences type is Rhea
-  (select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences | .[]) |= select(.type == "Rhea")
+  [
+    del(.comments), 
+    {
+      comments: [
+        select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences = [.reaction.dbReferences | .[] | select(.type == "Rhea")]
+      ]
+    }
+  ] | add
   `,
   ctd: `
   # Split pubMedIDs by |

From c37e7c7f616b278c686397c2432013f0a6674dfc Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 28 Oct 2022 17:36:47 -0700
Subject: [PATCH 10/51] make jq strings cleaner

---
 src/transformers/jq_transfomer.ts | 44 ++++++++++++-------------------
 1 file changed, 17 insertions(+), 27 deletions(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index ce2bd50..f66184d 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -6,14 +6,9 @@ const jq = require('node-jq');
 const filterStrings = {
   ebi: `
   # only take comments where dbReferences type is Rhea
-  [
-    del(.comments), 
-    {
-      comments: [
-        select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences = [.reaction.dbReferences | .[] | select(.type == "Rhea")]
-      ]
-    }
-  ] | add
+  .comments = [
+    select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences = [.reaction.dbReferences | .[] | select(.type == "Rhea")]
+  ]
   `,
   ctd: `
   # Split pubMedIDs by |
@@ -26,25 +21,20 @@ const filterStrings = {
   (.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)
   `,
   biolink: `
-  [
-    del(.associations),
-    {
-      associations: (
-        [
-          # take associations that aren't null
-          (select(.associations != null) | .associations | .[] | 
-          # split association object ids & take last (only for CHEMBL, REACT, HGNC)
-          select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
-          # take publications with PMID & for IDs take last element after splitting by :
-          .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)])
-          # delete publications if empty array
-          | delifempty(.publications)
-        ] +
-        # include associations with null object ids
-        [select(.associations != null) | .associations | .[] | select(.object.id == null)]
-      )
-    }
-  ] | add
+  .associations = (
+    [
+      # take associations that aren't null
+      (select(.associations != null) | .associations | .[] | 
+      # split association object ids & take last (only for CHEMBL, REACT, HGNC)
+      select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
+      # take publications with PMID & for IDs take last element after splitting by :
+      .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)])
+      # delete publications if empty array
+      | delifempty(.publications)
+    ] +
+    # include associations with null object ids
+    [select(.associations != null) | .associations | .[] | select(.object.id == null)]
+  )
   # delete association if empty array
   | delifempty(.associations)
   `

From ca62d2d4e4bb3a76a95b9905de202921aa839168 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 7 Nov 2022 18:28:35 -0800
Subject: [PATCH 11/51] allow custom JQ strings from the query_operation

---
 src/index.ts                      | 10 +++++++++-
 src/transformers/jq_transfomer.ts |  3 ++-
 src/types.ts                      |  1 +
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index 37a2d7d..d86d926 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -27,7 +27,15 @@ export class Transformer {
         debug(`api name ${api}`);
         let tags = this.data.edge.query_operation.tags;
         debug(`api tags: ${tags}`);
-        if (tags.includes('bte-trapi')) {
+
+        if (!this.data.edge.query_operation.transformer) {
+          console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
+        } 
+
+        if (this.data.edge.query_operation.transformer) {
+          console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
+          this.tf = new JQTransformer(this.data, { ...this.config, custom: this.data.edge.query_operation.transformer })
+        } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);
         } else if (api.startsWith('SEMMED')) {
             this.tf = new SemmedTransformer(this.data, this.config);
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index f66184d..7529c5d 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -42,7 +42,8 @@ const filterStrings = {
 
 export default class JQTransformer extends BaseTransformer {
   async wrap (res) {
-    res = JSON.parse(await jq.run(functions+"\n"+filterStrings[this.config.type], res, { input: 'json' }));
+    if (this.config.custom) res = JSON.parse(await jq.run(functions+"\n"+this.config.custom, res, { input: 'json' }));
+    else res = JSON.parse(await jq.run(functions+"\n"+filterStrings[this.config.type], res, { input: 'json' }));
     return res;
   }
 }
diff --git a/src/types.ts b/src/types.ts
index ebbada7..762ab40 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -24,6 +24,7 @@ interface QueryOperationInterface {
     request_body: object;
     supportBatch: boolean;
     inputSeparator: string;
+    transformer: string;
 }
 
 

From e6a12cc5a5d4627ccacb4a79c5634166a4cc9b87 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 14 Nov 2022 17:52:12 -0800
Subject: [PATCH 12/51] add edge variable to be used in filter strings

---
 src/jq_utils.ts                   | 24 ++++++++++++++++++++++--
 src/transformers/jq_transfomer.ts |  6 +++---
 src/types.ts                      |  5 +++++
 3 files changed, 30 insertions(+), 5 deletions(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index 0a5c5f1..e9e9550 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -1,7 +1,27 @@
-export const functions = `
+import { JQVariable, BTEKGOperationObject } from "./types"
+
+const functions = `
 # example increment function
 def increment: . + 1;
 
 # deletes key if empty array
 def delifempty(k): (if k == [] then del(k) | . else . end);
-`
\ No newline at end of file
+`
+
+function generateVariables(variables: JQVariable[]) {
+    let variableString = '';
+    for (const variable of variables) {
+      variableString += `${variable.value} as ${variable.name} | `;
+    }
+    return variableString;
+}
+
+export function generateFilterString(filterString: string, edge: BTEKGOperationObject) {
+  const variables = [
+    {
+      name: '$edge',
+      value: JSON.stringify(edge)
+    }
+  ];
+  return `${functions}\n${generateVariables(variables)}${filterString}`
+} 
\ No newline at end of file
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 7529c5d..a7d2114 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -1,5 +1,5 @@
 import BaseTransformer from "./transformer";
-import { functions } from "../jq_utils";
+import { generateFilterString } from "../jq_utils";
 
 const jq = require('node-jq');
 
@@ -42,8 +42,8 @@ const filterStrings = {
 
 export default class JQTransformer extends BaseTransformer {
   async wrap (res) {
-    if (this.config.custom) res = JSON.parse(await jq.run(functions+"\n"+this.config.custom, res, { input: 'json' }));
-    else res = JSON.parse(await jq.run(functions+"\n"+filterStrings[this.config.type], res, { input: 'json' }));
+    if (this.config.custom) res = JSON.parse(await jq.run(generateFilterString(this.config.custom, this.edge), res, { input: 'json' }));
+    else res = JSON.parse(await jq.run(generateFilterString(filterStrings[this.config.type], this.edge), res, { input: 'json' }));
     return res;
   }
 }
diff --git a/src/types.ts b/src/types.ts
index 762ab40..38c4f6e 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -52,3 +52,8 @@ export interface BTEQueryObject {
     response: JSONDoc | JSONDoc[];
     edge: BTEKGOperationObject;
 }
+
+export interface JQVariable {
+    name: string;
+    value: string;
+}
\ No newline at end of file

From e6bc9a339add69cd553230d453ce0f64f48be8ce Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 14 Nov 2022 17:52:21 -0800
Subject: [PATCH 13/51] clean up

---
 src/index.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index d86d926..89a084b 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -28,12 +28,12 @@ export class Transformer {
         let tags = this.data.edge.query_operation.tags;
         debug(`api tags: ${tags}`);
 
-        if (!this.data.edge.query_operation.transformer) {
-          console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
-        } 
+        // if (!this.data.edge.query_operation.transformer) {
+        //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
+        // } 
 
         if (this.data.edge.query_operation.transformer) {
-          console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
+          // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
           this.tf = new JQTransformer(this.data, { ...this.config, custom: this.data.edge.query_operation.transformer })
         } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);

From 6693fe28de12c8be42e6b2f85bd57c807306d8c7 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 21 Nov 2022 18:02:11 -0800
Subject: [PATCH 14/51] start on a semmedb transformer

---
 src/jq_utils.ts                   |  3 +++
 src/transformers/jq_transfomer.ts | 33 +++++++++++++++++++++++++------
 2 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index e9e9550..71b24e0 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -6,6 +6,9 @@ def increment: . + 1;
 
 # deletes key if empty array
 def delifempty(k): (if k == [] then del(k) | . else . end);
+
+# sets inputted value to "empty" if empty array
+def remifempty: (if . == [] then empty else . end);
 `
 
 function generateVariables(variables: JQVariable[]) {
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index a7d2114..664c9f1 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -23,12 +23,14 @@ const filterStrings = {
   biolink: `
   .associations = (
     [
-      # take associations that aren't null
-      (select(.associations != null) | .associations | .[] | 
-      # split association object ids & take last (only for CHEMBL, REACT, HGNC)
-      select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
-      # take publications with PMID & for IDs take last element after splitting by :
-      .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)])
+      (
+        # take associations that aren't null
+        select(.associations != null) | .associations | .[] | 
+        # split association object ids & take last (only for CHEMBL, REACT, HGNC)
+        select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
+        # take publications with PMID & for IDs take last element after splitting by :
+        .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)]
+      )
       # delete publications if empty array
       | delifempty(.publications)
     ] +
@@ -37,6 +39,25 @@ const filterStrings = {
   )
   # delete association if empty array
   | delifempty(.associations)
+  `,
+  semmedb: `
+  # NOTE: Currently this still needs some functions from Biothings transformer so that needs to be figured out
+  map_values(
+    # checks if value is array and nonzero length
+    if (. | type) == "array" and (. | length) != 0 then 
+      [
+        # check the type for each element against edge type
+        .[] | if (.["@type"] == $edge.association.output_type) or (.["@type"] == "DiseaseOrPhenotypicFeature" and $edge.association.output_type == "Disease") then
+          # rename appropriate fields
+          (.UMLS = .umls | .pubmed = .pmid | del(.umls) | del (.pmid) | .)
+        # empty for unecessary fields
+        else empty end
+      # remove key if empty array
+      ] | remifempty
+    else 
+      empty 
+    end
+  )
   `
 }
 

From 9b5070b1a3a08e96414b6184d0abafe4474e9fa9 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 22 Nov 2022 18:02:42 -0800
Subject: [PATCH 15/51] create  jq string for pairCurieWithAPIResponse

---
 src/transformers/jq_transfomer.ts | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 664c9f1..6a12220 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -68,3 +68,29 @@ export default class JQTransformer extends BaseTransformer {
     return res;
   }
 }
+
+/* 
+  COULD BE ADDED (pairCurieWithAPIResponse for BioThings Transformer):
+  def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
+
+  {"query_operation": {"method": "get"}, "assocation": {"input_id": "test"}, "input": {"queryInputs": "woahsfd"}} as $edge | 
+
+  if $edge.query_operation.method == "post" then
+    # if response is not an array, then use response.hits
+    if (.response | type) == "array" then .response else .response.hits end |
+    reduce .[] as $item ({};
+      # if the item is notfound, then proceed to next item & keep current object
+      if ($item | keys | contains(["notfound"])) then
+        .
+      else
+        generateCurie($edge.assocation.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+      end
+    )
+  else
+    if ($edge.input | type) == "object" then
+      .response as $res | generateCurie($edge.assocation.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = $res
+    else
+      .response as $res | generateCurie($edge.assocation.input_id; $edge.input) as $curie | {} | .[$curie] = $res
+    end
+  end
+*/
\ No newline at end of file

From 90bb34474024511eff612bf102a68becb7277c01 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 28 Nov 2022 17:43:24 -0800
Subject: [PATCH 16/51] Use jq_wrap parameter

---
 src/index.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index 89a084b..c029f60 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -32,9 +32,9 @@ export class Transformer {
         //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
         // } 
 
-        if (this.data.edge.query_operation.transformer) {
+        if (this.data.edge.query_operation?.transformer?.wrap_jq) {
           // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
-          this.tf = new JQTransformer(this.data, { ...this.config, custom: this.data.edge.query_operation.transformer })
+          this.tf = new JQTransformer(this.data, { ...this.config, custom: this.data.edge.query_operation.transformer.wrap_jq })
         } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);
         } else if (api.startsWith('SEMMED')) {

From ce17e57846e7264cc3060fcbbdb32ad3022d01b3 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 28 Nov 2022 17:48:17 -0800
Subject: [PATCH 17/51] making transformer into object

---
 src/types.ts | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/types.ts b/src/types.ts
index 38c4f6e..f7bc3d3 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -14,6 +14,11 @@ interface XBTEParametersObject {
     [key: string]: string | number;
 }
 
+interface TransformerObject {
+    wrap_jq: string;
+    pair_jq: string;
+}
+
 interface QueryOperationInterface {
     path: string;
     method: string;
@@ -24,7 +29,7 @@ interface QueryOperationInterface {
     request_body: object;
     supportBatch: boolean;
     inputSeparator: string;
-    transformer: string;
+    transformer: TransformerObject;
 }
 
 

From ffaccc60020030f881481f9509748e286d1b85d6 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 28 Nov 2022 17:58:28 -0800
Subject: [PATCH 18/51] add generate curie function

---
 src/jq_utils.ts | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index 71b24e0..c341b25 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -9,6 +9,9 @@ def delifempty(k): (if k == [] then del(k) | . else . end);
 
 # sets inputted value to "empty" if empty array
 def remifempty: (if . == [] then empty else . end);
+
+# generates a curie from a type and id
+def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
 `
 
 function generateVariables(variables: JQVariable[]) {

From ac4778243653858e1488a24ee6be36e23268e27d Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 28 Nov 2022 18:16:29 -0800
Subject: [PATCH 19/51] allow pair_jq option

---
 src/index.ts                              | 10 +++++++---
 src/transformers/biothings_transformer.ts |  2 +-
 src/transformers/jq_transfomer.ts         | 15 +++++++++++----
 src/transformers/transformer.ts           | 12 ++++++++++--
 src/types.ts                              |  4 ++--
 5 files changed, 31 insertions(+), 12 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index c029f60..36f6d46 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -32,9 +32,13 @@ export class Transformer {
         //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
         // } 
 
-        if (this.data.edge.query_operation?.transformer?.wrap_jq) {
-          // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
-          this.tf = new JQTransformer(this.data, { ...this.config, custom: this.data.edge.query_operation.transformer.wrap_jq })
+        if (this.data.edge.query_operation?.transformer) {
+            // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
+            this.tf = new JQTransformer(this.data, { 
+              ...this.config, 
+              wrap: this.data.edge.query_operation.transformer.wrap_jq, 
+              pair: this.data.edge.query_operation.transformer.pair_jq 
+            })
         } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);
         } else if (api.startsWith('SEMMED')) {
diff --git a/src/transformers/biothings_transformer.ts b/src/transformers/biothings_transformer.ts
index a3170da..b7adc18 100644
--- a/src/transformers/biothings_transformer.ts
+++ b/src/transformers/biothings_transformer.ts
@@ -2,7 +2,7 @@ import BaseTransformer from "./transformer";
 import { generateCurie } from '../utils';
 
 export default class BioThingsTransformer extends BaseTransformer {
-    pairCurieWithAPIResponse() {
+    async pairCurieWithAPIResponse() {
         if (this.edge.query_operation.method === "post") {
             let res = {};
             this.data.response.map(item => {
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 6a12220..ffb66d4 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -63,10 +63,17 @@ const filterStrings = {
 
 export default class JQTransformer extends BaseTransformer {
   async wrap (res) {
-    if (this.config.custom) res = JSON.parse(await jq.run(generateFilterString(this.config.custom, this.edge), res, { input: 'json' }));
-    else res = JSON.parse(await jq.run(generateFilterString(filterStrings[this.config.type], this.edge), res, { input: 'json' }));
+    if (this.config.wrap) res = JSON.parse(await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: 'json' }));
+    else if (filterStrings[this.config.type]) res = JSON.parse(await jq.run(generateFilterString(filterStrings[this.config.type], this.edge), res, { input: 'json' }));
+    else res = super.wrap(res);
+
     return res;
   }
+
+  async pairCurieWithAPIResponse () {
+    if (this.config.pair) return JSON.parse(await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: 'json' }));
+    return super.pairCurieWithAPIResponse();
+  }
 }
 
 /* 
@@ -88,9 +95,9 @@ export default class JQTransformer extends BaseTransformer {
     )
   else
     if ($edge.input | type) == "object" then
-      .response as $res | generateCurie($edge.assocation.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = $res
+      .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
     else
-      .response as $res | generateCurie($edge.assocation.input_id; $edge.input) as $curie | {} | .[$curie] = $res
+      .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = [$res]
     end
   end
 */
\ No newline at end of file
diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts
index 8c3d59c..18c7777 100644
--- a/src/transformers/transformer.ts
+++ b/src/transformers/transformer.ts
@@ -23,7 +23,7 @@ export default class BaseTransformer {
     /**
      * Create an object with key representing input, and value representing the output of API
      */
-    pairCurieWithAPIResponse() {
+    async pairCurieWithAPIResponse() {
         let input = generateCurie(
             this.edge.association.input_id,
             this.edge.input.hasOwnProperty('queryInputs') ? this.edge.input["queryInputs"] : this.edge.input as string
@@ -33,6 +33,14 @@ export default class BaseTransformer {
         };
     }
 
+    /*
+      if 4edge.input | keys | contains(["queryInputs"]) then
+        {[generateCurie($edge.assocation.input_id, $edge.input.queryInputs)]: .response}
+      else
+        {[generateCurie($edge.assocation.input_id, $edge.input)]: .response}
+      end
+    */
+
     /**
      * Wrapper functions to transform API response before passing to JSON Transformer
      * @return {Object} - key is curie representing input, value is an array of outputs.
@@ -164,7 +172,7 @@ export default class BaseTransformer {
      */
     async transform() {
         let transformedRecords = [];
-        let responses = this.pairCurieWithAPIResponse();
+        let responses = await this.pairCurieWithAPIResponse();
 
         await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
             if (Array.isArray(curieResponses) && curieResponses.length > 0) {
diff --git a/src/types.ts b/src/types.ts
index f7bc3d3..6152b00 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -15,8 +15,8 @@ interface XBTEParametersObject {
 }
 
 interface TransformerObject {
-    wrap_jq: string;
-    pair_jq: string;
+    wrap_jq?: string;
+    pair_jq?: string;
 }
 
 interface QueryOperationInterface {

From 27f631ec10e14426cbea369f3433c336dcf506a7 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 2 Dec 2022 18:45:29 -0800
Subject: [PATCH 20/51] fix checking for transformer

---
 src/index.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/index.ts b/src/index.ts
index 36f6d46..e6bbb56 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -32,7 +32,7 @@ export class Transformer {
         //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
         // } 
 
-        if (this.data.edge.query_operation?.transformer) {
+        if (this.data.edge.query_operation?.transformer?.pair_jq || this.data.edge.query_operation?.transformer?.wrap_jq) {
             // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
             this.tf = new JQTransformer(this.data, { 
               ...this.config, 

From c897fd04a3e02eceace0c6bd7ae634e370000da2 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 5 Dec 2022 17:52:56 -0800
Subject: [PATCH 21/51] More merge changes from main

---
 __test__/base_transformer.test.ts        |  4 ++--
 __test__/biolink_transformers.test.ts    |  2 +-
 __test__/biothings_transformer.test.ts   | 12 ++++++------
 __test__/ebi_protein_transformer.test.ts |  2 +-
 __test__/semmed_transformer.test.ts      |  6 +++---
 __test__/transformers.test.ts            |  4 ++--
 6 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/__test__/base_transformer.test.ts b/__test__/base_transformer.test.ts
index aa0bf0b..d7e8286 100644
--- a/__test__/base_transformer.test.ts
+++ b/__test__/base_transformer.test.ts
@@ -21,9 +21,9 @@ describe("test base transformer", () => {
         }
     })
 
-    test("Test pairInputWithAPIResponse function", () => {
+    test("Test pairInputWithAPIResponse function", async () => {
         const tf = new base_tf(input, {});
-        const res = tf.pairCurieWithAPIResponse();
+        const res = await tf.pairCurieWithAPIResponse();
         expect(res).toHaveProperty("DOID:9562");
         expect(res["DOID:9562"]).toHaveLength(1);
     })
diff --git a/__test__/biolink_transformers.test.ts b/__test__/biolink_transformers.test.ts
index f364ed4..c00be7c 100644
--- a/__test__/biolink_transformers.test.ts
+++ b/__test__/biolink_transformers.test.ts
@@ -84,7 +84,7 @@ describe("test biolink transformer", () => {
     test("test biolink jsonTransform function", async () => {
         let tf = new jq_tf(input, { type: "biolink" });
         const wrapped_response = await tf.wrap(response);
-        let res = tf.jsonTransform(wrapped_response);
+        let res: JSONDoc = tf.jsonTransform(wrapped_response);
         expect(res).toHaveProperty("related_to");
         expect(res.related_to[0].HGNC).toEqual("10956");
         expect(res.related_to[0].pubmed[0]).toEqual("21685912");
diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts
index 6308e39..a730bf7 100644
--- a/__test__/biothings_transformer.test.ts
+++ b/__test__/biothings_transformer.test.ts
@@ -21,9 +21,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
+        test("test biothings wrapper", async () => {
             let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(2);
             expect(res).toHaveProperty("DRUGBANK:DB00188");
             expect(res["DRUGBANK:DB00188"]).toHaveLength(2);
@@ -46,9 +46,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
+        test("test biothings wrapper", async () => {
             let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("NCBIGene:1017");
             expect(res["NCBIGene:1017"]).toHaveLength(1);
@@ -78,9 +78,9 @@ describe("test biothings transformer", () => {
             }
         })
 
-        test("test biothings wrapper", () => {
+        test("test biothings wrapper", async () => {
             let tf = new biothings_tf(input, {});
-            let res = tf.pairCurieWithAPIResponse();
+            let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("PUBCHEM:11373846");
             expect(res["PUBCHEM:11373846"]).toHaveLength(1);
diff --git a/__test__/ebi_protein_transformer.test.ts b/__test__/ebi_protein_transformer.test.ts
index ea2344c..d2ad3f6 100644
--- a/__test__/ebi_protein_transformer.test.ts
+++ b/__test__/ebi_protein_transformer.test.ts
@@ -19,7 +19,7 @@ describe("test EBI Protein transformer", () => {
   });
 
   test("test ebi wrapper", async () => {
-    let tf = new jq_tf(input, {});
+    let tf = new jq_tf(input, {type: "ebi"});
     let res = await tf.wrap(response);
     expect(res.comments[0].reaction.dbReferences).toHaveLength(1);
   });
diff --git a/__test__/semmed_transformer.test.ts b/__test__/semmed_transformer.test.ts
index 7fd7c26..674c247 100644
--- a/__test__/semmed_transformer.test.ts
+++ b/__test__/semmed_transformer.test.ts
@@ -76,9 +76,9 @@ describe("test semmed transformer", () => {
         }
     });
 
-    test("test semmed pairCurieWithAPIResponse", () => {
+    test("test semmed pairCurieWithAPIResponse", async () => {
         let tf = new semmed_tf(input, {});
-        let res = tf.pairCurieWithAPIResponse();
+        let res = await tf.pairCurieWithAPIResponse();
         expect(res["UMLS:C1332823"][0]['umls']).toBe("C1332823");
         expect(res).toHaveProperty('UMLS:C1332823');
         expect(res["UMLS:123"]).toBeUndefined();
@@ -98,7 +98,7 @@ describe("test semmed transformer", () => {
 
     test("add edge info", async () => {
         let tf = new semmed_tf(input, {});
-        let res = tf.pairCurieWithAPIResponse();
+        let res = await tf.pairCurieWithAPIResponse();
         let rec = res["UMLS:C1332823"][0];
         rec = tf.wrap(rec);
         let result = await tf.formatRecords("UMLS:C1332823", rec["positively_regulates"][0]);
diff --git a/__test__/transformers.test.ts b/__test__/transformers.test.ts
index 3a61919..75b4ecc 100644
--- a/__test__/transformers.test.ts
+++ b/__test__/transformers.test.ts
@@ -147,9 +147,9 @@ describe("test biothings transformer", () => {
         }
     });
 
-    test("test biothings pairCurieWithAPIResponse", () => {
+    test("test biothings pairCurieWithAPIResponse", async () => {
         let tf = new biothings_tf(input, {});
-        let res = tf.pairCurieWithAPIResponse();
+        let res = await tf.pairCurieWithAPIResponse();
         expect(res["UMLS:C1332823"][0]['umls']).toBe("C1332823");
         expect(res).toHaveProperty('UMLS:C1332823');
         expect(res["123"]).toBeUndefined();

From 1c63e48d723cc1c55f9b6d90c7269b88e201c2b7 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 5 Dec 2022 17:54:37 -0800
Subject: [PATCH 22/51] Add jq filter string for pairCurie biothings

---
 src/transformers/biothings_transformer.ts | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/transformers/biothings_transformer.ts b/src/transformers/biothings_transformer.ts
index cec7629..683ae1b 100644
--- a/src/transformers/biothings_transformer.ts
+++ b/src/transformers/biothings_transformer.ts
@@ -2,6 +2,26 @@ import BaseTransformer from "./transformer";
 import { generateCurie } from '../utils';
 
 export default class BioThingsTransformer extends BaseTransformer {
+    // IN JQ:
+    // if $edge.query_operation.method == "post" then
+    //   # if response is not an array, then use response.hits
+    //   if (.response | type) == "array" then .response else .response.hits end |
+    //   reduce .[] as $item ({};
+    //     # if the item is notfound, then proceed to next item & keep current object
+    //     if ($item | keys | contains(["notfound"])) then
+    //       .
+    //     else
+    //       generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+    //     end
+    //   )
+    // else
+    //   if ($edge.input | type) == "object" then
+    //     .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = $res
+    //   else
+    //     .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = $res
+    //   end
+    // end
+
     async pairCurieWithAPIResponse() {
         if (this.edge.query_operation.method === "post") {
             let res = {};

From 0ce7b80098077bb4b9e1e5f927af0d59d193fd5a Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 5 Jan 2023 18:19:53 -0800
Subject: [PATCH 23/51] initial list filter function (untested)

---
 src/jq_utils.ts | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index c341b25..5222c61 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -12,6 +12,24 @@ def remifempty: (if . == [] then empty else . end);
 
 # generates a curie from a type and id
 def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
+
+# checks if object meets any filter string
+def any_filter(filter_strs):
+. as $obj | . |= foreach filter_strs as $filter_str (false; . or $obj.[filter_str | split(":") | first] == filter_str | split(":") | last; .);
+
+# checks if object meets all filter strings
+def all_filter(filter_strs):
+. as $obj | . |= foreach filter_strs as $filter_str (false; . or $obj.[filter_str | split(":") | first] == filter_str | split(":") | last; .);
+
+# filters the list that is supplied on all conditions
+def list_filter_all(filter_strs): 
+(filter_str | split(":") | first) as $key | (filter_str | split(":") | last) as $value |
+. |= [.[] | if . | all_filter(filter_strs) then . else empty end];
+
+# filters the list that is supplied on any conditions
+def list_filter_any(filter_strs): 
+(filter_str | split(":") | first) as $key | (filter_str | split(":") | last) as $value |
+. |= [.[] | if . | any_filter(filter_strs) then . else empty end];
 `
 
 function generateVariables(variables: JQVariable[]) {

From d5e985ea7b440900f4314f7356c6a59c3a89bf2c Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 6 Jan 2023 17:42:32 -0800
Subject: [PATCH 24/51] Fix list filter all/any

---
 src/jq_utils.ts | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index 5222c61..97256ca 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -15,21 +15,17 @@ def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end
 
 # checks if object meets any filter string
 def any_filter(filter_strs):
-. as $obj | . |= foreach filter_strs as $filter_str (false; . or $obj.[filter_str | split(":") | first] == filter_str | split(":") | last; .);
+. as $obj | foreach (filter_strs | .[]) as $filter_str (false; . or (($obj | .[$filter_str | split(":") | first]) == ($filter_str | split(":") | last)); .);
 
 # checks if object meets all filter strings
 def all_filter(filter_strs):
-. as $obj | . |= foreach filter_strs as $filter_str (false; . or $obj.[filter_str | split(":") | first] == filter_str | split(":") | last; .);
+. as $obj | foreach (filter_strs | .[]) as $filter_str (true; . and (($obj | .[$filter_str | split(":") | first]) == ($filter_str | split(":") | last)); .);
 
 # filters the list that is supplied on all conditions
-def list_filter_all(filter_strs): 
-(filter_str | split(":") | first) as $key | (filter_str | split(":") | last) as $value |
-. |= [.[] | if . | all_filter(filter_strs) then . else empty end];
+def list_filter_all(filter_strs): [.[] | if . | all_filter(filter_strs) then . else empty end];
 
 # filters the list that is supplied on any conditions
-def list_filter_any(filter_strs): 
-(filter_str | split(":") | first) as $key | (filter_str | split(":") | last) as $value |
-. |= [.[] | if . | any_filter(filter_strs) then . else empty end];
+def list_filter_any(filter_strs): [.[] | if . | any_filter(filter_strs) then . else empty end];
 `
 
 function generateVariables(variables: JQVariable[]) {

From c00c5afc6a0a00d0388c3b712cceffa9c8d303af Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 6 Jan 2023 18:15:23 -0800
Subject: [PATCH 25/51] nesting

---
 src/jq_utils.ts | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index 97256ca..dcac114 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -13,19 +13,23 @@ def remifempty: (if . == [] then empty else . end);
 # generates a curie from a type and id
 def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
 
+# getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity)
+def get_nested_field(field):
+. as $obj | reduce (field | split(".") | .[]) as $subfield ($obj; .[$subfield]?);
+
 # checks if object meets any filter string
 def any_filter(filter_strs):
-. as $obj | foreach (filter_strs | .[]) as $filter_str (false; . or (($obj | .[$filter_str | split(":") | first]) == ($filter_str | split(":") | last)); .);
+. as $obj | reduce (filter_strs | .[]) as $filter_str (false; . or (($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)));
 
 # checks if object meets all filter strings
 def all_filter(filter_strs):
-. as $obj | foreach (filter_strs | .[]) as $filter_str (true; . and (($obj | .[$filter_str | split(":") | first]) == ($filter_str | split(":") | last)); .);
+. as $obj | reduce (filter_strs | .[]) as $filter_str (true; . and (($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)));
 
 # filters the list that is supplied on all conditions
-def list_filter_all(filter_strs): [.[] | if . | all_filter(filter_strs) then . else empty end];
+def list_filter_all(filter_strs): if (. | type) == "array" then [.[] | if . | all_filter(filter_strs) then . else empty end] else empty end;
 
 # filters the list that is supplied on any conditions
-def list_filter_any(filter_strs): [.[] | if . | any_filter(filter_strs) then . else empty end];
+def list_filter_any(filter_strs): if (. | type) == "array" then [.[] | if . | any_filter(filter_strs) then . else empty end] else empty end;
 `
 
 function generateVariables(variables: JQVariable[]) {

From 2bace62c7ee644304ec9dcd6c5d327b5617677af Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Fri, 6 Jan 2023 18:22:42 -0800
Subject: [PATCH 26/51] add node-jq dependency

---
 package.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 39d5e7b..558cd41 100644
--- a/package.json
+++ b/package.json
@@ -54,7 +54,8 @@
     "common-path-prefix": "^3.0.0",
     "husky": "^4.3.8",
     "jsonata": "^1.8.4",
-    "lodash": "^4.17.21"
+    "lodash": "^4.17.21",
+    "node-jq": "^2.3.4"
   },
   "husky": {
     "hooks": {

From 9e541c6f17204da0d7b6b0efba5af1dd06833233 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 12 Jan 2023 17:19:26 -0800
Subject: [PATCH 27/51] Multiple allowed values for list_filter_all

---
 src/jq_utils.ts | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index dcac114..3558daf 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -19,11 +19,21 @@ def get_nested_field(field):
 
 # checks if object meets any filter string
 def any_filter(filter_strs):
-. as $obj | reduce (filter_strs | .[]) as $filter_str (false; . or (($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)));
+. as $obj | reduce (filter_strs | .[]) as $filter_str (
+  false; 
+  . or (
+    ($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)
+  )
+);
 
 # checks if object meets all filter strings
 def all_filter(filter_strs):
-. as $obj | reduce (filter_strs | .[]) as $filter_str (true; . and (($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)));
+. as $obj | reduce (filter_strs | .[]) as $filter_str (
+  true; 
+  . and (
+    $obj | any_filter([$filter_str | split(":") | last | split(",") | .[] | ($filter_str | split(":") | first) + ":" + .])
+  )
+);
 
 # filters the list that is supplied on all conditions
 def list_filter_all(filter_strs): if (. | type) == "array" then [.[] | if . | all_filter(filter_strs) then . else empty end] else empty end;

From 78aecaf7d65a0e3f2e1fa236139856925ff26fea Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 14 Mar 2023 21:03:06 -0700
Subject: [PATCH 28/51] Fix ctd
 https://github.com/biothings/BioThings_Explorer_TRAPI/issues/583

---
 src/index.ts                      | 2 +-
 src/transformers/jq_transfomer.ts | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index e6bbb56..1a486f8 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -52,7 +52,7 @@ export class Transformer {
         } else if (tags.includes("biothings")) {
             this.tf = new BioThingsTransformer(this.data, this.config);
         } else if (tags.includes("ctd")) {
-            this.tf = new CTDTransformer(this.data, this.config);
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" });
         } else if (tags.includes("opentarget")) {
             this.tf = new OpenTargetTransformer(this.data, this.config)
         } else {
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index ffb66d4..7e59884 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -13,8 +13,10 @@ const filterStrings = {
   ctd: `
   # Split pubMedIDs by |
   ((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | 
+  ((.[] | select(.PubMedIds != null) | .PubMedIds) |= split("|")) | 
   # take last element of disease ids after spliting by :
-  ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) | {data: .}
+  ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) |
+  ((.[] | select(.DiseaseId != null) | .DiseaseId) |= (split(":") | last)) | {data: .}
   `,
   opentarget: `
   # split drug IDs with CHEMBL by /

From a59b35a7f2c5030dd82ae9c1ecc1f7a814652773 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 14 Mar 2023 22:25:35 -0700
Subject: [PATCH 29/51] handle direct evidence split by |

---
 src/transformers/jq_transfomer.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 7e59884..b383832 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -14,6 +14,8 @@ const filterStrings = {
   # Split pubMedIDs by |
   ((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | 
   ((.[] | select(.PubMedIds != null) | .PubMedIds) |= split("|")) | 
+  # Split Direct Evidence by |
+  ((.[] | select(.DirectEvidence != null) | .DirectEvidence) |= split("|")) | 
   # take last element of disease ids after spliting by :
   ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) |
   ((.[] | select(.DiseaseId != null) | .DiseaseId) |= (split(":") | last)) | {data: .}

From 3df9e405e5e80e8314b8a78506f5049c8819c245 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 22 Mar 2023 18:04:03 -0700
Subject: [PATCH 30/51] biothings support

---
 src/index.ts                      |  4 +-
 src/transformers/jq_transfomer.ts | 71 +++++++++++--------------------
 2 files changed, 27 insertions(+), 48 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index 1a486f8..4348587 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -41,8 +41,6 @@ export class Transformer {
             })
         } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);
-        } else if (api.startsWith('SEMMED')) {
-            this.tf = new SemmedTransformer(this.data, this.config);
         } else if (api === 'BioLink API') {
             // this.tf = new BiolinkTransformer(this.data, this.config);
             this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" })
@@ -50,7 +48,7 @@ export class Transformer {
             // this.tf = new EBIProteinTransformer(this.data, this.config)
             this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" })
         } else if (tags.includes("biothings")) {
-            this.tf = new BioThingsTransformer(this.data, this.config);
+            this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" })
         } else if (tags.includes("ctd")) {
             this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" });
         } else if (tags.includes("opentarget")) {
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index b383832..cb2c518 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -3,7 +3,7 @@ import { generateFilterString } from "../jq_utils";
 
 const jq = require('node-jq');
 
-const filterStrings = {
+const filterStringsWrap = {
   ebi: `
   # only take comments where dbReferences type is Rhea
   .comments = [
@@ -43,49 +43,11 @@ const filterStrings = {
   )
   # delete association if empty array
   | delifempty(.associations)
-  `,
-  semmedb: `
-  # NOTE: Currently this still needs some functions from Biothings transformer so that needs to be figured out
-  map_values(
-    # checks if value is array and nonzero length
-    if (. | type) == "array" and (. | length) != 0 then 
-      [
-        # check the type for each element against edge type
-        .[] | if (.["@type"] == $edge.association.output_type) or (.["@type"] == "DiseaseOrPhenotypicFeature" and $edge.association.output_type == "Disease") then
-          # rename appropriate fields
-          (.UMLS = .umls | .pubmed = .pmid | del(.umls) | del (.pmid) | .)
-        # empty for unecessary fields
-        else empty end
-      # remove key if empty array
-      ] | remifempty
-    else 
-      empty 
-    end
-  )
   `
 }
 
-export default class JQTransformer extends BaseTransformer {
-  async wrap (res) {
-    if (this.config.wrap) res = JSON.parse(await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: 'json' }));
-    else if (filterStrings[this.config.type]) res = JSON.parse(await jq.run(generateFilterString(filterStrings[this.config.type], this.edge), res, { input: 'json' }));
-    else res = super.wrap(res);
-
-    return res;
-  }
-
-  async pairCurieWithAPIResponse () {
-    if (this.config.pair) return JSON.parse(await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: 'json' }));
-    return super.pairCurieWithAPIResponse();
-  }
-}
-
-/* 
-  COULD BE ADDED (pairCurieWithAPIResponse for BioThings Transformer):
-  def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
-
-  {"query_operation": {"method": "get"}, "assocation": {"input_id": "test"}, "input": {"queryInputs": "woahsfd"}} as $edge | 
-
+const filterStringsPair = {
+  biothings: `
   if $edge.query_operation.method == "post" then
     # if response is not an array, then use response.hits
     if (.response | type) == "array" then .response else .response.hits end |
@@ -94,14 +56,33 @@ export default class JQTransformer extends BaseTransformer {
       if ($item | keys | contains(["notfound"])) then
         .
       else
-        generateCurie($edge.assocation.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+        generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
       end
     )
   else
     if ($edge.input | type) == "object" then
-      .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
+      .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = $res
     else
-      .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = [$res]
+      .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = $res
     end
   end
-*/
\ No newline at end of file
+  `,
+  ctd: ``
+}
+
+export default class JQTransformer extends BaseTransformer {
+  async wrap (res) {
+    if (this.config.wrap) res = JSON.parse(await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: 'json' }));
+    else if (filterStringsWrap[this.config.type]) res = JSON.parse(await jq.run(generateFilterString(filterStringsWrap[this.config.type], this.edge), res, { input: 'json' }));
+    else res = super.wrap(res);
+
+    return res;
+  }
+
+  async pairCurieWithAPIResponse () {
+    if (this.config.pair) return JSON.parse(await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: 'json' }));
+    else if (filterStringsPair[this.config.type]) return JSON.parse(await jq.run(generateFilterString(filterStringsPair[this.config.type], this.edge), this.data, { input: 'json' }));
+
+    return super.pairCurieWithAPIResponse();
+  }
+}
\ No newline at end of file

From 4fd7e3187d0b32bcc094470cf8ddc964c3d002c0 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 22 Mar 2023 18:08:15 -0700
Subject: [PATCH 31/51] add ctd pair

---
 src/transformers/jq_transfomer.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index cb2c518..61c2ec0 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -67,7 +67,7 @@ const filterStringsPair = {
     end
   end
   `,
-  ctd: ``
+  ctd: `reduce (.response | .[]) as $item ({}; .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] = [] + .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] + [$item]) | map_values([.])`
 }
 
 export default class JQTransformer extends BaseTransformer {

From 934eb368d31a7beae5daa4f94ec6e508dc4de35f Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 23 Mar 2023 19:24:19 -0700
Subject: [PATCH 32/51] spelling fixes

---
 src/transformers/transformer.ts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts
index fb156d5..460d122 100644
--- a/src/transformers/transformer.ts
+++ b/src/transformers/transformer.ts
@@ -34,10 +34,10 @@ export default class BaseTransformer {
     }
 
     /*
-      if 4edge.input | keys | contains(["queryInputs"]) then
-        {[generateCurie($edge.assocation.input_id, $edge.input.queryInputs)]: .response}
+      if $edge.input | keys | contains(["queryInputs"]) then
+        {[generateCurie($edge.association.input_id, $edge.input.queryInputs)]: .response}
       else
-        {[generateCurie($edge.assocation.input_id, $edge.input)]: .response}
+        {[generateCurie($edge.association.input_id, $edge.input)]: .response}
       end
     */
 

From 8a6ac89da3b2ea11c396861d1575399679acc1ce Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 28 Mar 2023 18:30:50 -0700
Subject: [PATCH 33/51] remove disease id parsing from ctd

---
 src/transformers/jq_transfomer.ts | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 61c2ec0..af2ce26 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -16,9 +16,7 @@ const filterStringsWrap = {
   ((.[] | select(.PubMedIds != null) | .PubMedIds) |= split("|")) | 
   # Split Direct Evidence by |
   ((.[] | select(.DirectEvidence != null) | .DirectEvidence) |= split("|")) | 
-  # take last element of disease ids after spliting by :
-  ((.[] | select(.DiseaseID != null) | .DiseaseID) |= (split(":") | last)) |
-  ((.[] | select(.DiseaseId != null) | .DiseaseId) |= (split(":") | last)) | {data: .}
+  {data: .}
   `,
   opentarget: `
   # split drug IDs with CHEMBL by /
@@ -85,4 +83,4 @@ export default class JQTransformer extends BaseTransformer {
 
     return super.pairCurieWithAPIResponse();
   }
-}
\ No newline at end of file
+}

From 9fbcb38dc527136cb67b21b29d7510a22dfe72b1 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 28 Mar 2023 18:36:22 -0700
Subject: [PATCH 34/51] test fix

---
 __test__/ctd_transformer.test.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/__test__/ctd_transformer.test.ts b/__test__/ctd_transformer.test.ts
index 16590bb..7d9b9f7 100644
--- a/__test__/ctd_transformer.test.ts
+++ b/__test__/ctd_transformer.test.ts
@@ -25,7 +25,7 @@ describe("test ctd transformer", () => {
         expect(res).toHaveProperty("data");
         expect(res.data).toHaveLength(2);
         expect(res.data[0].PubMedIDs).toEqual(["21559390"]);
-        expect(res.data[0].DiseaseID).toEqual("D008545");
+        expect(res.data[0].DiseaseID).toEqual("MESH:D008545");
     })
 
     test("test ctd wrapper if pubmed id field is not string", async () => {

From ea9db147795f69884ef05983c4f038a511a60772 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 29 Mar 2023 17:37:23 -0700
Subject: [PATCH 35/51] fix
 https://github.com/biothings/BioThings_Explorer_TRAPI/issues/592

---
 src/jq_utils.ts                   | 6 ++++++
 src/transformers/jq_transfomer.ts | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index 3558daf..2ce8b64 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -4,6 +4,9 @@ const functions = `
 # example increment function
 def increment: . + 1;
 
+# converts value to array if not already
+def toArray: if (. | type) == "array" then . else [.] end;
+
 # deletes key if empty array
 def delifempty(k): (if k == [] then del(k) | . else . end);
 
@@ -13,6 +16,9 @@ def remifempty: (if . == [] then empty else . end);
 # generates a curie from a type and id
 def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
 
+# generates a curie from a type and id [string] (by checking queryInputs)
+def generateCurieWithInputs(idType; id; queryInputs): reduce (queryInputs | toArray | .[]) as $input (""; if (id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
+
 # getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity)
 def get_nested_field(field):
 . as $obj | reduce (field | split(".") | .[]) as $subfield ($obj; .[$subfield]?);
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index af2ce26..589fadd 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -54,7 +54,7 @@ const filterStringsPair = {
       if ($item | keys | contains(["notfound"])) then
         .
       else
-        generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
       end
     )
   else

From f49766ca9d836454b9fd635ca103d9fef82cd8fb Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 2 Aug 2023 15:29:47 -0700
Subject: [PATCH 36/51] fix generateCurieWithInputs to handle array

---
 src/jq_utils.ts | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index 2ce8b64..c7ef400 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -13,11 +13,14 @@ def delifempty(k): (if k == [] then del(k) | . else . end);
 # sets inputted value to "empty" if empty array
 def remifempty: (if . == [] then empty else . end);
 
+# gets first element of array (if array)
+def getfirst: if (. | type) == "array" then .[0] else . end;
+
 # generates a curie from a type and id
-def generateCurie(idType; id): if (id | type) == "array" then id[0] else id end | split(":") | last | idType + ":" + .;
+def generateCurie(idType; id): id | getfirst | split(":") | last | idType + ":" + .;
 
 # generates a curie from a type and id [string] (by checking queryInputs)
-def generateCurieWithInputs(idType; id; queryInputs): reduce (queryInputs | toArray | .[]) as $input (""; if (id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
+def generateCurieWithInputs(idType; id; queryInputs): (id | getfirst) as $id | reduce (queryInputs | toArray | .[]) as $input (""; if ($id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
 
 # getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity)
 def get_nested_field(field):
@@ -64,4 +67,4 @@ export function generateFilterString(filterString: string, edge: BTEKGOperationO
     }
   ];
   return `${functions}\n${generateVariables(variables)}${filterString}`
-} 
\ No newline at end of file
+} 

From 55b48c998eb9975f8369ccc0dd040453fa5748d8 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 2 Aug 2023 15:32:34 -0700
Subject: [PATCH 37/51] migrate biothings transformer test to jq

---
 __test__/biothings_transformer.test.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts
index a730bf7..ea211ef 100644
--- a/__test__/biothings_transformer.test.ts
+++ b/__test__/biothings_transformer.test.ts
@@ -1,5 +1,5 @@
 
-import biothings_tf from "../src/transformers/biothings_transformer";
+import jq_tf from "../src/transformers/jq_transfomer";
 import {describe, expect, test} from '@jest/globals';
 import fs from "fs";
 import path from "path";
@@ -22,7 +22,7 @@ describe("test biothings transformer", () => {
         })
 
         test("test biothings wrapper", async () => {
-            let tf = new biothings_tf(input, {});
+            let tf = new jq_tf(input, {type: "biothings"});
             let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(2);
             expect(res).toHaveProperty("DRUGBANK:DB00188");
@@ -47,7 +47,7 @@ describe("test biothings transformer", () => {
         })
 
         test("test biothings wrapper", async () => {
-            let tf = new biothings_tf(input, {});
+            let tf = new jq_tf(input, {type: "biothings"});
             let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("NCBIGene:1017");
@@ -79,7 +79,7 @@ describe("test biothings transformer", () => {
         })
 
         test("test biothings wrapper", async () => {
-            let tf = new biothings_tf(input, {});
+            let tf = new jq_tf(input, {type: "biothings"});
             let res = await tf.pairCurieWithAPIResponse();
             expect(Object.keys(res)).toHaveLength(1);
             expect(res).toHaveProperty("PUBCHEM:11373846");

From f2fc0d638782cf44756ca93ed957562a230170f0 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 2 Aug 2023 15:37:11 -0700
Subject: [PATCH 38/51] update biothings test more for jq

---
 __test__/biothings_transformer.test.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts
index ea211ef..9cb98f4 100644
--- a/__test__/biothings_transformer.test.ts
+++ b/__test__/biothings_transformer.test.ts
@@ -55,7 +55,7 @@ describe("test biothings transformer", () => {
         })
 
         test("test biothings transform", async () => {
-            let tf = new biothings_tf(input, {});
+            let tf = new jq_tf(input, {type: "biothings"});
             let res = await tf.transform();
             expect(res).toHaveLength(27);
             expect(res[0]).not.toHaveProperty('pubmed');

From 7e3b524f9b2533e213b6de578771aff656c73bc0 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 2 Aug 2023 15:41:03 -0700
Subject: [PATCH 39/51] add back semmed transformer

---
 src/index.ts | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/index.ts b/src/index.ts
index 4348587..1289948 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -41,6 +41,8 @@ export class Transformer {
             })
         } else if (tags.includes('bte-trapi')) {
             this.tf = new TRAPITransformer(this.data, this.config);
+        } else if (api.startsWith('SEMMED')) {
+            this.tf = new SemmedTransformer(this.data, this.config);
         } else if (api === 'BioLink API') {
             // this.tf = new BiolinkTransformer(this.data, this.config);
             this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" })

From 76b52e211012aebda978b807f4478a4c696d68bd Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 2 Aug 2023 16:05:11 -0700
Subject: [PATCH 40/51] update biothings jq

---
 src/transformers/jq_transfomer.ts | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
index 589fadd..472e4ad 100644
--- a/src/transformers/jq_transfomer.ts
+++ b/src/transformers/jq_transfomer.ts
@@ -54,14 +54,18 @@ const filterStringsPair = {
       if ($item | keys | contains(["notfound"])) then
         .
       else
-        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
+        if $edge.input | type == "object" and $edge.input.queryInputs | type == "object" then
+          generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
+        else
+          generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+        end
       end
     )
   else
     if ($edge.input | type) == "object" then
-      .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = $res
+      .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
     else
-      .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = $res
+      .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = [$res]
     end
   end
   `,

From 77f6c7fe597de4eb52b74f7a0f73aee972f7a633 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 14 Sep 2023 17:40:47 -0700
Subject: [PATCH 41/51] clean up files

---
 src/transformers/biothings_transformer.ts  | 20 --------------------
 src/transformers/opentarget_transformer.ts |  7 -------
 2 files changed, 27 deletions(-)

diff --git a/src/transformers/biothings_transformer.ts b/src/transformers/biothings_transformer.ts
index 683ae1b..cec7629 100644
--- a/src/transformers/biothings_transformer.ts
+++ b/src/transformers/biothings_transformer.ts
@@ -2,26 +2,6 @@ import BaseTransformer from "./transformer";
 import { generateCurie } from '../utils';
 
 export default class BioThingsTransformer extends BaseTransformer {
-    // IN JQ:
-    // if $edge.query_operation.method == "post" then
-    //   # if response is not an array, then use response.hits
-    //   if (.response | type) == "array" then .response else .response.hits end |
-    //   reduce .[] as $item ({};
-    //     # if the item is notfound, then proceed to next item & keep current object
-    //     if ($item | keys | contains(["notfound"])) then
-    //       .
-    //     else
-    //       generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
-    //     end
-    //   )
-    // else
-    //   if ($edge.input | type) == "object" then
-    //     .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = $res
-    //   else
-    //     .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = $res
-    //   end
-    // end
-
     async pairCurieWithAPIResponse() {
         if (this.edge.query_operation.method === "post") {
             let res = {};
diff --git a/src/transformers/opentarget_transformer.ts b/src/transformers/opentarget_transformer.ts
index d5011d8..69e13a9 100644
--- a/src/transformers/opentarget_transformer.ts
+++ b/src/transformers/opentarget_transformer.ts
@@ -3,13 +3,6 @@ import jq from "node-jq";
 
 export default class OpenTargetTransformer extends BaseTransformer {
     async wrap(res) {
-//         res.data = res.data.map(item => {
-//             if ('drug' in item && "id" in item.drug && typeof item.drug.id === "string" && item.drug.id.includes("CHEMBL")) {
-//                 item.drug.id = item.drug.id.split('/').slice(-1)[0];
-//             }
-//             return item;
-//         });
-//         return res;
         const filterString = '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)';
         return await jq.run(filterString, res);
     }

From 237524581fdbf2ac1449ad599e05304378213f68 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 18 Sep 2023 14:08:48 -0400
Subject: [PATCH 42/51] fix: typo, mv jq string to data/, ts formatting

---
 __test__/biolink_transformers.test.ts    |  2 +-
 __test__/biothings_transformer.test.ts   |  2 +-
 __test__/ctd_transformer.test.ts         |  2 +-
 __test__/ebi_protein_transformer.test.ts |  2 +-
 __test__/opentarget_transformer.test.ts  |  2 +-
 data/jq/pair/biothings.jq                | 22 ++++++
 data/jq/pair/ctd.jq                      |  1 +
 data/jq/wrap/biolink.jq                  | 18 +++++
 data/jq/wrap/ctd.jq                      |  6 ++
 data/jq/wrap/ebi.jq                      |  4 ++
 data/jq/wrap/opentarget.jq               |  2 +
 src/index.ts                             |  2 +-
 src/transformers/jq_transfomer.ts        | 90 ------------------------
 src/transformers/jq_transformer.ts       | 57 +++++++++++++++
 14 files changed, 116 insertions(+), 96 deletions(-)
 create mode 100644 data/jq/pair/biothings.jq
 create mode 100644 data/jq/pair/ctd.jq
 create mode 100644 data/jq/wrap/biolink.jq
 create mode 100644 data/jq/wrap/ctd.jq
 create mode 100644 data/jq/wrap/ebi.jq
 create mode 100644 data/jq/wrap/opentarget.jq
 delete mode 100644 src/transformers/jq_transfomer.ts
 create mode 100644 src/transformers/jq_transformer.ts

diff --git a/__test__/biolink_transformers.test.ts b/__test__/biolink_transformers.test.ts
index c00be7c..cd1d8e1 100644
--- a/__test__/biolink_transformers.test.ts
+++ b/__test__/biolink_transformers.test.ts
@@ -1,6 +1,6 @@
 import {describe, expect, test} from '@jest/globals';
 
-import jq_tf from "../built/transformers/jq_transfomer";
+import jq_tf from "../built/transformers/jq_transformer";
 import fs from "fs";
 import path from "path";
 import { JSONDoc } from '../src/json_transform/types';
diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts
index 9cb98f4..8b3719a 100644
--- a/__test__/biothings_transformer.test.ts
+++ b/__test__/biothings_transformer.test.ts
@@ -1,5 +1,5 @@
 
-import jq_tf from "../src/transformers/jq_transfomer";
+import jq_tf from "../src/transformers/jq_transformer";
 import {describe, expect, test} from '@jest/globals';
 import fs from "fs";
 import path from "path";
diff --git a/__test__/ctd_transformer.test.ts b/__test__/ctd_transformer.test.ts
index 7d9b9f7..089ef2e 100644
--- a/__test__/ctd_transformer.test.ts
+++ b/__test__/ctd_transformer.test.ts
@@ -1,7 +1,7 @@
 import {describe, expect, test} from '@jest/globals';
 import fs from "fs";
 import path from "path";
-import jq_tf from "../built/transformers/jq_transfomer";
+import jq_tf from "../built/transformers/jq_transformer";
 
 describe("test ctd transformer", () => {
 
diff --git a/__test__/ebi_protein_transformer.test.ts b/__test__/ebi_protein_transformer.test.ts
index d2ad3f6..f3bc9a6 100644
--- a/__test__/ebi_protein_transformer.test.ts
+++ b/__test__/ebi_protein_transformer.test.ts
@@ -1,7 +1,7 @@
 import { describe, expect, test } from "@jest/globals";
 import fs from "fs";
 import path from "path";
-import jq_tf from "../src/transformers/jq_transfomer";
+import jq_tf from "../src/transformers/jq_transformer";
 
 describe("test EBI Protein transformer", () => {
   let response;
diff --git a/__test__/opentarget_transformer.test.ts b/__test__/opentarget_transformer.test.ts
index fe38203..470316f 100644
--- a/__test__/opentarget_transformer.test.ts
+++ b/__test__/opentarget_transformer.test.ts
@@ -1,5 +1,5 @@
 import {describe, expect, test} from '@jest/globals';
-import jq_tf from "../built/transformers/jq_transfomer";
+import jq_tf from "../built/transformers/jq_transformer";
 import fs from "fs";
 import path from "path";
 
diff --git a/data/jq/pair/biothings.jq b/data/jq/pair/biothings.jq
new file mode 100644
index 0000000..00d25b8
--- /dev/null
+++ b/data/jq/pair/biothings.jq
@@ -0,0 +1,22 @@
+if $edge.query_operation.method == "post" then
+  # if response is not an array, then use response.hits
+  if (.response | type) == "array" then .response else .response.hits end |
+  reduce .[] as $item ({};
+    # if the item is notfound, then proceed to next item & keep current object
+    if ($item | keys | contains(["notfound"])) then
+      .
+    else
+      if $edge.input | type == "object" and $edge.input.queryInputs | type == "object" then
+        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
+      else
+        generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+      end
+    end
+  )
+else
+  if ($edge.input | type) == "object" then
+    .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
+  else
+    .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = [$res]
+  end
+end
diff --git a/data/jq/pair/ctd.jq b/data/jq/pair/ctd.jq
new file mode 100644
index 0000000..830c945
--- /dev/null
+++ b/data/jq/pair/ctd.jq
@@ -0,0 +1 @@
+reduce (.response | .[]) as $item ({}; .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] = [] + .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] + [$item]) | map_values([.])
diff --git a/data/jq/wrap/biolink.jq b/data/jq/wrap/biolink.jq
new file mode 100644
index 0000000..696d9d1
--- /dev/null
+++ b/data/jq/wrap/biolink.jq
@@ -0,0 +1,18 @@
+.associations = (
+  [
+    (
+      # take associations that aren't null
+      select(.associations != null) | .associations | .[] | 
+      # split association object ids & take last (only for CHEMBL, REACT, HGNC)
+      select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
+      # take publications with PMID & for IDs take last element after splitting by :
+      .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)]
+    )
+    # delete publications if empty array
+    | delifempty(.publications)
+  ] +
+  # include associations with null object ids
+  [select(.associations != null) | .associations | .[] | select(.object.id == null)]
+)
+# delete association if empty array
+| delifempty(.associations)
diff --git a/data/jq/wrap/ctd.jq b/data/jq/wrap/ctd.jq
new file mode 100644
index 0000000..7ffd766
--- /dev/null
+++ b/data/jq/wrap/ctd.jq
@@ -0,0 +1,6 @@
+# Split pubMedIDs by |
+((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | 
+((.[] | select(.PubMedIds != null) | .PubMedIds) |= split("|")) | 
+# Split Direct Evidence by |
+((.[] | select(.DirectEvidence != null) | .DirectEvidence) |= split("|")) | 
+{data: .}
diff --git a/data/jq/wrap/ebi.jq b/data/jq/wrap/ebi.jq
new file mode 100644
index 0000000..7494d30
--- /dev/null
+++ b/data/jq/wrap/ebi.jq
@@ -0,0 +1,4 @@
+# only take comments where dbReferences type is Rhea
+.comments = [
+  select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences = [.reaction.dbReferences | .[] | select(.type == "Rhea")]
+]
diff --git a/data/jq/wrap/opentarget.jq b/data/jq/wrap/opentarget.jq
new file mode 100644
index 0000000..b437ee1
--- /dev/null
+++ b/data/jq/wrap/opentarget.jq
@@ -0,0 +1,2 @@
+# split drug IDs with CHEMBL by /
+(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)
diff --git a/src/index.ts b/src/index.ts
index 1289948..9d5b1cc 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -7,7 +7,7 @@ import OpenTargetTransformer from "./transformers/opentarget_transformer";
 import BaseTransformer from "./transformers/transformer";
 import TRAPITransformer from './transformers/trapi_transformer';
 import EBIProteinTransformer from './transformers/ebi_protein_transformer'
-import JQTransformer from "./transformers/jq_transfomer";
+import JQTransformer from "./transformers/jq_transformer";
 import { BTEQueryObject } from "./types";
 const debug = require("debug")("bte:api-response-transform:index");
 export { Record } from "./record";
diff --git a/src/transformers/jq_transfomer.ts b/src/transformers/jq_transfomer.ts
deleted file mode 100644
index 472e4ad..0000000
--- a/src/transformers/jq_transfomer.ts
+++ /dev/null
@@ -1,90 +0,0 @@
-import BaseTransformer from "./transformer";
-import { generateFilterString } from "../jq_utils";
-
-const jq = require('node-jq');
-
-const filterStringsWrap = {
-  ebi: `
-  # only take comments where dbReferences type is Rhea
-  .comments = [
-    select(.comments != null) | .comments | .[] | select(.reaction != null) | .reaction.dbReferences = [.reaction.dbReferences | .[] | select(.type == "Rhea")]
-  ]
-  `,
-  ctd: `
-  # Split pubMedIDs by |
-  ((.[] | select(.PubMedIDs != null) | .PubMedIDs) |= split("|")) | 
-  ((.[] | select(.PubMedIds != null) | .PubMedIds) |= split("|")) | 
-  # Split Direct Evidence by |
-  ((.[] | select(.DirectEvidence != null) | .DirectEvidence) |= split("|")) | 
-  {data: .}
-  `,
-  opentarget: `
-  # split drug IDs with CHEMBL by /
-  (.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)
-  `,
-  biolink: `
-  .associations = (
-    [
-      (
-        # take associations that aren't null
-        select(.associations != null) | .associations | .[] | 
-        # split association object ids & take last (only for CHEMBL, REACT, HGNC)
-        select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
-        # take publications with PMID & for IDs take last element after splitting by :
-        .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)]
-      )
-      # delete publications if empty array
-      | delifempty(.publications)
-    ] +
-    # include associations with null object ids
-    [select(.associations != null) | .associations | .[] | select(.object.id == null)]
-  )
-  # delete association if empty array
-  | delifempty(.associations)
-  `
-}
-
-const filterStringsPair = {
-  biothings: `
-  if $edge.query_operation.method == "post" then
-    # if response is not an array, then use response.hits
-    if (.response | type) == "array" then .response else .response.hits end |
-    reduce .[] as $item ({};
-      # if the item is notfound, then proceed to next item & keep current object
-      if ($item | keys | contains(["notfound"])) then
-        .
-      else
-        if $edge.input | type == "object" and $edge.input.queryInputs | type == "object" then
-          generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
-        else
-          generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
-        end
-      end
-    )
-  else
-    if ($edge.input | type) == "object" then
-      .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
-    else
-      .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = [$res]
-    end
-  end
-  `,
-  ctd: `reduce (.response | .[]) as $item ({}; .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] = [] + .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] + [$item]) | map_values([.])`
-}
-
-export default class JQTransformer extends BaseTransformer {
-  async wrap (res) {
-    if (this.config.wrap) res = JSON.parse(await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: 'json' }));
-    else if (filterStringsWrap[this.config.type]) res = JSON.parse(await jq.run(generateFilterString(filterStringsWrap[this.config.type], this.edge), res, { input: 'json' }));
-    else res = super.wrap(res);
-
-    return res;
-  }
-
-  async pairCurieWithAPIResponse () {
-    if (this.config.pair) return JSON.parse(await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: 'json' }));
-    else if (filterStringsPair[this.config.type]) return JSON.parse(await jq.run(generateFilterString(filterStringsPair[this.config.type], this.edge), this.data, { input: 'json' }));
-
-    return super.pairCurieWithAPIResponse();
-  }
-}
diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
new file mode 100644
index 0000000..861c621
--- /dev/null
+++ b/src/transformers/jq_transformer.ts
@@ -0,0 +1,57 @@
+import BaseTransformer from "./transformer";
+import { generateFilterString } from "../jq_utils";
+import fs from "fs";
+import Path from "path";
+
+import * as jq from "node-jq"; // If converted to import, ts compile breaks it (imports default as undefined)
+import { JSONDoc } from "../json_transform/types";
+
+// Get prefab JQ strings from data/jq
+const filterStringsWrap = Object.fromEntries(
+  fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/wrap`)).map(file => {
+    const filePath = Path.resolve(`${__dirname}/../../data/jq/wrap/${file}`);
+    return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })];
+  }),
+);
+
+const filterStringsPair = Object.fromEntries(
+  fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/pair`)).map(file => {
+    const filePath = Path.resolve(`${__dirname}/../../data/jq/pair/${file}`);
+    return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })];
+  }),
+);
+
+export default class JQTransformer extends BaseTransformer {
+  // TODO more specific typing?
+  async wrap(res: JSONDoc | JSONDoc[]): Promise<JSONDoc | JSONDoc[]> {
+    if (this.config.wrap)
+      res = JSON.parse(
+        (await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: "json" })) as string,
+      );
+    else if (filterStringsWrap[this.config.type])
+      res = JSON.parse(
+        (await jq.run(generateFilterString(filterStringsWrap[this.config.type], this.edge), res, {
+          input: "json",
+        })) as string,
+      );
+    else res = super.wrap(res);
+
+    return res;
+  }
+
+  // TODO more specific typing?
+  async pairCurieWithAPIResponse(): Promise<JSONDoc> {
+    if (this.config.pair)
+      return JSON.parse(
+        (await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: "json" })) as string,
+      );
+    else if (filterStringsPair[this.config.type])
+      return JSON.parse(
+        (await jq.run(generateFilterString(filterStringsPair[this.config.type], this.edge), this.data, {
+          input: "json",
+        })) as string,
+      );
+
+    return super.pairCurieWithAPIResponse();
+  }
+}

From f9a9689e779e881c829eb3407931c7878f1a5ce9 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 18 Sep 2023 17:41:10 -0700
Subject: [PATCH 43/51] Fix handling of biothings JQ,
 biothings/biothings_explorer#489

---
 data/jq/pair/biothings.jq | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/jq/pair/biothings.jq b/data/jq/pair/biothings.jq
index 00d25b8..eec14bc 100644
--- a/data/jq/pair/biothings.jq
+++ b/data/jq/pair/biothings.jq
@@ -1,4 +1,4 @@
-if $edge.query_operation.method == "post" then
+if $edge.query_operation._method == "post" then
   # if response is not an array, then use response.hits
   if (.response | type) == "array" then .response else .response.hits end |
   reduce .[] as $item ({};
@@ -6,7 +6,7 @@ if $edge.query_operation.method == "post" then
     if ($item | keys | contains(["notfound"])) then
       .
     else
-      if $edge.input | type == "object" and $edge.input.queryInputs | type == "object" then
+      if $edge.input | type == "object" then
         generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
       else
         generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]

From e729a8a144ef903724715c7574ec05253a678b66 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 28 Sep 2023 17:27:47 -0700
Subject: [PATCH 44/51] better typing

---
 src/json_transform/types.ts        | 4 ++++
 src/transformers/jq_transformer.ts | 5 ++---
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/json_transform/types.ts b/src/json_transform/types.ts
index 475f3e5..bf5fe2e 100644
--- a/src/json_transform/types.ts
+++ b/src/json_transform/types.ts
@@ -17,4 +17,8 @@ export interface BaseTransformedObject {
 export interface JSONDoc {
     [key1: string]: any;
     [key2: number]: any;
+}
+
+export interface PairedResponse {
+    [curie: string]: JSONDoc[]
 }
\ No newline at end of file
diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
index 861c621..320811d 100644
--- a/src/transformers/jq_transformer.ts
+++ b/src/transformers/jq_transformer.ts
@@ -4,7 +4,7 @@ import fs from "fs";
 import Path from "path";
 
 import * as jq from "node-jq"; // If converted to import, ts compile breaks it (imports default as undefined)
-import { JSONDoc } from "../json_transform/types";
+import { JSONDoc, PairedResponse } from "../json_transform/types";
 
 // Get prefab JQ strings from data/jq
 const filterStringsWrap = Object.fromEntries(
@@ -39,8 +39,7 @@ export default class JQTransformer extends BaseTransformer {
     return res;
   }
 
-  // TODO more specific typing?
-  async pairCurieWithAPIResponse(): Promise<JSONDoc> {
+  async pairCurieWithAPIResponse(): Promise<PairedResponse> {
     if (this.config.pair)
       return JSON.parse(
         (await jq.run(generateFilterString(this.config.pair, this.edge), this.data, { input: "json" })) as string,

From 7ab4e7486bae568ffb8b72cef0465a978aeaef0c Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 28 Sep 2023 18:02:13 -0700
Subject: [PATCH 45/51] fix most tests

---
 __test__/data/biothings/drug_response_example_edge.json | 2 +-
 __test__/data/biothings/mychem_example_edge.json        | 2 +-
 __test__/data/biothings/mygene_example_edge.json        | 2 +-
 data/jq/pair/biothings.jq                               | 4 ++--
 src/transformers/jq_transformer.ts                      | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/__test__/data/biothings/drug_response_example_edge.json b/__test__/data/biothings/drug_response_example_edge.json
index 16456cb..4b6da4f 100644
--- a/__test__/data/biothings/drug_response_example_edge.json
+++ b/__test__/data/biothings/drug_response_example_edge.json
@@ -8,7 +8,7 @@
             "size": "1000"
         },
         "_supportBatch": false,
-        "method": "get",
+        "_method": "get",
         "_pathParams": [],
         "_server": "https://biothings.ncats.io/drug_response_kp",
         "_path": "/query",
diff --git a/__test__/data/biothings/mychem_example_edge.json b/__test__/data/biothings/mychem_example_edge.json
index 2dce07d..47d58b9 100644
--- a/__test__/data/biothings/mychem_example_edge.json
+++ b/__test__/data/biothings/mychem_example_edge.json
@@ -17,7 +17,7 @@
         },
         "_supportBatch": true,
         "_inputSeparator": ",",
-        "method": "post",
+        "_method": "post",
         "_pathParams": [],
         "_server": "https://mychem.info/v1",
         "_path": "/query",
diff --git a/__test__/data/biothings/mygene_example_edge.json b/__test__/data/biothings/mygene_example_edge.json
index 36d44e2..b01b575 100644
--- a/__test__/data/biothings/mygene_example_edge.json
+++ b/__test__/data/biothings/mygene_example_edge.json
@@ -12,7 +12,7 @@
         },
         "_supportBatch": true,
         "_inputSeparator": ",",
-        "method": "post",
+        "_method": "post",
         "_pathParams": [],
         "_server": "https://mygene.info/v3",
         "_path": "/query",
diff --git a/data/jq/pair/biothings.jq b/data/jq/pair/biothings.jq
index eec14bc..cf57f40 100644
--- a/data/jq/pair/biothings.jq
+++ b/data/jq/pair/biothings.jq
@@ -9,7 +9,7 @@ if $edge.query_operation._method == "post" then
       if $edge.input | type == "object" then
         generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input.queryInputs) as $curie | .[$curie] = .[$curie] + [$item]
       else
-        generateCurie($edge.association.input_id; $item.query) as $curie | .[$curie] = .[$curie] + [$item]
+        generateCurieWithInputs($edge.association.input_id; $item.query; $edge.input | toArray) as $curie | .[$curie] = .[$curie] + [$item]
       end
     end
   )
@@ -17,6 +17,6 @@ else
   if ($edge.input | type) == "object" then
     .response as $res | generateCurie($edge.association.input_id; $edge.input.queryInputs) as $curie | {} | .[$curie] = [$res]
   else
-    .response as $res | generateCurie($edge.association.input_id; $edge.input) as $curie | {} | .[$curie] = [$res]
+    .response as $res | generateCurie($edge.association.input_id; ($edge.input | toArray)[0]) as $curie | {} | .[$curie] = [$res]
   end
 end
diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
index 320811d..1489fde 100644
--- a/src/transformers/jq_transformer.ts
+++ b/src/transformers/jq_transformer.ts
@@ -23,7 +23,7 @@ const filterStringsPair = Object.fromEntries(
 
 export default class JQTransformer extends BaseTransformer {
   // TODO more specific typing?
-  async wrap(res: JSONDoc | JSONDoc[]): Promise<JSONDoc | JSONDoc[]> {
+  async wrap(res: JSONDoc | JSONDoc[]): Promise<JSONDoc> {
     if (this.config.wrap)
       res = JSON.parse(
         (await jq.run(generateFilterString(this.config.wrap, this.edge), res, { input: "json" })) as string,

From 1e3844d0d1b5bd1f0a64e1416e21c82c4c27b6da Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Tue, 3 Oct 2023 16:43:14 -0400
Subject: [PATCH 46/51] chore: move jq utils string to data/

---
 data/jq/utils.jq | 48 +++++++++++++++++++++++++++++++
 src/jq_utils.ts  | 75 +++++++++---------------------------------------
 2 files changed, 62 insertions(+), 61 deletions(-)
 create mode 100644 data/jq/utils.jq

diff --git a/data/jq/utils.jq b/data/jq/utils.jq
new file mode 100644
index 0000000..220755c
--- /dev/null
+++ b/data/jq/utils.jq
@@ -0,0 +1,48 @@
+# example increment function
+def increment: . + 1;
+
+# converts value to array if not already
+def toArray: if (. | type) == "array" then . else [.] end;
+
+# deletes key if empty array
+def delifempty(k): (if k == [] then del(k) | . else . end);
+
+# sets inputted value to "empty" if empty array
+def remifempty: (if . == [] then empty else . end);
+
+# gets first element of array (if array)
+def getfirst: if (. | type) == "array" then .[0] else . end;
+
+# generates a curie from a type and id
+def generateCurie(idType; id): id | getfirst | split(":") | last | idType + ":" + .;
+
+# generates a curie from a type and id [string] (by checking queryInputs)
+def generateCurieWithInputs(idType; id; queryInputs): (id | getfirst) as $id | reduce (queryInputs | toArray | .[]) as $input (""; if ($id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
+
+# getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity)
+def get_nested_field(field):
+. as $obj | reduce (field | split(".") | .[]) as $subfield ($obj; .[$subfield]?);
+
+# checks if object meets any filter string
+def any_filter(filter_strs):
+. as $obj | reduce (filter_strs | .[]) as $filter_str (
+  false; 
+  . or (
+    ($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)
+  )
+);
+
+# checks if object meets all filter strings
+def all_filter(filter_strs):
+. as $obj | reduce (filter_strs | .[]) as $filter_str (
+  true; 
+  . and (
+    $obj | any_filter([$filter_str | split(":") | last | split(",") | .[] | ($filter_str | split(":") | first) + ":" + .])
+  )
+);
+
+# filters the list that is supplied on all conditions
+def list_filter_all(filter_strs): if (. | type) == "array" then [.[] | if . | all_filter(filter_strs) then . else empty end] else empty end;
+
+# filters the list that is supplied on any conditions
+def list_filter_any(filter_strs): if (. | type) == "array" then [.[] | if . | any_filter(filter_strs) then . else empty end] else empty end;
diff --git a/src/jq_utils.ts b/src/jq_utils.ts
index c7ef400..d6c4d7b 100644
--- a/src/jq_utils.ts
+++ b/src/jq_utils.ts
@@ -1,70 +1,23 @@
-import { JQVariable, BTEKGOperationObject } from "./types"
+import { JQVariable, BTEKGOperationObject } from "./types";
+import Path from "path";
+import fs from "fs";
 
-const functions = `
-# example increment function
-def increment: . + 1;
-
-# converts value to array if not already
-def toArray: if (. | type) == "array" then . else [.] end;
-
-# deletes key if empty array
-def delifempty(k): (if k == [] then del(k) | . else . end);
-
-# sets inputted value to "empty" if empty array
-def remifempty: (if . == [] then empty else . end);
-
-# gets first element of array (if array)
-def getfirst: if (. | type) == "array" then .[0] else . end;
-
-# generates a curie from a type and id
-def generateCurie(idType; id): id | getfirst | split(":") | last | idType + ":" + .;
-
-# generates a curie from a type and id [string] (by checking queryInputs)
-def generateCurieWithInputs(idType; id; queryInputs): (id | getfirst) as $id | reduce (queryInputs | toArray | .[]) as $input (""; if ($id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
-
-# getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity)
-def get_nested_field(field):
-. as $obj | reduce (field | split(".") | .[]) as $subfield ($obj; .[$subfield]?);
-
-# checks if object meets any filter string
-def any_filter(filter_strs):
-. as $obj | reduce (filter_strs | .[]) as $filter_str (
-  false; 
-  . or (
-    ($obj | get_nested_field($filter_str | split(":") | first)) == ($filter_str | split(":") | last)
-  )
-);
-
-# checks if object meets all filter strings
-def all_filter(filter_strs):
-. as $obj | reduce (filter_strs | .[]) as $filter_str (
-  true; 
-  . and (
-    $obj | any_filter([$filter_str | split(":") | last | split(",") | .[] | ($filter_str | split(":") | first) + ":" + .])
-  )
-);
-
-# filters the list that is supplied on all conditions
-def list_filter_all(filter_strs): if (. | type) == "array" then [.[] | if . | all_filter(filter_strs) then . else empty end] else empty end;
-
-# filters the list that is supplied on any conditions
-def list_filter_any(filter_strs): if (. | type) == "array" then [.[] | if . | any_filter(filter_strs) then . else empty end] else empty end;
-`
+const functions = fs.readFileSync(Path.resolve(`${__dirname}/../data/jq/utils.jq`), { encoding: "utf8" });
 
 function generateVariables(variables: JQVariable[]) {
-    let variableString = '';
-    for (const variable of variables) {
-      variableString += `${variable.value} as ${variable.name} | `;
-    }
-    return variableString;
+  let variableString = "";
+  for (const variable of variables) {
+    variableString += `${variable.value} as ${variable.name} | `;
+  }
+  return variableString;
 }
 
 export function generateFilterString(filterString: string, edge: BTEKGOperationObject) {
   const variables = [
     {
-      name: '$edge',
-      value: JSON.stringify(edge)
-    }
+      name: "$edge",
+      value: JSON.stringify(edge),
+    },
   ];
-  return `${functions}\n${generateVariables(variables)}${filterString}`
-} 
+  return `${functions}\n${generateVariables(variables)}${filterString}`;
+}

From 7df862e79a2aa3a09a354e209bde18d6c8984a11 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Tue, 3 Oct 2023 16:43:34 -0400
Subject: [PATCH 47/51] fix: ctd jq pair function

---
 data/jq/pair/ctd.jq | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/data/jq/pair/ctd.jq b/data/jq/pair/ctd.jq
index 830c945..017fba1 100644
--- a/data/jq/pair/ctd.jq
+++ b/data/jq/pair/ctd.jq
@@ -1 +1,18 @@
-reduce (.response | .[]) as $item ({}; .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] = [] + .[generateCurie($edge.association.input_id; $item.Input | ascii_upcase)] + [$item]) | map_values([.])
+reduce (.response | .[]) as $item (
+  {}; .[generateCurie($edge.association.input_id; (
+    if ($edge.input | type) == "object" then
+      ($edge.input.queryInputs | toArray)[] | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
+    else
+      ($edge.input | toArray) | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
+    end
+  ))] = [] 
+  + .[generateCurie($edge.association.input_id; (
+    if ($edge.input | type) == "object" then
+    ($edge.input.queryInputs | toArray)[] | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
+    else
+    ($edge.input | toArray) | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
+    end
+  ))] 
+  + [$item]
+) | map_values([.])
+# TODO: current setup doesn't error, but only grabs one item.

From 00f7c6e40242989b7fdbd82830b68f564a6325ba Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 12 Oct 2023 13:06:21 -0400
Subject: [PATCH 48/51] style: indent 2

---
 src/index.ts | 94 ++++++++++++++++++++++++++--------------------------
 1 file changed, 47 insertions(+), 47 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index 9d5b1cc..0ed1f0c 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -5,62 +5,62 @@ import CTDTransformer from "./transformers/ctd_transformer";
 import SemmedTransformer from "./transformers/semmed_transformer";
 import OpenTargetTransformer from "./transformers/opentarget_transformer";
 import BaseTransformer from "./transformers/transformer";
-import TRAPITransformer from './transformers/trapi_transformer';
-import EBIProteinTransformer from './transformers/ebi_protein_transformer'
+import TRAPITransformer from "./transformers/trapi_transformer";
+import EBIProteinTransformer from "./transformers/ebi_protein_transformer";
 import JQTransformer from "./transformers/jq_transformer";
 import { BTEQueryObject } from "./types";
 const debug = require("debug")("bte:api-response-transform:index");
 export { Record } from "./record";
 
 export class Transformer {
-    private data: BTEQueryObject;
-    private tf: BaseTransformer;
-    config: any;
-    constructor(data: BTEQueryObject, config: any) {
-        this.data = data;
-        this.config = config;
-        this.route();
-    }
+  private data: BTEQueryObject;
+  private tf: BaseTransformer;
+  config: any;
+  constructor(data: BTEQueryObject, config: any) {
+    this.data = data;
+    this.config = config;
+    this.route();
+  }
 
-    route() {
-        let api = this.data.edge.association.api_name;
-        debug(`api name ${api}`);
-        let tags = this.data.edge.query_operation.tags;
-        debug(`api tags: ${tags}`);
+  route() {
+    const api = this.data.edge.association.api_name;
+    debug(`api name ${api}`);
+    const tags = this.data.edge.query_operation.tags;
+    debug(`api tags: ${tags}`);
 
-        // if (!this.data.edge.query_operation.transformer) {
-        //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
-        // } 
+    // if (!this.data.edge.query_operation.transformer) {
+    //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
+    // }
 
-        if (this.data.edge.query_operation?.transformer?.pair_jq || this.data.edge.query_operation?.transformer?.wrap_jq) {
-            // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
-            this.tf = new JQTransformer(this.data, { 
-              ...this.config, 
-              wrap: this.data.edge.query_operation.transformer.wrap_jq, 
-              pair: this.data.edge.query_operation.transformer.pair_jq 
-            })
-        } else if (tags.includes('bte-trapi')) {
-            this.tf = new TRAPITransformer(this.data, this.config);
-        } else if (api.startsWith('SEMMED')) {
-            this.tf = new SemmedTransformer(this.data, this.config);
-        } else if (api === 'BioLink API') {
-            // this.tf = new BiolinkTransformer(this.data, this.config);
-            this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" })
-        } else if (api === 'EBI Proteins API') {
-            // this.tf = new EBIProteinTransformer(this.data, this.config)
-            this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" })
-        } else if (tags.includes("biothings")) {
-            this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" })
-        } else if (tags.includes("ctd")) {
-            this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" });
-        } else if (tags.includes("opentarget")) {
-            this.tf = new OpenTargetTransformer(this.data, this.config)
-        } else {
-            this.tf = new BaseTransformer(this.data, this.config)
-        }
+    if (this.data.edge.query_operation?.transformer?.pair_jq || this.data.edge.query_operation?.transformer?.wrap_jq) {
+      // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
+      this.tf = new JQTransformer(this.data, {
+        ...this.config,
+        wrap: this.data.edge.query_operation.transformer.wrap_jq,
+        pair: this.data.edge.query_operation.transformer.pair_jq,
+      });
+    } else if (tags.includes("bte-trapi")) {
+      this.tf = new TRAPITransformer(this.data, this.config);
+    } else if (api.startsWith("SEMMED")) {
+      this.tf = new SemmedTransformer(this.data, this.config);
+    } else if (api === "BioLink API") {
+      // this.tf = new BiolinkTransformer(this.data, this.config);
+      this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" });
+    } else if (api === "EBI Proteins API") {
+      // this.tf = new EBIProteinTransformer(this.data, this.config)
+      this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" });
+    } else if (tags.includes("biothings")) {
+      this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" });
+    } else if (tags.includes("ctd")) {
+      this.tf = new JQTransformer(this.data, { ...this.config, type: "ctd" });
+    } else if (tags.includes("opentarget")) {
+      this.tf = new OpenTargetTransformer(this.data, this.config);
+    } else {
+      this.tf = new BaseTransformer(this.data, this.config);
     }
+  }
 
-    async transform() {
-        return await this.tf.transform();
-    }
+  async transform() {
+    return await this.tf.transform();
+  }
 }

From 8d7b43731c13ced63ffc9a8d382508fecf1483c8 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 12 Oct 2023 13:06:53 -0400
Subject: [PATCH 49/51] fix: CTD pair function batch support

---
 data/jq/pair/ctd.jq | 37 +++++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 16 deletions(-)

diff --git a/data/jq/pair/ctd.jq b/data/jq/pair/ctd.jq
index 017fba1..a912f1f 100644
--- a/data/jq/pair/ctd.jq
+++ b/data/jq/pair/ctd.jq
@@ -1,18 +1,23 @@
-reduce (.response | .[]) as $item (
-  {}; .[generateCurie($edge.association.input_id; (
-    if ($edge.input | type) == "object" then
-      ($edge.input.queryInputs | toArray)[] | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
-    else
-      ($edge.input | toArray) | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
-    end
-  ))] = [] 
-  + .[generateCurie($edge.association.input_id; (
-    if ($edge.input | type) == "object" then
-    ($edge.input.queryInputs | toArray)[] | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
-    else
-    ($edge.input | toArray) | select(($item.Input | ascii_upcase) | contains(. | ascii_upcase))
-    end
-  ))] 
+reduce .response[] as $item (
+  {}; .[(
+      if ($edge.input | type) == "object" then
+        ($edge.input.queryInputs | toArray)[]
+      else
+        ($edge.input | toArray)[]
+      end
+    ) 
+    | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase))
+    | generateCurie($edge.association.input_id; .)
+  ] = [] 
+  + .[(
+      if ($edge.input | type) == "object" then
+        ($edge.input.queryInputs | toArray)[]
+      else
+        ($edge.input | toArray)[]
+      end
+    )
+    | select(($item.Input | ascii_upcase | split(":") | last) == (. | ascii_upcase))
+    | generateCurie($edge.association.input_id; .)
+  ] 
   + [$item]
 ) | map_values([.])
-# TODO: current setup doesn't error, but only grabs one item.

From 549e4158a4da9da51acb05287ac29765dede65bb Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Fri, 13 Oct 2023 13:24:45 -0400
Subject: [PATCH 50/51] fix: obtain jq wrap/pair from annotation

---
 src/index.ts |  6 +++---
 src/types.ts | 16 ++++++++++------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/index.ts b/src/index.ts
index 0ed1f0c..50cf253 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -32,12 +32,12 @@ export class Transformer {
     //   console.log(`WE DONT DO THE OP ${api}, ${this.data.edge.query_operation}`)
     // }
 
-    if (this.data.edge.query_operation?.transformer?.pair_jq || this.data.edge.query_operation?.transformer?.wrap_jq) {
+    if (this.data.edge.query_operation?.transformer?.jq) {
       // console.log("WE DO THE OP", this.data.edge.query_operation.transformer)
       this.tf = new JQTransformer(this.data, {
         ...this.config,
-        wrap: this.data.edge.query_operation.transformer.wrap_jq,
-        pair: this.data.edge.query_operation.transformer.pair_jq,
+        wrap: this.data.edge.query_operation.transformer.jq.wrap,
+        pair: this.data.edge.query_operation.transformer.jq.pair,
       });
     } else if (tags.includes("bte-trapi")) {
       this.tf = new TRAPITransformer(this.data, this.config);
diff --git a/src/types.ts b/src/types.ts
index 417f5c4..384457d 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -15,8 +15,12 @@ interface XBTEParametersObject {
 }
 
 interface TransformerObject {
-    wrap_jq?: string;
-    pair_jq?: string;
+  wrap?: string;
+  pair?: string;
+}
+
+interface TransformerSet {
+  [transformerPattern: string]: TransformerObject;
 }
 
 interface QueryOperationInterface {
@@ -29,7 +33,7 @@ interface QueryOperationInterface {
   request_body: object;
   supportBatch: boolean;
   inputSeparator: string;
-  transformer: TransformerObject;
+  transformer: TransformerSet;
 }
 
 interface SmartAPIKGOperationObject {
@@ -58,6 +62,6 @@ export interface BTEQueryObject {
 }
 
 export interface JQVariable {
-    name: string;
-    value: string;
-}
\ No newline at end of file
+  name: string;
+  value: string;
+}

From 521504790115b11b88e7d170737ef4f9f0744873 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:43:05 -0400
Subject: [PATCH 51/51] style: prettier formatting

---
 __test__/base_transformer.test.ts             |   205 +-
 __test__/biolink_transformers.test.ts         |   161 +-
 __test__/biothings_transformer.test.ts        |   148 +-
 __test__/ctd_transformer.test.ts              |    93 +-
 __test__/data/biolink/edge.json               |    96 +-
 __test__/data/biolink/response.json           |  7456 +++--
 .../biothings/drug_response_example_edge.json |   117 +-
 .../biothings/drug_response_get_response.json | 23707 ++++++++--------
 .../data/biothings/mychem_example_edge.json   |   104 +-
 __test__/data/biothings/mychem_post.json      |   579 +-
 .../data/biothings/mygene_example_edge.json   |    96 +-
 __test__/data/biothings/mygene_post.json      |   383 +-
 __test__/data/ctd/edge.json                   |    82 +-
 __test__/data/ctd/response.json               |    42 +-
 __test__/data/ctd/response2.json              |  1483 +-
 __test__/data/ebi_protein/edge.json           |    87 +-
 __test__/data/ebi_protein/response.json       |  9357 +++---
 __test__/data/ols/edge.json                   |    76 +-
 __test__/data/ols/response.json               |  3688 ++-
 __test__/data/opentarget/edge.json            |    82 +-
 __test__/data/opentarget/response.json        |  1439 +-
 __test__/data/semmedgene/edge.json            |   103 +-
 __test__/data/semmedgene/response.json        |   436 +-
 __test__/ebi_protein_transformer.test.ts      |     2 +-
 __test__/opentarget_transformer.test.ts       |    74 +-
 __test__/record.test.ts                       |   101 +-
 __test__/semmed_transformer.test.ts           |   110 +-
 __test__/transformers.test.ts                 |   248 +-
 __test__/utils.test.ts                        |    72 +-
 src/json_transform/index.ts                   |    30 +-
 src/json_transform/types.ts                   |    16 +-
 src/json_transform/utils.ts                   |   209 +-
 src/transformers/biolink_transformer.ts       |    66 +-
 src/transformers/biothings_transformer.ts     |    51 +-
 src/transformers/cord_transformer.ts          |    54 +-
 src/transformers/ctd_transformer.ts           |    39 +-
 src/transformers/ebi_protein_transformer.ts   |    25 +-
 src/transformers/opentarget_transformer.ts    |    11 +-
 src/transformers/semmed_transformer.ts        |    54 +-
 src/transformers/transformer.ts               |   433 +-
 src/transformers/trapi_transformer.ts         |    16 +-
 src/utils.ts                                  |    24 +-
 42 files changed, 26010 insertions(+), 25645 deletions(-)

diff --git a/__test__/base_transformer.test.ts b/__test__/base_transformer.test.ts
index 7d7214a..db6a758 100644
--- a/__test__/base_transformer.test.ts
+++ b/__test__/base_transformer.test.ts
@@ -1,121 +1,120 @@
-import {describe, expect, test} from '@jest/globals';
+import { describe, expect, test } from "@jest/globals";
 
 import base_tf from "../src/transformers/transformer";
 import fs from "fs";
 import path from "path";
-import { JSONDoc } from '../src/json_transform/types';
+import { JSONDoc } from "../src/json_transform/types";
 
 describe("test base transformer", () => {
+  let response;
+  let input;
 
-    let response;
-    let input;
+  beforeEach(() => {
+    const response_path = path.resolve(__dirname, "./data/ols/response.json");
+    response = JSON.parse(fs.readFileSync(response_path, { encoding: "utf8" }));
+    const edge_path = path.resolve(__dirname, "./data/ols/edge.json");
+    const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+    input = {
+      response,
+      edge,
+    };
+  });
 
-    beforeEach(() => {
-        const response_path = path.resolve(__dirname, './data/ols/response.json');
-        response = JSON.parse(fs.readFileSync(response_path, { encoding: 'utf8' }));
-        const edge_path = path.resolve(__dirname, './data/ols/edge.json');
-        const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-        input = {
-            response,
-            edge
-        }
-    })
+  test("Test pairInputWithAPIResponse function", async () => {
+    const tf = new base_tf(input, {});
+    const res = await tf.pairCurieWithAPIResponse();
+    expect(res).toHaveProperty("DOID:9562");
+    expect(res["DOID:9562"]).toHaveLength(1);
+  });
 
-    test("Test pairInputWithAPIResponse function", async () => {
-        const tf = new base_tf(input, {});
-        const res = await tf.pairCurieWithAPIResponse();
-        expect(res).toHaveProperty("DOID:9562");
-        expect(res["DOID:9562"]).toHaveLength(1);
-    })
+  test("Test wrap function if response is not an array", () => {
+    const tf = new base_tf(input, {});
+    const res = tf.wrap(response);
+    expect(res).toHaveProperty("_embedded");
+  });
 
-    test("Test wrap function if response is not an array", () => {
-        const tf = new base_tf(input, {});
-        const res = tf.wrap(response);
-        expect(res).toHaveProperty("_embedded");
-    })
+  test("Test wrap function if response is an array", () => {
+    const tf = new base_tf(input, {});
+    const fake = ["1"];
+    const res = tf.wrap(fake);
+    expect(res).toHaveProperty("data");
+    expect(res.data).toEqual(["1"]);
+  });
 
-    test("Test wrap function if response is an array", () => {
-        const tf = new base_tf(input, {});
-        const fake = ["1"]
-        const res = tf.wrap(fake);
-        expect(res).toHaveProperty("data");
-        expect(res.data).toEqual(["1"])
-    })
+  test("Test jsonTransform function", () => {
+    const tf = new base_tf(input, {});
+    const res: JSONDoc = tf.jsonTransform(response);
+    expect(res).toHaveProperty("has_subclass");
+    expect(res.has_subclass[0]).toHaveProperty("DOID");
+    expect(res.has_subclass[0].DOID).toEqual("DOID:0110596");
+    expect(res.has_subclass[0].name).toEqual("primary ciliary dyskinesia 21");
+    expect(res.has_subclass[0].description).toEqual([
+      "A primary ciliary dyskinesia that is characterized by autosomal recessive inheritance with a missing Nexin link, infantile onset of chronic sinopulmonary infections, and has_material_basis_in homozygous mutation in the DRC1 gene on chromosome 2p23.",
+    ]);
+  });
 
-    test("Test jsonTransform function", () => {
-        const tf = new base_tf(input, {});
-        const res: JSONDoc = tf.jsonTransform(response);
-        expect(res).toHaveProperty("has_subclass");
-        expect(res.has_subclass[0]).toHaveProperty("DOID");
-        expect(res.has_subclass[0].DOID).toEqual("DOID:0110596");
-        expect(res.has_subclass[0].name).toEqual("primary ciliary dyskinesia 21");
-        expect(res.has_subclass[0].description).toEqual([
-            "A primary ciliary dyskinesia that is characterized by autosomal recessive inheritance with a missing Nexin link, infantile onset of chronic sinopulmonary infections, and has_material_basis_in homozygous mutation in the DRC1 gene on chromosome 2p23."
-        ]);
-    })
+  test("Test _updatePublications function if pubmed id is prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmid: "PMID:1233",
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmid");
+    expect(res.publications).toEqual(["PMID:1233"]);
+  });
 
-    test("Test _updatePublications function if pubmed id is prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmid: "PMID:1233"
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmid');
-        expect(res.publications).toEqual(["PMID:1233"]);
-    })
+  test("Test _updatePublications function if pubmed id is NOT prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmid: 1233,
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmid");
+    expect(res.publications).toEqual(["PMID:1233"]);
+  });
 
-    test("Test _updatePublications function if pubmed id is NOT prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmid: 1233
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmid');
-        expect(res.publications).toEqual(["PMID:1233"])
-    })
+  test("Test _updatePublications function if pmc id is prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmcid: "PMCID:1233",
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmcid");
+    expect(res.publications).toEqual(["PMCID:1233"]);
+  });
 
-    test("Test _updatePublications function if pmc id is prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmcid: "PMCID:1233"
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmcid');
-        expect(res.publications).toEqual(["PMCID:1233"]);
-    })
+  test("Test _updatePublications function if pmc id is NOT prefixed", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      ref_pmcid: 123,
+    };
+    const res = tf._updatePublications(fake);
+    expect(res).not.toHaveProperty("ref_pmcid");
+    expect(res.publications).toEqual(["PMCID:123"]);
+  });
 
-    test("Test _updatePublications function if pmc id is NOT prefixed", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            ref_pmcid: 123
-        }
-        const res = tf._updatePublications(fake);
-        expect(res).not.toHaveProperty('ref_pmcid');
-        expect(res.publications).toEqual(["PMCID:123"])
-    })
+  test("Test extractObjectIDs function if output id type not in result", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      kk: 1,
+    };
+    const res = tf.extractObjectIDs(fake);
+    expect(res).toEqual([]);
+  });
 
-    test("Test extractObjectIDs function if output id type not in result", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            kk: 1
-        };
-        const res = tf.extractObjectIDs(fake);
-        expect(res).toEqual([]);
-    })
+  test("Test extractObjectIDs function if output id type is in result", () => {
+    const tf = new base_tf(input, {});
+    const fake = {
+      DOID: 1,
+    };
+    const res = tf.extractObjectIDs(fake);
+    expect(res).toEqual(["DOID:1"]);
+  });
 
-    test("Test extractObjectIDs function if output id type is in result", () => {
-        const tf = new base_tf(input, {});
-        const fake = {
-            DOID: 1
-        };
-        const res = tf.extractObjectIDs(fake);
-        expect(res).toEqual(["DOID:1"]);
-    })
-
-    test("Test formatRecords function if result is empty", async () => {
-        const tf = new base_tf(input, {});
-        const fake = {};
-        const res = await tf.formatRecords("NCBIGene:1017", fake);
-        expect(res).toEqual([]);
-    })
-})
+  test("Test formatRecords function if result is empty", async () => {
+    const tf = new base_tf(input, {});
+    const fake = {};
+    const res = await tf.formatRecords("NCBIGene:1017", fake);
+    expect(res).toEqual([]);
+  });
+});
diff --git a/__test__/biolink_transformers.test.ts b/__test__/biolink_transformers.test.ts
index cd1d8e1..57214c7 100644
--- a/__test__/biolink_transformers.test.ts
+++ b/__test__/biolink_transformers.test.ts
@@ -1,96 +1,93 @@
-import {describe, expect, test} from '@jest/globals';
+import { describe, expect, test } from "@jest/globals";
 
 import jq_tf from "../built/transformers/jq_transformer";
 import fs from "fs";
 import path from "path";
-import { JSONDoc } from '../src/json_transform/types';
+import { JSONDoc } from "../src/json_transform/types";
 
 describe("test biolink transformer", () => {
+  let response;
+  let input;
 
-    let response;
-    let input;
+  beforeEach(() => {
+    const response_path = path.resolve(__dirname, "./data/biolink/response.json");
+    response = JSON.parse(fs.readFileSync(response_path, { encoding: "utf8" }));
+    const edge_path = path.resolve(__dirname, "./data/biolink/edge.json");
+    const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+    input = {
+      response,
+      edge,
+    };
+  });
 
-    beforeEach(() => {
-        const response_path = path.resolve(__dirname, './data/biolink/response.json');
-        response = JSON.parse(fs.readFileSync(response_path, {encoding: 'utf8'}));
-        const edge_path = path.resolve(__dirname, './data/biolink/edge.json');
-        const edge = JSON.parse(fs.readFileSync(edge_path, {encoding: 'utf8'}));
-        input = {
-            response,
-            edge
-        }
-    })
+  test("test biolink wrapper", async () => {
+    let tf = new jq_tf(input, { type: "biolink" });
+    let res = await tf.wrap(response);
+    expect(res.associations[0].object.HGNC).toBe("10956");
+    expect(res.associations[0].publications[0].id).toBe("21685912");
+    expect(res.associations[1]).not.toHaveProperty("publications");
+    expect(res.associations[1]).not.toHaveProperty("provided_by");
+  });
 
-    test("test biolink wrapper", async () => {
-        let tf = new jq_tf(input, { type: "biolink" });
-        let res = await tf.wrap(response);
-        expect(res.associations[0].object.HGNC).toBe("10956");
-        expect(res.associations[0].publications[0].id).toBe("21685912");
-        expect(res.associations[1]).not.toHaveProperty("publications");
-        expect(res.associations[1]).not.toHaveProperty("provided_by");
-    });
-
-    test("test biolink wrapper if no association field as root key", async () => {
-        let tf = new jq_tf(input, { type: "biolink" });
-        let res = await tf.wrap({ "data": [] });
-        expect(res).toEqual({ "data": [] })
-    });
+  test("test biolink wrapper if no association field as root key", async () => {
+    let tf = new jq_tf(input, { type: "biolink" });
+    let res = await tf.wrap({ data: [] });
+    expect(res).toEqual({ data: [] });
+  });
 
-    test("test biolink wrapper if no object id should be prefixed", async () => {
-        const tf = new jq_tf(input, { type: "biolink" });
-        const res = await tf.wrap(
-            {
-                associations: [
-                    {
-                        object: {
-                            id: "MONDO:12345"
-                        }
-                    }
-                ]
-            });
-        expect(res.associations[0].object.MONDO).toEqual("MONDO:12345")
+  test("test biolink wrapper if no object id should be prefixed", async () => {
+    const tf = new jq_tf(input, { type: "biolink" });
+    const res = await tf.wrap({
+      associations: [
+        {
+          object: {
+            id: "MONDO:12345",
+          },
+        },
+      ],
     });
+    expect(res.associations[0].object.MONDO).toEqual("MONDO:12345");
+  });
 
-    test("test biolink wrapper if no object field present", async () => {
-        const tf = new jq_tf(input, { type: "biolink" });
-        const fake_response = {
-            associations: [
-                {
-                    object1: {
-                        id: "MONDO:12345"
-                    }
-                }
-            ]
-        }
-        const res = await tf.wrap(fake_response);
-        expect(res).toEqual(fake_response)
-    });
+  test("test biolink wrapper if no object field present", async () => {
+    const tf = new jq_tf(input, { type: "biolink" });
+    const fake_response = {
+      associations: [
+        {
+          object1: {
+            id: "MONDO:12345",
+          },
+        },
+      ],
+    };
+    const res = await tf.wrap(fake_response);
+    expect(res).toEqual(fake_response);
+  });
 
-    test("test biolink wrapper if no object.id field present", async () => {
-        const tf = new jq_tf(input, { type: "biolink" });
-        const fake_response = {
-            associations: [
-                {
-                    object: {
-                        id1: "MONDO:12345"
-                    }
-                }
-            ]
-        }
-        const res = await tf.wrap(fake_response);
-        expect(res).toEqual(fake_response)
-    });
-
-    test("test biolink jsonTransform function", async () => {
-        let tf = new jq_tf(input, { type: "biolink" });
-        const wrapped_response = await tf.wrap(response);
-        let res: JSONDoc = tf.jsonTransform(wrapped_response);
-        expect(res).toHaveProperty("related_to");
-        expect(res.related_to[0].HGNC).toEqual("10956");
-        expect(res.related_to[0].pubmed[0]).toEqual("21685912");
-        expect(res.related_to[0].relation).toEqual("contributes to condition");
-        expect(res.related_to[0].source[0]).toEqual("https://archive.monarchinitiative.org/#gwascatalog");
-        expect(res.related_to[0].taxid).toEqual("NCBITaxon:9606")
-    });
+  test("test biolink wrapper if no object.id field present", async () => {
+    const tf = new jq_tf(input, { type: "biolink" });
+    const fake_response = {
+      associations: [
+        {
+          object: {
+            id1: "MONDO:12345",
+          },
+        },
+      ],
+    };
+    const res = await tf.wrap(fake_response);
+    expect(res).toEqual(fake_response);
+  });
 
-})
+  test("test biolink jsonTransform function", async () => {
+    let tf = new jq_tf(input, { type: "biolink" });
+    const wrapped_response = await tf.wrap(response);
+    let res: JSONDoc = tf.jsonTransform(wrapped_response);
+    expect(res).toHaveProperty("related_to");
+    expect(res.related_to[0].HGNC).toEqual("10956");
+    expect(res.related_to[0].pubmed[0]).toEqual("21685912");
+    expect(res.related_to[0].relation).toEqual("contributes to condition");
+    expect(res.related_to[0].source[0]).toEqual("https://archive.monarchinitiative.org/#gwascatalog");
+    expect(res.related_to[0].taxid).toEqual("NCBITaxon:9606");
+  });
+});
diff --git a/__test__/biothings_transformer.test.ts b/__test__/biothings_transformer.test.ts
index 5c194fc..1af7ce7 100644
--- a/__test__/biothings_transformer.test.ts
+++ b/__test__/biothings_transformer.test.ts
@@ -1,89 +1,87 @@
-
 import jq_tf from "../src/transformers/jq_transformer";
-import {describe, expect, test} from '@jest/globals';
+import { describe, expect, test } from "@jest/globals";
 import fs from "fs";
 import path from "path";
 
 describe("test biothings transformer", () => {
+  describe("test biothings transformer for post query", () => {
+    let input;
+    let response;
 
-    describe("test biothings transformer for post query", () => {
-        let input;
-        let response;
-
-        beforeAll(() => {
-            const post_query_response_path = path.resolve(__dirname, './data/biothings/mychem_post.json');
-            response = JSON.parse(fs.readFileSync(post_query_response_path, { encoding: 'utf8' }));
-            const edge_path = path.resolve(__dirname, './data/biothings/mychem_example_edge.json');
-            const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-            input = {
-                response,
-                edge
-            }
-        })
+    beforeAll(() => {
+      const post_query_response_path = path.resolve(__dirname, "./data/biothings/mychem_post.json");
+      response = JSON.parse(fs.readFileSync(post_query_response_path, { encoding: "utf8" }));
+      const edge_path = path.resolve(__dirname, "./data/biothings/mychem_example_edge.json");
+      const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+      input = {
+        response,
+        edge,
+      };
+    });
 
-        test("test biothings wrapper", async () => {
-            let tf = new jq_tf(input, {type: "biothings"});
-            let res = await tf.pairCurieWithAPIResponse();
-            expect(Object.keys(res)).toHaveLength(2);
-            expect(res).toHaveProperty("DRUGBANK:DB00188");
-            expect(res["DRUGBANK:DB00188"]).toHaveLength(2);
-            expect(res).not.toHaveProperty("DRUGBANK:DB0000");
-        })
-    })
+    test("test biothings wrapper", async () => {
+      let tf = new jq_tf(input, { type: "biothings" });
+      let res = await tf.pairCurieWithAPIResponse();
+      expect(Object.keys(res)).toHaveLength(2);
+      expect(res).toHaveProperty("DRUGBANK:DB00188");
+      expect(res["DRUGBANK:DB00188"]).toHaveLength(2);
+      expect(res).not.toHaveProperty("DRUGBANK:DB0000");
+    });
+  });
 
-    describe("test biothings transformer for post query using mygene", () => {
-        let input;
-        let response;
+  describe("test biothings transformer for post query using mygene", () => {
+    let input;
+    let response;
 
-        beforeAll(() => {
-            const post_query_response_path = path.resolve(__dirname, './data/biothings/mygene_post.json');
-            response = JSON.parse(fs.readFileSync(post_query_response_path, { encoding: 'utf8' }));
-            const edge_path = path.resolve(__dirname, './data/biothings/mygene_example_edge.json');
-            const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-            input = {
-                response,
-                edge
-            }
-        })
+    beforeAll(() => {
+      const post_query_response_path = path.resolve(__dirname, "./data/biothings/mygene_post.json");
+      response = JSON.parse(fs.readFileSync(post_query_response_path, { encoding: "utf8" }));
+      const edge_path = path.resolve(__dirname, "./data/biothings/mygene_example_edge.json");
+      const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+      input = {
+        response,
+        edge,
+      };
+    });
 
-        test("test biothings wrapper", async () => {
-            let tf = new jq_tf(input, {type: "biothings"});
-            let res = await tf.pairCurieWithAPIResponse();
-            expect(Object.keys(res)).toHaveLength(1);
-            expect(res).toHaveProperty("NCBIGene:1017");
-            expect(res["NCBIGene:1017"]).toHaveLength(1);
-        })
+    test("test biothings wrapper", async () => {
+      let tf = new jq_tf(input, { type: "biothings" });
+      let res = await tf.pairCurieWithAPIResponse();
+      expect(Object.keys(res)).toHaveLength(1);
+      expect(res).toHaveProperty("NCBIGene:1017");
+      expect(res["NCBIGene:1017"]).toHaveLength(1);
+    });
 
-        test("test biothings transform", async () => {
-            let tf = new jq_tf(input, {type: "biothings"});
-            let res = await tf.transform();
-            expect(res).toHaveLength(27);
-            expect(res[0]).not.toHaveProperty('ref_pmid');
-            expect(res[0]).toHaveProperty('publications', ["PMID:21873635"]);
-        })
-    })
+    test("test biothings transform", async () => {
+      let tf = new jq_tf(input, { type: "biothings" });
+      let res = await tf.transform();
+      expect(res).toHaveLength(27);
+      expect(res[0]).not.toHaveProperty("ref_pmid");
+      expect(res[0]).toHaveProperty("publications", ["PMID:21873635"]);
+    });
+  });
 
-    describe("test biothings transformer for get query", () => {
-        let input;
-        let response;
+  describe("test biothings transformer for get query", () => {
+    let input;
+    let response;
 
-        beforeAll(() => {
-            const get_query_response_path = path.resolve(__dirname, './data/biothings/drug_response_get_response.json');
-            response = JSON.parse(fs.readFileSync(get_query_response_path, { encoding: 'utf8' }));
-            const edge_path = path.resolve(__dirname, './data/biothings/drug_response_example_edge.json');
-            const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-            input = {
-                response,
-                edge
-            }
-        })
+    beforeAll(() => {
+      const get_query_response_path = path.resolve(__dirname, "./data/biothings/drug_response_get_response.json");
+      response = JSON.parse(fs.readFileSync(get_query_response_path, { encoding: "utf8" }));
+      const edge_path = path.resolve(__dirname, "./data/biothings/drug_response_example_edge.json");
+      const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+      input = {
+        response,
+        edge,
+      };
+    });
 
-        test("test biothings wrapper", async () => {
-            let tf = new jq_tf(input, {type: "biothings"});
-            let res = await tf.pairCurieWithAPIResponse();
-            expect(Object.keys(res)).toHaveLength(1);
-            expect(res).toHaveProperty("PUBCHEM:11373846");
-            expect(res["PUBCHEM:11373846"]).toHaveLength(1);
-        })
-    })
-})
+    test("test biothings wrapper", async () => {
+      let tf = new jq_tf(input, { type: "biothings" });
+      let res = await tf.pairCurieWithAPIResponse();
+      expect(Object.keys(res)).toHaveLength(1);
+      expect(res).toHaveProperty("PUBCHEM:11373846");
+      expect(res["PUBCHEM:11373846"]).toHaveLength(1);
+    });
+  });
+});
diff --git a/__test__/ctd_transformer.test.ts b/__test__/ctd_transformer.test.ts
index 089ef2e..eca2c93 100644
--- a/__test__/ctd_transformer.test.ts
+++ b/__test__/ctd_transformer.test.ts
@@ -1,56 +1,55 @@
-import {describe, expect, test} from '@jest/globals';
+import { describe, expect, test } from "@jest/globals";
 import fs from "fs";
 import path from "path";
 import jq_tf from "../built/transformers/jq_transformer";
 
 describe("test ctd transformer", () => {
+  let response;
+  let input;
 
-    let response;
-    let input;
+  beforeEach(() => {
+    const response_path = path.resolve(__dirname, "./data/ctd/response.json");
+    response = JSON.parse(fs.readFileSync(response_path, { encoding: "utf8" }));
+    const edge_path = path.resolve(__dirname, "./data/ctd/edge.json");
+    const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+    input = {
+      response,
+      edge,
+    };
+  });
 
-    beforeEach(() => {
-        const response_path = path.resolve(__dirname, './data/ctd/response.json');
-        response = JSON.parse(fs.readFileSync(response_path, { encoding: 'utf8' }));
-        const edge_path = path.resolve(__dirname, './data/ctd/edge.json');
-        const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-        input = {
-            response,
-            edge
-        }
-    })
+  test("test ctd wrapper", async () => {
+    let tf = new jq_tf(input, { type: "ctd" });
+    let res = await tf.wrap(response);
+    expect(res).toHaveProperty("data");
+    expect(res.data).toHaveLength(2);
+    expect(res.data[0].PubMedIDs).toEqual(["21559390"]);
+    expect(res.data[0].DiseaseID).toEqual("MESH:D008545");
+  });
 
-    test("test ctd wrapper", async () => {
-        let tf = new jq_tf(input, { type: "ctd" });
-        let res = await tf.wrap(response);
-        expect(res).toHaveProperty("data");
-        expect(res.data).toHaveLength(2);
-        expect(res.data[0].PubMedIDs).toEqual(["21559390"]);
-        expect(res.data[0].DiseaseID).toEqual("MESH:D008545");
-    })
+  test("test ctd wrapper if pubmed id field is not string", async () => {
+    const tf = new jq_tf(input, { type: "ctd" });
+    const fake = [
+      {
+        DiseaseID: "MESH:D008545",
+      },
+    ];
+    const res = await tf.wrap(fake);
+    expect(res).toHaveProperty("data");
+    expect(res.data).toHaveLength(1);
+    expect(res.data[0].PubMedIDs).toBeUndefined;
+  });
 
-    test("test ctd wrapper if pubmed id field is not string", async () => {
-        const tf = new jq_tf(input, { type: "ctd" });
-        const fake = [
-            {
-                DiseaseID: "MESH:D008545"
-            }
-        ]
-        const res = await tf.wrap(fake);
-        expect(res).toHaveProperty("data");
-        expect(res.data).toHaveLength(1);
-        expect(res.data[0].PubMedIDs).toBeUndefined;
-    })
-
-    test("test ctd wrapper if disease id field is not string", async () => {
-        const tf = new jq_tf(input, { type: "ctd" });
-        const fake = [
-            {
-                PubMedID: "12345"
-            }
-        ]
-        const res = await tf.wrap(fake);
-        expect(res).toHaveProperty("data");
-        expect(res.data).toHaveLength(1);
-        expect(res.data[0].DiseaseIDs).toBeUndefined;
-    })
-})
+  test("test ctd wrapper if disease id field is not string", async () => {
+    const tf = new jq_tf(input, { type: "ctd" });
+    const fake = [
+      {
+        PubMedID: "12345",
+      },
+    ];
+    const res = await tf.wrap(fake);
+    expect(res).toHaveProperty("data");
+    expect(res.data).toHaveLength(1);
+    expect(res.data[0].DiseaseIDs).toBeUndefined;
+  });
+});
diff --git a/__test__/data/biolink/edge.json b/__test__/data/biolink/edge.json
index 23c59cb..ae7099b 100644
--- a/__test__/data/biolink/edge.json
+++ b/__test__/data/biolink/edge.json
@@ -1,56 +1,44 @@
 {
-    "input": "DOID:678",
-    "query_operation": {
-        "params": {
-            "disease_id": "{inputs[0]}",
-            "rows": 200
-        },
-        "path": "/bioentity/disease/{disease_id}/genes",
-        "path_params": [
-            "disease_id"
-        ],
-        "method": "get",
-        "server": "https://api.monarchinitiative.org/api",
-        "tags": [
-            "anatomy",
-            "disease",
-            "gene",
-            "phenotype",
-            "pathway",
-            "annotation",
-            "query",
-            "translator",
-            "biolink"
-        ],
-        "supportBatch": false
+  "input": "DOID:678",
+  "query_operation": {
+    "params": {
+      "disease_id": "{inputs[0]}",
+      "rows": 200
     },
-    "association": {
-        "input_id": "MONDO",
-        "input_type": "Disease",
-        "output_id": "HGNC",
-        "output_type": "Gene",
-        "predicate": "related_to",
-        "api_name": "BioLink API",
-        "smartapi": {
-            "id": "d22b657426375a5295e7da8a303b9893",
-            "meta": {
-                "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d",
-                "github_username": "newgene",
-                "timestamp": "2020-05-28T00:02:40.483712",
-                "uptime_status": "good",
-                "uptime_ts": "2020-06-11T00:05:38.030503",
-                "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml"
-            }
-        }
-    },
-    "response_mapping": {
-        "related_to": {
-            "HGNC": "associations.object.HGNC",
-            "pubmed": "associations.publications.id",
-            "relation": "associations.relation.label",
-            "source": "associations.provided_by",
-            "taxid": "associations.object.taxon.id"
-        }
-    },
-    "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
-}
\ No newline at end of file
+    "path": "/bioentity/disease/{disease_id}/genes",
+    "path_params": ["disease_id"],
+    "method": "get",
+    "server": "https://api.monarchinitiative.org/api",
+    "tags": ["anatomy", "disease", "gene", "phenotype", "pathway", "annotation", "query", "translator", "biolink"],
+    "supportBatch": false
+  },
+  "association": {
+    "input_id": "MONDO",
+    "input_type": "Disease",
+    "output_id": "HGNC",
+    "output_type": "Gene",
+    "predicate": "related_to",
+    "api_name": "BioLink API",
+    "smartapi": {
+      "id": "d22b657426375a5295e7da8a303b9893",
+      "meta": {
+        "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d",
+        "github_username": "newgene",
+        "timestamp": "2020-05-28T00:02:40.483712",
+        "uptime_status": "good",
+        "uptime_ts": "2020-06-11T00:05:38.030503",
+        "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml"
+      }
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "HGNC": "associations.object.HGNC",
+      "pubmed": "associations.publications.id",
+      "relation": "associations.relation.label",
+      "source": "associations.provided_by",
+      "taxid": "associations.object.taxon.id"
+    }
+  },
+  "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
+}
diff --git a/__test__/data/biolink/response.json b/__test__/data/biolink/response.json
index b707993..6d272c6 100644
--- a/__test__/data/biolink/response.json
+++ b/__test__/data/biolink/response.json
@@ -1,4227 +1,3303 @@
 {
-    "associations": [
+  "associations": [
+    {
+      "id": "235d96fe-7a99-4554-8cae-ed2d04e2c0c5",
+      "type": null,
+      "subject": {
+        "taxon": {
+          "id": null,
+          "label": null
+        },
+        "id": "MONDO:0019037",
+        "label": "progressive supranuclear palsy",
+        "iri": "http://purl.obolibrary.org/obo/MONDO_0019037",
+        "category": ["disease"]
+      },
+      "subject_eq": null,
+      "subject_extensions": null,
+      "object": {
+        "taxon": {
+          "id": "NCBITaxon:9606",
+          "label": "Homo sapiens"
+        },
+        "id": "HGNC:10956",
+        "label": "SLCO1A2",
+        "iri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10956",
+        "category": ["gene"]
+      },
+      "object_eq": null,
+      "object_extensions": null,
+      "relation": {
+        "inverse": true,
+        "id": "RO:0003304",
+        "label": "contributes to condition",
+        "iri": "http://purl.obolibrary.org/obo/RO_0003304",
+        "category": null
+      },
+      "slim": null,
+      "negated": false,
+      "qualifiers": null,
+      "evidence_graph": {
+        "nodes": [
+          {
+            "id": "MONARCH:b8d5e5d72e9364f0e46e",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "MONARCH:bff6d3cb1c2f75352e05",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "RO:0003304",
+            "lbl": "contributes to condition",
+            "meta": {}
+          },
+          {
+            "id": "PMID:30089514",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "MONDO:0019037",
+            "lbl": "progressive supranuclear palsy",
+            "meta": {}
+          },
+          {
+            "id": "ECO:0000213",
+            "lbl": "combinatorial evidence used in automatic assertion",
+            "meta": {}
+          },
+          {
+            "id": "PMID:21685912",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "HGNC:10956",
+            "lbl": "SLCO1A2",
+            "meta": {}
+          },
+          {
+            "id": "dbSNP:rs11568563",
+            "lbl": "rs11568563-?",
+            "meta": {}
+          },
+          {
+            "id": "dbSNP:rs7966334",
+            "lbl": "rs7966334-?",
+            "meta": {}
+          }
+        ],
+        "edges": [
+          {
+            "sub": "MONARCH:b8d5e5d72e9364f0e46e",
+            "pred": "RO:0002558",
+            "obj": "ECO:0000213",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["has evidence"]
+            }
+          },
+          {
+            "sub": "MONARCH:b8d5e5d72e9364f0e46e",
+            "pred": "OBAN:association_has_predicate",
+            "obj": "RO:0003304",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["association has predicate"]
+            }
+          },
+          {
+            "sub": "MONARCH:bff6d3cb1c2f75352e05",
+            "pred": "dc:source",
+            "obj": "PMID:30089514",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["source"]
+            }
+          },
+          {
+            "sub": "MONARCH:bff6d3cb1c2f75352e05",
+            "pred": "OBAN:association_has_object",
+            "obj": "MONDO:0019037",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["association has object"],
+              "equivalentOriginalNodeTarget": ["http://www.orpha.net/ORDO/Orphanet_683"]
+            }
+          },
+          {
+            "sub": "dbSNP:rs11568563",
+            "pred": "RO:0003304",
+            "obj": "MONDO:0019037",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["contributes to condition"],
+              "equivalentOriginalNodeTarget": ["http://www.orpha.net/ORDO/Orphanet_683"]
+            }
+          },
+          {
+            "sub": "MONARCH:bff6d3cb1c2f75352e05",
+            "pred": "RO:0002558",
+            "obj": "ECO:0000213",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["has evidence"]
+            }
+          },
+          {
+            "sub": "MONARCH:bff6d3cb1c2f75352e05",
+            "pred": "OBAN:association_has_subject",
+            "obj": "dbSNP:rs7966334",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["association has subject"]
+            }
+          },
+          {
+            "sub": "MONARCH:b8d5e5d72e9364f0e46e",
+            "pred": "OBAN:association_has_subject",
+            "obj": "dbSNP:rs11568563",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["association has subject"]
+            }
+          },
+          {
+            "sub": "dbSNP:rs7966334",
+            "pred": "RO:0003304",
+            "obj": "MONDO:0019037",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["contributes to condition"],
+              "equivalentOriginalNodeTarget": ["http://www.orpha.net/ORDO/Orphanet_683"]
+            }
+          },
+          {
+            "sub": "MONARCH:b8d5e5d72e9364f0e46e",
+            "pred": "dc:source",
+            "obj": "PMID:21685912",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["source"]
+            }
+          },
+          {
+            "sub": "MONARCH:b8d5e5d72e9364f0e46e",
+            "pred": "OBAN:association_has_object",
+            "obj": "MONDO:0019037",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["association has object"],
+              "equivalentOriginalNodeTarget": ["http://www.orpha.net/ORDO/Orphanet_683"]
+            }
+          },
+          {
+            "sub": "dbSNP:rs11568563",
+            "pred": "GENO:0000418",
+            "obj": "HGNC:10956",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["has_affected_feature"],
+              "equivalentOriginalNodeTarget": ["http://ensembl.org/id/ENSG00000084453"]
+            }
+          },
+          {
+            "sub": "dbSNP:rs7966334",
+            "pred": "GENO:0000418",
+            "obj": "HGNC:10956",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["has_affected_feature"],
+              "equivalentOriginalNodeTarget": ["http://ensembl.org/id/ENSG00000084453"]
+            }
+          },
+          {
+            "sub": "MONARCH:bff6d3cb1c2f75352e05",
+            "pred": "OBAN:association_has_predicate",
+            "obj": "RO:0003304",
+            "meta": {
+              "isDefinedBy": ["https://archive.monarchinitiative.org/#gwascatalog"],
+              "lbl": ["association has predicate"]
+            }
+          }
+        ]
+      },
+      "evidence_types": [
+        {
+          "id": "ECO:0000213",
+          "label": "combinatorial evidence used in automatic assertion"
+        }
+      ],
+      "provided_by": ["https://archive.monarchinitiative.org/#gwascatalog"],
+      "publications": [
+        {
+          "id": "PMID:21685912",
+          "label": null
+        },
+        {
+          "id": "PMID:30089514",
+          "label": null
+        }
+      ]
+    },
+    {
+      "id": "235d96fe-7a99-4554-8cae-ed2d04e2c0c5",
+      "type": null,
+      "subject": {
+        "taxon": {
+          "id": null,
+          "label": null
+        },
+        "id": "MONDO:0019037",
+        "label": "progressive supranuclear palsy",
+        "iri": "http://purl.obolibrary.org/obo/MONDO_0019037",
+        "category": ["disease"]
+      },
+      "subject_eq": null,
+      "subject_extensions": null,
+      "object": {
+        "taxon": {
+          "id": "NCBITaxon:9606",
+          "label": "Homo sapiens"
+        },
+        "id": "HGNC:10956",
+        "label": "SLCO1A2",
+        "iri": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10956",
+        "category": ["gene"]
+      },
+      "object_eq": null,
+      "object_extensions": null,
+      "relation": {
+        "inverse": true,
+        "id": "RO:0003304",
+        "label": "contributes to condition",
+        "iri": "http://purl.obolibrary.org/obo/RO_0003304",
+        "category": null
+      },
+      "slim": null,
+      "negated": false,
+      "qualifiers": null,
+      "evidence_graph": {
+        "nodes": [
+          {
+            "id": "MONARCH:b8d5e5d72e9364f0e46e",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "MONARCH:bff6d3cb1c2f75352e05",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "RO:0003304",
+            "lbl": "contributes to condition",
+            "meta": {}
+          },
+          {
+            "id": "PMID:30089514",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "MONDO:0019037",
+            "lbl": "progressive supranuclear palsy",
+            "meta": {}
+          },
+          {
+            "id": "ECO:0000213",
+            "lbl": "combinatorial evidence used in automatic assertion",
+            "meta": {}
+          },
+          {
+            "id": "PMID:21685912",
+            "lbl": null,
+            "meta": {}
+          },
+          {
+            "id": "HGNC:10956",
+            "lbl": "SLCO1A2",
+            "meta": {}
+          },
+          {
+            "id": "dbSNP:rs11568563",
+            "lbl": "rs11568563-?",
+            "meta": {}
+          },
+          {
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diff --git a/__test__/data/biothings/drug_response_example_edge.json b/__test__/data/biothings/drug_response_example_edge.json
index 4b6da4f..af77535 100644
--- a/__test__/data/biothings/drug_response_example_edge.json
+++ b/__test__/data/biothings/drug_response_example_edge.json
@@ -1,63 +1,60 @@
 {
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-    "query_operation": {
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-            "q": "object.PUBCHEM:{inputs[0]} AND association.effect_size:<0 AND association.pvalue:<0.05",
-            "sort": "association.pvalue",
-            "size": "1000"
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-        "_supportBatch": false,
-        "_method": "get",
-        "_pathParams": [],
-        "_server": "https://biothings.ncats.io/drug_response_kp",
-        "_path": "/query",
-        "_tags": [
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-            "disease",
-            "chemical",
-            "association",
-            "annotation",
-            "query",
-            "translator",
-            "biothings",
-            "biothings_graph"
-        ]
+  "input": "11373846",
+  "query_operation": {
+    "_params": {
+      "fields": "association.context.disease.mondo,subject.NCBIGene,association.effect_size,association.pvalue",
+      "q": "object.PUBCHEM:{inputs[0]} AND association.effect_size:<0 AND association.pvalue:<0.05",
+      "sort": "association.pvalue",
+      "size": "1000"
     },
-    "association": {
-        "input_id": "PUBCHEM",
-        "input_type": "ChemicalSubstance",
-        "output_id": "NCBIGene",
-        "output_type": "Gene",
-        "predicate": "gene_has_variant_that_contributes_to_drug_response_association",
-        "source": "Multiomics Provider",
-        "api_name": "Drug Response KP API",
-        "smartapi": {},
-        "x-translator": {
-            "component": "KP",
-            "team": [
-                "Multiomics Provider",
-                "Service Provider"
-            ]
-        }
-    },
-    "response_mapping": {
-        "gene_has_variant_that_contributes_to_drug_response_association": {
-            "NCBIGene": "hits.subject.NCBIGene",
-            "effect_size": "hits.association.effect_size",
-            "pvalue": "hits.association.pvalue",
-            "disease_context": "hits.association.context.disease.mondo"
-        }
-    },
-    "tags": [
-        "gene",
-        "disease",
-        "chemical",
-        "association",
-        "annotation",
-        "query",
-        "translator",
-        "biothings",
-        "biothings_graph"
+    "_supportBatch": false,
+    "_method": "get",
+    "_pathParams": [],
+    "_server": "https://biothings.ncats.io/drug_response_kp",
+    "_path": "/query",
+    "_tags": [
+      "gene",
+      "disease",
+      "chemical",
+      "association",
+      "annotation",
+      "query",
+      "translator",
+      "biothings",
+      "biothings_graph"
     ]
-}
\ No newline at end of file
+  },
+  "association": {
+    "input_id": "PUBCHEM",
+    "input_type": "ChemicalSubstance",
+    "output_id": "NCBIGene",
+    "output_type": "Gene",
+    "predicate": "gene_has_variant_that_contributes_to_drug_response_association",
+    "source": "Multiomics Provider",
+    "api_name": "Drug Response KP API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": ["Multiomics Provider", "Service Provider"]
+    }
+  },
+  "response_mapping": {
+    "gene_has_variant_that_contributes_to_drug_response_association": {
+      "NCBIGene": "hits.subject.NCBIGene",
+      "effect_size": "hits.association.effect_size",
+      "pvalue": "hits.association.pvalue",
+      "disease_context": "hits.association.context.disease.mondo"
+    }
+  },
+  "tags": [
+    "gene",
+    "disease",
+    "chemical",
+    "association",
+    "annotation",
+    "query",
+    "translator",
+    "biothings",
+    "biothings_graph"
+  ]
+}
diff --git a/__test__/data/biothings/drug_response_get_response.json b/__test__/data/biothings/drug_response_get_response.json
index d3e75f4..8f64b73 100644
--- a/__test__/data/biothings/drug_response_get_response.json
+++ b/__test__/data/biothings/drug_response_get_response.json
@@ -1,11925 +1,11784 @@
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+    {
+      "_id": "CCDC33-GSK429286A-0.04855926388149771-1.755181757745865",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0004967"
+          }
+        },
+        "effect_size": -1.1789911744795678,
+        "pvalue": 0.04855926388149771
+      },
+      "subject": {
+        "NCBIGene": "80125"
+      }
+    },
+    {
+      "_id": "HDAC7-GSK429286A-0.048619188590668695-4.10433443432677",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0006256"
+          }
+        },
+        "effect_size": -1.231713273897983,
+        "pvalue": 0.048619188590668695
+      },
+      "subject": {
+        "NCBIGene": "51564"
+      }
+    },
+    {
+      "_id": "CSPG4-GSK429286A-0.04865338698113973-2.68383961724685",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0018874"
+          }
+        },
+        "effect_size": -1.088482270729775,
+        "pvalue": 0.04865338698113973
+      },
+      "subject": {
+        "NCBIGene": "1464"
+      }
+    },
+    {
+      "_id": "YTHDC1-GSK429286A-0.04866540748223191-4.10562176192737",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": ["MONDO:0003093", "MONDO:0005580"]
+          }
+        },
+        "effect_size": -1.2707266393149135,
+        "pvalue": 0.04866540748223191
+      },
+      "subject": {
+        "NCBIGene": "91746"
+      }
+    },
+    {
+      "_id": "CNGA1-GSK429286A-0.048761515681429675-3.69493914020001",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0006256"
+          }
+        },
+        "effect_size": -1.2399577462600304,
+        "pvalue": 0.048761515681429675
+      },
+      "subject": {
+        "NCBIGene": "1259"
+      }
+    },
+    {
+      "_id": "UGT1A5-GSK429286A-0.048785268169691476-5.02355415654748",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0005061"
+          }
+        },
+        "effect_size": -0.9577330383825109,
+        "pvalue": 0.048785268169691476
+      },
+      "subject": {
+        "NCBIGene": "54579"
+      }
+    },
+    {
+      "_id": "BTN1A1-GSK429286A-0.049265812114825815-3.69493914020001",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0006256"
+          }
+        },
+        "effect_size": -1.237011934161722,
+        "pvalue": 0.049265812114825815
+      },
+      "subject": {
+        "NCBIGene": "696"
+      }
+    },
+    {
+      "_id": "ABCB8-GSK429286A-0.04928693839886909-4.37380800230499",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0005012"
+          }
+        },
+        "effect_size": -1.2189629893925908,
+        "pvalue": 0.04928693839886909
+      },
+      "subject": {
+        "NCBIGene": "11194"
+      }
+    },
+    {
+      "_id": "PRDM9-GSK429286A-0.049356046574943885-4.228177103746241",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": ["MONDO:0003093", "MONDO:0005580"]
+          }
+        },
+        "effect_size": -1.1095832287302332,
+        "pvalue": 0.049356046574943885
+      },
+      "subject": {
+        "NCBIGene": "56979"
+      }
+    },
+    {
+      "_id": "OPLAH-GSK429286A-0.04940215075788177-4.95941623100301",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0008433"
+          }
+        },
+        "effect_size": -1.284292348654776,
+        "pvalue": 0.04940215075788177
+      },
+      "subject": {
+        "NCBIGene": "26873"
+      }
+    },
+    {
+      "_id": "NUP205-GSK429286A-0.049630820107970805-4.10433443432677",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0006256"
+          }
+        },
+        "effect_size": -0.9784872126877439,
+        "pvalue": 0.049630820107970805
+      },
+      "subject": {
+        "NCBIGene": "23165"
+      }
+    },
+    {
+      "_id": "STAMBPL1-GSK429286A-0.04986829476647059-4.23660382002562",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0005061"
+          }
+        },
+        "effect_size": -1.2027206907980774,
+        "pvalue": 0.04986829476647059
+      },
+      "subject": {
+        "NCBIGene": "57559"
+      }
+    },
+    {
+      "_id": "MCM6-GSK429286A-0.04999095614425051-4.37380800230499",
+      "_score": null,
+      "association": {
+        "context": {
+          "disease": {
+            "mondo": "MONDO:0005012"
+          }
+        },
+        "effect_size": -1.2632984088415444,
+        "pvalue": 0.04999095614425051
+      },
+      "subject": {
+        "NCBIGene": "4175"
+      }
+    }
+  ]
+}
diff --git a/__test__/data/biothings/mychem_example_edge.json b/__test__/data/biothings/mychem_example_edge.json
index 47d58b9..b7f8586 100644
--- a/__test__/data/biothings/mychem_example_edge.json
+++ b/__test__/data/biothings/mychem_example_edge.json
@@ -1,65 +1,45 @@
 {
-    "input": [
-        "DB00188",
-        "DB00184",
-        "DB0000"
-    ],
-    "query_operation": {
-        "_params": {
-            "fields": "drugbank.enzymes"
-        },
-        "_requestBody": {
-            "body": {
-                "q": "{inputs[0]}",
-                "scopes": "drugbank.id"
-            },
-            "header": "application/x-www-form-urlencoded"
-        },
-        "_supportBatch": true,
-        "_inputSeparator": ",",
-        "_method": "post",
-        "_pathParams": [],
-        "_server": "https://mychem.info/v1",
-        "_path": "/query",
-        "_tags": [
-            "chemical",
-            "drug",
-            "annotation",
-            "query",
-            "translator",
-            "biothings"
-        ]
+  "input": ["DB00188", "DB00184", "DB0000"],
+  "query_operation": {
+    "_params": {
+      "fields": "drugbank.enzymes"
     },
-    "association": {
-        "input_id": "DRUGBANK",
-        "input_type": "ChemicalSubstance",
-        "output_id": "SYMBOL",
-        "output_type": "Gene",
-        "predicate": "metabolic_processing_affected_by",
-        "source": "drugbank",
-        "api_name": "MyChem.info API",
-        "smartapi": {},
-        "x-translator": {
-            "component": "KP",
-            "team": [
-                "Service Provider"
-            ]
-        }
+    "_requestBody": {
+      "body": {
+        "q": "{inputs[0]}",
+        "scopes": "drugbank.id"
+      },
+      "header": "application/x-www-form-urlencoded"
     },
-    "response_mapping": {
-        "metabolic_processing_affected_by": {
-            "name": "drugbank.enzymes.name",
-            "SYMBOL": "drugbank.enzymes.gene_name",
-            "function": "drugbank.enzymes.general_function",
-            "action": "drugbank.enzymes.actions"
-        }
-    },
-    "tags": [
-        "chemical",
-        "drug",
-        "annotation",
-        "query",
-        "translator",
-        "biothings"
-    ]
-}
\ No newline at end of file
+    "_supportBatch": true,
+    "_inputSeparator": ",",
+    "_method": "post",
+    "_pathParams": [],
+    "_server": "https://mychem.info/v1",
+    "_path": "/query",
+    "_tags": ["chemical", "drug", "annotation", "query", "translator", "biothings"]
+  },
+  "association": {
+    "input_id": "DRUGBANK",
+    "input_type": "ChemicalSubstance",
+    "output_id": "SYMBOL",
+    "output_type": "Gene",
+    "predicate": "metabolic_processing_affected_by",
+    "source": "drugbank",
+    "api_name": "MyChem.info API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": ["Service Provider"]
+    }
+  },
+  "response_mapping": {
+    "metabolic_processing_affected_by": {
+      "name": "drugbank.enzymes.name",
+      "SYMBOL": "drugbank.enzymes.gene_name",
+      "function": "drugbank.enzymes.general_function",
+      "action": "drugbank.enzymes.actions"
+    }
+  },
+  "tags": ["chemical", "drug", "annotation", "query", "translator", "biothings"]
+}
diff --git a/__test__/data/biothings/mychem_post.json b/__test__/data/biothings/mychem_post.json
index 48a751e..2136214 100644
--- a/__test__/data/biothings/mychem_post.json
+++ b/__test__/data/biothings/mychem_post.json
@@ -1,337 +1,250 @@
 [
-    {
-        "query": "DB00188",
-        "fake": true
-    },
-    {
-        "query": "DB00188",
-        "_id": "GXJABQQUPOEUTA-RDJZCZTQSA-N",
-        "_score": 6.163889,
-        "drugbank": {
-            "_license": "http://bit.ly/2PSfZTD",
-            "enzymes": [
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP3A4",
-                    "general_function": "Vitamin d3 25-hydroxylase activity",
-                    "id": "BE0002638",
-                    "known_action": "no",
-                    "name": "Cytochrome P450 3A4",
-                    "organism": "Humans",
-                    "pmids": [
-                        22087865,
-                        26622646,
-                        15764713,
-                        16443666
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).",
-                    "uniprot": "P08684"
-                },
-                {
-                    "actions": [
-                        "substrate",
-                        "inhibitor"
-                    ],
-                    "gene_name": "CYP2C19",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0003536",
-                    "known_action": "no",
-                    "name": "Cytochrome P450 2C19",
-                    "organism": "Humans",
-                    "pmids": [
-                        19515014,
-                        15764713,
-                        16103134,
-                        16443666
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.",
-                    "uniprot": "P33261"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2D6",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0002363",
-                    "name": "Cytochrome P450 2D6",
-                    "organism": "Humans",
-                    "pmids": [
-                        19515014,
-                        16103134,
-                        15764713
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.",
-                    "uniprot": "P10635"
-                },
-                {
-                    "actions": [
-                        "substrate",
-                        "inhibitor"
-                    ],
-                    "gene_name": "CYP1A2",
-                    "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen",
-                    "id": "BE0002433",
-                    "known_action": "no",
-                    "name": "Cytochrome P450 1A2",
-                    "organism": "Humans",
-                    "pmids": [
-                        15764713
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.",
-                    "uniprot": "P05177"
-                },
-                {
-                    "actions": [
-                        "substrate",
-                        "inhibitor"
-                    ],
-                    "gene_name": "CYP2C9",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0002793",
-                    "known_action": "no",
-                    "name": "Cytochrome P450 2C9",
-                    "organism": "Humans",
-                    "pmids": [
-                        15764713,
-                        16443666,
-                        16103134
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.",
-                    "uniprot": "P11712"
-                }
-            ]
+  {
+    "query": "DB00188",
+    "fake": true
+  },
+  {
+    "query": "DB00188",
+    "_id": "GXJABQQUPOEUTA-RDJZCZTQSA-N",
+    "_score": 6.163889,
+    "drugbank": {
+      "_license": "http://bit.ly/2PSfZTD",
+      "enzymes": [
+        {
+          "actions": "substrate",
+          "gene_name": "CYP3A4",
+          "general_function": "Vitamin d3 25-hydroxylase activity",
+          "id": "BE0002638",
+          "known_action": "no",
+          "name": "Cytochrome P450 3A4",
+          "organism": "Humans",
+          "pmids": [22087865, 26622646, 15764713, 16443666],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).",
+          "uniprot": "P08684"
+        },
+        {
+          "actions": ["substrate", "inhibitor"],
+          "gene_name": "CYP2C19",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0003536",
+          "known_action": "no",
+          "name": "Cytochrome P450 2C19",
+          "organism": "Humans",
+          "pmids": [19515014, 15764713, 16103134, 16443666],
+          "source": "Swiss-Prot",
+          "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.",
+          "uniprot": "P33261"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2D6",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0002363",
+          "name": "Cytochrome P450 2D6",
+          "organism": "Humans",
+          "pmids": [19515014, 16103134, 15764713],
+          "source": "Swiss-Prot",
+          "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.",
+          "uniprot": "P10635"
+        },
+        {
+          "actions": ["substrate", "inhibitor"],
+          "gene_name": "CYP1A2",
+          "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen",
+          "id": "BE0002433",
+          "known_action": "no",
+          "name": "Cytochrome P450 1A2",
+          "organism": "Humans",
+          "pmids": [15764713],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.",
+          "uniprot": "P05177"
+        },
+        {
+          "actions": ["substrate", "inhibitor"],
+          "gene_name": "CYP2C9",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0002793",
+          "known_action": "no",
+          "name": "Cytochrome P450 2C9",
+          "organism": "Humans",
+          "pmids": [15764713, 16443666, 16103134],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.",
+          "uniprot": "P11712"
         }
-    },
-    {
-        "query": "DB00184",
-        "_id": "SNICXCGAKADSCV-JTQLQIEISA-N",
-        "_score": 6.411114,
-        "drugbank": {
-            "_license": "http://bit.ly/2PSfZTD",
-            "enzymes": [
-                {
-                    "actions": [
-                        "substrate",
-                        "inhibitor"
-                    ],
-                    "gene_name": "CYP2A6",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0003336",
-                    "name": "Cytochrome P450 2A6",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185,
-                        22869927,
-                        11678779,
-                        14757175
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Exhibits a high coumarin 7-hydroxylase activity. Can act in the hydroxylation of the anti-cancer drugs cyclophosphamide and ifosphamide. Competent in the metabolic activation of aflatoxin B1. Constitutes the major nicotine C-oxidase. Acts as a 1,4-cineole 2-exo-monooxygenase. Possesses low phenacetin O-deethylation activity.",
-                    "uniprot": "P11509"
-                },
-                {
-                    "actions": [
-                        "substrate",
-                        "inhibitor",
-                        "inducer"
-                    ],
-                    "gene_name": "CYP2E1",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0003533",
-                    "name": "Cytochrome P450 2E1",
-                    "organism": "Humans",
-                    "pmids": [
-                        12711639,
-                        11719700,
-                        10350185,
-                        12750430,
-                        20233178,
-                        8328992
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.",
-                    "uniprot": "P05181"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2A13",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0003534",
-                    "name": "Cytochrome P450 2A13",
-                    "organism": "Humans",
-                    "pmids": [
-                        16188955,
-                        15196988,
-                        15528319
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Exhibits a coumarin 7-hydroxylase activity. Active in the metabolic activation of hexamethylphosphoramide, N,N-dimethylaniline, 2'-methoxyacetophenone, N-nitrosomethylphenylamine, and the tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Possesses phenacetin O-deethylation activity.",
-                    "uniprot": "Q16696"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2B6",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0003549",
-                    "name": "Cytochrome P450 2B6",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185,
-                        11996015
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,4-cineole 2-exo-monooxygenase.",
-                    "uniprot": "P20813"
-                },
-                {
-                    "actions": [
-                        "substrate",
-                        "inducer"
-                    ],
-                    "gene_name": "CYP1A1",
-                    "general_function": "Vitamin d 24-hydroxylase activity",
-                    "id": "BE0003543",
-                    "name": "Cytochrome P450 1A1",
-                    "organism": "Humans",
-                    "pmids": [
-                        11849738,
-                        10427467,
-                        10350185
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.",
-                    "uniprot": "P04798"
-                },
-                {
-                    "actions": [
-                        "substrate",
-                        "inducer"
-                    ],
-                    "gene_name": "CYP1A2",
-                    "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen",
-                    "id": "BE0002433",
-                    "name": "Cytochrome P450 1A2",
-                    "organism": "Humans",
-                    "pmids": [
-                        21599724,
-                        10427467,
-                        10350185,
-                        20932495
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.",
-                    "uniprot": "P05177"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2C19",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0003536",
-                    "name": "Cytochrome P450 2C19",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.",
-                    "uniprot": "P33261"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2C8",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0002887",
-                    "name": "Cytochrome P450 2C8",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it generates only 14,15- and 11,12-cis-epoxyeicosatrienoic acids. It is the principal enzyme responsible for the metabolism the anti-cancer drug paclitaxel (taxol).",
-                    "uniprot": "P10632"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2C9",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0002793",
-                    "name": "Cytochrome P450 2C9",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.",
-                    "uniprot": "P11712"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP2D6",
-                    "general_function": "Steroid hydroxylase activity",
-                    "id": "BE0002363",
-                    "name": "Cytochrome P450 2D6",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185,
-                        8807663,
-                        26287939
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.",
-                    "uniprot": "P10635"
-                },
-                {
-                    "actions": "substrate",
-                    "gene_name": "CYP3A4",
-                    "general_function": "Vitamin d3 25-hydroxylase activity",
-                    "id": "BE0002638",
-                    "name": "Cytochrome P450 3A4",
-                    "organism": "Humans",
-                    "pmids": [
-                        10350185
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).",
-                    "uniprot": "P08684"
-                },
-                {
-                    "actions": "inhibitor",
-                    "gene_name": "MAOA",
-                    "general_function": "Serotonin binding",
-                    "id": "BE0002198",
-                    "name": "Amine oxidase [flavin-containing] A",
-                    "organism": "Humans",
-                    "pmids": [
-                        21636610,
-                        19142115
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.",
-                    "uniprot": "P21397"
-                },
-                {
-                    "actions": "inhibitor",
-                    "gene_name": "MAOB",
-                    "general_function": "Primary amine oxidase activity",
-                    "id": "BE0002196",
-                    "name": "Amine oxidase [flavin-containing] B",
-                    "organism": "Humans",
-                    "pmids": [
-                        21636610
-                    ],
-                    "source": "Swiss-Prot",
-                    "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.",
-                    "uniprot": "P27338"
-                }
-            ]
+      ]
+    }
+  },
+  {
+    "query": "DB00184",
+    "_id": "SNICXCGAKADSCV-JTQLQIEISA-N",
+    "_score": 6.411114,
+    "drugbank": {
+      "_license": "http://bit.ly/2PSfZTD",
+      "enzymes": [
+        {
+          "actions": ["substrate", "inhibitor"],
+          "gene_name": "CYP2A6",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0003336",
+          "name": "Cytochrome P450 2A6",
+          "organism": "Humans",
+          "pmids": [10350185, 22869927, 11678779, 14757175],
+          "source": "Swiss-Prot",
+          "specific_function": "Exhibits a high coumarin 7-hydroxylase activity. Can act in the hydroxylation of the anti-cancer drugs cyclophosphamide and ifosphamide. Competent in the metabolic activation of aflatoxin B1. Constitutes the major nicotine C-oxidase. Acts as a 1,4-cineole 2-exo-monooxygenase. Possesses low phenacetin O-deethylation activity.",
+          "uniprot": "P11509"
+        },
+        {
+          "actions": ["substrate", "inhibitor", "inducer"],
+          "gene_name": "CYP2E1",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0003533",
+          "name": "Cytochrome P450 2E1",
+          "organism": "Humans",
+          "pmids": [12711639, 11719700, 10350185, 12750430, 20233178, 8328992],
+          "source": "Swiss-Prot",
+          "specific_function": "Metabolizes several precarcinogens, drugs, and solvents to reactive metabolites. Inactivates a number of drugs and xenobiotics and also bioactivates many xenobiotic substrates to their hepatotoxic or carcinogenic forms.",
+          "uniprot": "P05181"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2A13",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0003534",
+          "name": "Cytochrome P450 2A13",
+          "organism": "Humans",
+          "pmids": [16188955, 15196988, 15528319],
+          "source": "Swiss-Prot",
+          "specific_function": "Exhibits a coumarin 7-hydroxylase activity. Active in the metabolic activation of hexamethylphosphoramide, N,N-dimethylaniline, 2'-methoxyacetophenone, N-nitrosomethylphenylamine, and the tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Possesses phenacetin O-deethylation activity.",
+          "uniprot": "Q16696"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2B6",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0003549",
+          "name": "Cytochrome P450 2B6",
+          "organism": "Humans",
+          "pmids": [10350185, 11996015],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,4-cineole 2-exo-monooxygenase.",
+          "uniprot": "P20813"
+        },
+        {
+          "actions": ["substrate", "inducer"],
+          "gene_name": "CYP1A1",
+          "general_function": "Vitamin d 24-hydroxylase activity",
+          "id": "BE0003543",
+          "name": "Cytochrome P450 1A1",
+          "organism": "Humans",
+          "pmids": [11849738, 10427467, 10350185],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.",
+          "uniprot": "P04798"
+        },
+        {
+          "actions": ["substrate", "inducer"],
+          "gene_name": "CYP1A2",
+          "general_function": "Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen",
+          "id": "BE0002433",
+          "name": "Cytochrome P450 1A2",
+          "organism": "Humans",
+          "pmids": [21599724, 10427467, 10350185, 20932495],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.",
+          "uniprot": "P05177"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2C19",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0003536",
+          "name": "Cytochrome P450 2C19",
+          "organism": "Humans",
+          "pmids": [10350185],
+          "source": "Swiss-Prot",
+          "specific_function": "Responsible for the metabolism of a number of therapeutic agents such as the anticonvulsant drug S-mephenytoin, omeprazole, proguanil, certain barbiturates, diazepam, propranolol, citalopram and imipramine.",
+          "uniprot": "P33261"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2C8",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0002887",
+          "name": "Cytochrome P450 2C8",
+          "organism": "Humans",
+          "pmids": [10350185],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. In the epoxidation of arachidonic acid it generates only 14,15- and 11,12-cis-epoxyeicosatrienoic acids. It is the principal enzyme responsible for the metabolism the anti-cancer drug paclitaxel (taxol).",
+          "uniprot": "P10632"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2C9",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0002793",
+          "name": "Cytochrome P450 2C9",
+          "organism": "Humans",
+          "pmids": [10350185],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.",
+          "uniprot": "P11712"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP2D6",
+          "general_function": "Steroid hydroxylase activity",
+          "id": "BE0002363",
+          "name": "Cytochrome P450 2D6",
+          "organism": "Humans",
+          "pmids": [10350185, 8807663, 26287939],
+          "source": "Swiss-Prot",
+          "specific_function": "Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.",
+          "uniprot": "P10635"
+        },
+        {
+          "actions": "substrate",
+          "gene_name": "CYP3A4",
+          "general_function": "Vitamin d3 25-hydroxylase activity",
+          "id": "BE0002638",
+          "name": "Cytochrome P450 3A4",
+          "organism": "Humans",
+          "pmids": [10350185],
+          "source": "Swiss-Prot",
+          "specific_function": "Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide (PubMed:11159812). Catalyzes 4-beta-hydroxylation of cholesterol. May catalyze 25-hydroxylation of cholesterol in vitro (PubMed:21576599).",
+          "uniprot": "P08684"
+        },
+        {
+          "actions": "inhibitor",
+          "gene_name": "MAOA",
+          "general_function": "Serotonin binding",
+          "id": "BE0002198",
+          "name": "Amine oxidase [flavin-containing] A",
+          "organism": "Humans",
+          "pmids": [21636610, 19142115],
+          "source": "Swiss-Prot",
+          "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.",
+          "uniprot": "P21397"
+        },
+        {
+          "actions": "inhibitor",
+          "gene_name": "MAOB",
+          "general_function": "Primary amine oxidase activity",
+          "id": "BE0002196",
+          "name": "Amine oxidase [flavin-containing] B",
+          "organism": "Humans",
+          "pmids": [21636610],
+          "source": "Swiss-Prot",
+          "specific_function": "Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.",
+          "uniprot": "P27338"
         }
-    },
-    {
-        "query": "DBOOOO",
-        "notfound": true
+      ]
     }
-]
\ No newline at end of file
+  },
+  {
+    "query": "DBOOOO",
+    "notfound": true
+  }
+]
diff --git a/__test__/data/biothings/mygene_example_edge.json b/__test__/data/biothings/mygene_example_edge.json
index b01b575..0ba1e8d 100644
--- a/__test__/data/biothings/mygene_example_edge.json
+++ b/__test__/data/biothings/mygene_example_edge.json
@@ -1,58 +1,44 @@
 {
-    "query_operation": {
-        "_params": {
-            "fields": "go.BP"
-        },
-        "_requestBody": {
-            "body": {
-                "q": "{inputs[0]}",
-                "scopes": "entrezgene"
-            },
-            "header": "application/x-www-form-urlencoded"
-        },
-        "_supportBatch": true,
-        "_inputSeparator": ",",
-        "_method": "post",
-        "_pathParams": [],
-        "_server": "https://mygene.info/v3",
-        "_path": "/query",
-        "_tags": [
-            "gene",
-            "annotation",
-            "query",
-            "translator",
-            "biothings"
-        ]
+  "query_operation": {
+    "_params": {
+      "fields": "go.BP"
     },
-    "association": {
-        "input_id": "NCBIGene",
-        "input_type": "Gene",
-        "output_id": "GO",
-        "output_type": "BiologicalProcess",
-        "predicate": "functional_association",
-        "source": "entrez",
-        "api_name": "MyGene.info API",
-        "smartapi": {},
-        "x-translator": {
-            "component": "KP",
-            "team": [
-                "Service Provider"
-            ]
-        }
+    "_requestBody": {
+      "body": {
+        "q": "{inputs[0]}",
+        "scopes": "entrezgene"
+      },
+      "header": "application/x-www-form-urlencoded"
     },
-    "response_mapping": {
-        "functional_association": {
-            "evidence": "go.BP.evidence",
-            "GO": "go.BP.id",
-            "pubmed": "go.BP.pubmed",
-            "term": "go.BP.term"
-        }
-    },
-    "tags": [
-        "gene",
-        "annotation",
-        "query",
-        "translator",
-        "biothings"
-    ]
-}
\ No newline at end of file
+    "_supportBatch": true,
+    "_inputSeparator": ",",
+    "_method": "post",
+    "_pathParams": [],
+    "_server": "https://mygene.info/v3",
+    "_path": "/query",
+    "_tags": ["gene", "annotation", "query", "translator", "biothings"]
+  },
+  "association": {
+    "input_id": "NCBIGene",
+    "input_type": "Gene",
+    "output_id": "GO",
+    "output_type": "BiologicalProcess",
+    "predicate": "functional_association",
+    "source": "entrez",
+    "api_name": "MyGene.info API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": ["Service Provider"]
+    }
+  },
+  "response_mapping": {
+    "functional_association": {
+      "evidence": "go.BP.evidence",
+      "GO": "go.BP.id",
+      "pubmed": "go.BP.pubmed",
+      "term": "go.BP.term"
+    }
+  },
+  "tags": ["gene", "annotation", "query", "translator", "biothings"]
+}
diff --git a/__test__/data/biothings/mygene_post.json b/__test__/data/biothings/mygene_post.json
index 2fb6c5c..3d3c897 100644
--- a/__test__/data/biothings/mygene_post.json
+++ b/__test__/data/biothings/mygene_post.json
@@ -1,196 +1,193 @@
 [
-    {
-        "query": "1017",
-        "_id": "1017",
-        "_score": 23.263514,
-        "go": {
-            "BP": [
-                {
-                    "evidence": "IBA",
-                    "gocategory": "BP",
-                    "id": "GO:0000082",
-                    "pubmed": 21873635,
-                    "term": "G1/S transition of mitotic cell cycle"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0000082",
-                    "term": "G1/S transition of mitotic cell cycle"
-                },
-                {
-                    "evidence": "NAS",
-                    "gocategory": "BP",
-                    "id": "GO:0000086",
-                    "pubmed": 1653904,
-                    "term": "G2/M transition of mitotic cell cycle"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0000086",
-                    "term": "G2/M transition of mitotic cell cycle"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0006260",
-                    "pubmed": 19238148,
-                    "term": "DNA replication"
-                },
-                {
-                    "evidence": "IEA",
-                    "gocategory": "BP",
-                    "id": "GO:0006281",
-                    "term": "DNA repair"
-                },
-                {
-                    "evidence": "IBA",
-                    "gocategory": "BP",
-                    "id": "GO:0006468",
-                    "pubmed": 21873635,
-                    "term": "protein phosphorylation"
-                },
-                {
-                    "evidence": "IDA",
-                    "gocategory": "BP",
-                    "id": "GO:0006468",
-                    "pubmed": [
-                        12944431,
-                        28666995
-                    ],
-                    "term": "protein phosphorylation"
-                },
-                {
-                    "evidence": "IMP",
-                    "gocategory": "BP",
-                    "id": "GO:0006468",
-                    "pubmed": 29203878,
-                    "term": "protein phosphorylation"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0006977",
-                    "term": "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest"
-                },
-                {
-                    "evidence": "IMP",
-                    "gocategory": "BP",
-                    "id": "GO:0007099",
-                    "pubmed": 26297806,
-                    "term": "centriole replication"
-                },
-                {
-                    "evidence": "IBA",
-                    "gocategory": "BP",
-                    "id": "GO:0007165",
-                    "pubmed": 21873635,
-                    "term": "signal transduction"
-                },
-                {
-                    "evidence": "IEP",
-                    "gocategory": "BP",
-                    "id": "GO:0007265",
-                    "pubmed": 9054499,
-                    "term": "Ras protein signal transduction"
-                },
-                {
-                    "evidence": "IBA",
-                    "gocategory": "BP",
-                    "id": "GO:0008284",
-                    "pubmed": 21873635,
-                    "term": "positive regulation of cell population proliferation"
-                },
-                {
-                    "evidence": "IDA",
-                    "gocategory": "BP",
-                    "id": "GO:0008284",
-                    "pubmed": 10767298,
-                    "term": "positive regulation of cell population proliferation"
-                },
-                {
-                    "evidence": "IBA",
-                    "gocategory": "BP",
-                    "id": "GO:0010389",
-                    "pubmed": 21873635,
-                    "term": "regulation of G2/M transition of mitotic cell cycle"
-                },
-                {
-                    "evidence": "IBA",
-                    "gocategory": "BP",
-                    "id": "GO:0010468",
-                    "pubmed": 21873635,
-                    "term": "regulation of gene expression"
-                },
-                {
-                    "evidence": "IDA",
-                    "gocategory": "BP",
-                    "id": "GO:0016572",
-                    "pubmed": 11746698,
-                    "term": "histone phosphorylation"
-                },
-                {
-                    "evidence": "IDA",
-                    "gocategory": "BP",
-                    "id": "GO:0018105",
-                    "pubmed": 23184662,
-                    "term": "peptidyl-serine phosphorylation"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0031145",
-                    "term": "anaphase-promoting complex-dependent catabolic process"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0031571",
-                    "pubmed": 21319273,
-                    "term": "mitotic G1 DNA damage checkpoint"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0051298",
-                    "pubmed": 19238148,
-                    "term": "centrosome duplication"
-                },
-                {
-                    "evidence": "IEA",
-                    "gocategory": "BP",
-                    "id": "GO:0051301",
-                    "term": "cell division"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0051321",
-                    "pubmed": 19238148,
-                    "term": "meiotic cell cycle"
-                },
-                {
-                    "evidence": "IDA",
-                    "gocategory": "BP",
-                    "id": "GO:0060968",
-                    "pubmed": 20935635,
-                    "term": "regulation of gene silencing"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:0071732",
-                    "pubmed": 20079829,
-                    "term": "cellular response to nitric oxide"
-                },
-                {
-                    "evidence": "TAS",
-                    "gocategory": "BP",
-                    "id": "GO:1901796",
-                    "term": "regulation of signal transduction by p53 class mediator"
-                }
-            ]
+  {
+    "query": "1017",
+    "_id": "1017",
+    "_score": 23.263514,
+    "go": {
+      "BP": [
+        {
+          "evidence": "IBA",
+          "gocategory": "BP",
+          "id": "GO:0000082",
+          "pubmed": 21873635,
+          "term": "G1/S transition of mitotic cell cycle"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0000082",
+          "term": "G1/S transition of mitotic cell cycle"
+        },
+        {
+          "evidence": "NAS",
+          "gocategory": "BP",
+          "id": "GO:0000086",
+          "pubmed": 1653904,
+          "term": "G2/M transition of mitotic cell cycle"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0000086",
+          "term": "G2/M transition of mitotic cell cycle"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0006260",
+          "pubmed": 19238148,
+          "term": "DNA replication"
+        },
+        {
+          "evidence": "IEA",
+          "gocategory": "BP",
+          "id": "GO:0006281",
+          "term": "DNA repair"
+        },
+        {
+          "evidence": "IBA",
+          "gocategory": "BP",
+          "id": "GO:0006468",
+          "pubmed": 21873635,
+          "term": "protein phosphorylation"
+        },
+        {
+          "evidence": "IDA",
+          "gocategory": "BP",
+          "id": "GO:0006468",
+          "pubmed": [12944431, 28666995],
+          "term": "protein phosphorylation"
+        },
+        {
+          "evidence": "IMP",
+          "gocategory": "BP",
+          "id": "GO:0006468",
+          "pubmed": 29203878,
+          "term": "protein phosphorylation"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0006977",
+          "term": "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest"
+        },
+        {
+          "evidence": "IMP",
+          "gocategory": "BP",
+          "id": "GO:0007099",
+          "pubmed": 26297806,
+          "term": "centriole replication"
+        },
+        {
+          "evidence": "IBA",
+          "gocategory": "BP",
+          "id": "GO:0007165",
+          "pubmed": 21873635,
+          "term": "signal transduction"
+        },
+        {
+          "evidence": "IEP",
+          "gocategory": "BP",
+          "id": "GO:0007265",
+          "pubmed": 9054499,
+          "term": "Ras protein signal transduction"
+        },
+        {
+          "evidence": "IBA",
+          "gocategory": "BP",
+          "id": "GO:0008284",
+          "pubmed": 21873635,
+          "term": "positive regulation of cell population proliferation"
+        },
+        {
+          "evidence": "IDA",
+          "gocategory": "BP",
+          "id": "GO:0008284",
+          "pubmed": 10767298,
+          "term": "positive regulation of cell population proliferation"
+        },
+        {
+          "evidence": "IBA",
+          "gocategory": "BP",
+          "id": "GO:0010389",
+          "pubmed": 21873635,
+          "term": "regulation of G2/M transition of mitotic cell cycle"
+        },
+        {
+          "evidence": "IBA",
+          "gocategory": "BP",
+          "id": "GO:0010468",
+          "pubmed": 21873635,
+          "term": "regulation of gene expression"
+        },
+        {
+          "evidence": "IDA",
+          "gocategory": "BP",
+          "id": "GO:0016572",
+          "pubmed": 11746698,
+          "term": "histone phosphorylation"
+        },
+        {
+          "evidence": "IDA",
+          "gocategory": "BP",
+          "id": "GO:0018105",
+          "pubmed": 23184662,
+          "term": "peptidyl-serine phosphorylation"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0031145",
+          "term": "anaphase-promoting complex-dependent catabolic process"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0031571",
+          "pubmed": 21319273,
+          "term": "mitotic G1 DNA damage checkpoint"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0051298",
+          "pubmed": 19238148,
+          "term": "centrosome duplication"
+        },
+        {
+          "evidence": "IEA",
+          "gocategory": "BP",
+          "id": "GO:0051301",
+          "term": "cell division"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0051321",
+          "pubmed": 19238148,
+          "term": "meiotic cell cycle"
+        },
+        {
+          "evidence": "IDA",
+          "gocategory": "BP",
+          "id": "GO:0060968",
+          "pubmed": 20935635,
+          "term": "regulation of gene silencing"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:0071732",
+          "pubmed": 20079829,
+          "term": "cellular response to nitric oxide"
+        },
+        {
+          "evidence": "TAS",
+          "gocategory": "BP",
+          "id": "GO:1901796",
+          "term": "regulation of signal transduction by p53 class mediator"
         }
+      ]
     }
-]
\ No newline at end of file
+  }
+]
diff --git a/__test__/data/ctd/edge.json b/__test__/data/ctd/edge.json
index 992f360..9eaa93a 100644
--- a/__test__/data/ctd/edge.json
+++ b/__test__/data/ctd/edge.json
@@ -1,47 +1,39 @@
 {
-    "input": "1017",
-    "query_operation": {
-        "_params": {
-            "inputType": "gene",
-            "report": "diseases_curated",
-            "format": "json",
-            "inputTerms": "{inputs[0]}"
-        },
-        "_supportBatch": false,
-        "method": "get",
-        "_pathParams": [],
-        "_server": "http://ctdbase.org/tools",
-        "_path": "/batchQuery.go",
-        "_tags": [
-            "translator",
-            "ctd"
-        ]
+  "input": "1017",
+  "query_operation": {
+    "_params": {
+      "inputType": "gene",
+      "report": "diseases_curated",
+      "format": "json",
+      "inputTerms": "{inputs[0]}"
     },
-    "association": {
-        "input_id": "NCBIGene",
-        "input_type": "Gene",
-        "output_id": "MESH",
-        "output_type": "Disease",
-        "predicate": "related_to",
-        "source": "CTD",
-        "api_name": "CTD API",
-        "smartapi": {},
-        "x-translator": {
-            "component": "KP",
-            "team": [
-                "Service Provider"
-            ]
-        }
-    },
-    "response_mapping": {
-        "related_to": {
-            "MESH": "data.DiseaseID",
-            "name": "data.DiseaseName",
-            "pubmed": "data.PubMedIDs"
-        }
-    },
-    "tags": [
-        "translator",
-        "ctd"
-    ]
-}
\ No newline at end of file
+    "_supportBatch": false,
+    "method": "get",
+    "_pathParams": [],
+    "_server": "http://ctdbase.org/tools",
+    "_path": "/batchQuery.go",
+    "_tags": ["translator", "ctd"]
+  },
+  "association": {
+    "input_id": "NCBIGene",
+    "input_type": "Gene",
+    "output_id": "MESH",
+    "output_type": "Disease",
+    "predicate": "related_to",
+    "source": "CTD",
+    "api_name": "CTD API",
+    "smartapi": {},
+    "x-translator": {
+      "component": "KP",
+      "team": ["Service Provider"]
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "MESH": "data.DiseaseID",
+      "name": "data.DiseaseName",
+      "pubmed": "data.PubMedIDs"
+    }
+  },
+  "tags": ["translator", "ctd"]
+}
diff --git a/__test__/data/ctd/response.json b/__test__/data/ctd/response.json
index 08a9a2b..9f2b67c 100644
--- a/__test__/data/ctd/response.json
+++ b/__test__/data/ctd/response.json
@@ -1,22 +1,22 @@
 [
-    {
-        "DirectEvidence": "marker/mechanism",
-        "DiseaseCategories": "Cancer",
-        "DiseaseID": "MESH:D008545",
-        "DiseaseName": "Melanoma",
-        "GeneID": "1017",
-        "GeneSymbol": "CDK2",
-        "Input": "1017",
-        "PubMedIDs": "21559390"
-    },
-    {
-        "DirectEvidence": "marker/mechanism",
-        "DiseaseCategories": "Cancer",
-        "DiseaseID": "MESH:D000077195",
-        "DiseaseName": "Squamous Cell Carcinoma of Head and Neck",
-        "GeneID": "1017",
-        "GeneSymbol": "CDK2",
-        "Input": "1017",
-        "PubMedIDs": "29464035"
-    }
-]
\ No newline at end of file
+  {
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Cancer",
+    "DiseaseID": "MESH:D008545",
+    "DiseaseName": "Melanoma",
+    "GeneID": "1017",
+    "GeneSymbol": "CDK2",
+    "Input": "1017",
+    "PubMedIDs": "21559390"
+  },
+  {
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Cancer",
+    "DiseaseID": "MESH:D000077195",
+    "DiseaseName": "Squamous Cell Carcinoma of Head and Neck",
+    "GeneID": "1017",
+    "GeneSymbol": "CDK2",
+    "Input": "1017",
+    "PubMedIDs": "29464035"
+  }
+]
diff --git a/__test__/data/ctd/response2.json b/__test__/data/ctd/response2.json
index 39c353e..8f0a95f 100644
--- a/__test__/data/ctd/response2.json
+++ b/__test__/data/ctd/response2.json
@@ -1 +1,1482 @@
-[{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Pregnancy complication","DiseaseID":"MESH:D000022","DiseaseName":"Abortion, Spontaneous","Input":"d003634","PubMedIDs":"16120699"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D018248","DiseaseName":"Adenoma, Liver Cell","Input":"d003634","PubMedIDs":"12597452"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Occupational disease","DiseaseID":"MESH:D000382","DiseaseName":"Agricultural Workers' Diseases","Input":"d003634","PubMedIDs":"12584743|16487989|17182642|17495700|17932376|17975796|19541724|20061368|20730623|24064777"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Urogenital disease (male)","DiseaseID":"MESH:D053627","DiseaseName":"Asthenozoospermia","Input":"d003634","PubMedIDs":"19303595"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Immune system disease|Respiratory tract disease","DiseaseID":"MESH:D001249","DiseaseName":"Asthma","Input":"d003634","PubMedIDs":"17932376|19541724"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Urogenital disease (male)","DiseaseID":"MESH:D053713","DiseaseName":"Azoospermia","Input":"d003634","PubMedIDs":"31682807"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Skin disease","DiseaseID":"MESH:D001943","DiseaseName":"Breast Neoplasms","Input":"d003634","PubMedIDs":"12709520|16792888|17938728"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Pathology (process)|Respiratory tract disease","DiseaseID":"MESH:D029481","DiseaseName":"Bronchitis, Chronic","Input":"d003634","PubMedIDs":"17495700|17975796"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D006528","DiseaseName":"Carcinoma, Hepatocellular","Input":"d003634","PubMedIDs":"12597452|21035526|6667461"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cardiovascular disease|Pathology (anatomical condition)","DiseaseID":"MESH:D006332","DiseaseName":"Cardiomegaly","Input":"d003634","PubMedIDs":"27325568"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease","DiseaseID":"MESH:D056486","DiseaseName":"Chemical and Drug Induced Liver Injury","Input":"d003634","PubMedIDs":"11272408|18675336"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder","DiseaseID":"MESH:D002653","DiseaseName":"Child Behavior Disorders","Input":"d003634","PubMedIDs":"27466755"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder","DiseaseID":"MESH:D003072","DiseaseName":"Cognition Disorders","Input":"d003634","PubMedIDs":"26630154"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D003110","DiseaseName":"Colonic Neoplasms","Input":"d003634","PubMedIDs":"20730623"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Congenital abnormality","DiseaseID":"MESH:D000013","DiseaseName":"Congenital Abnormalities","Input":"d003634","PubMedIDs":"15095906"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseID":"MESH:D009358","DiseaseName":"Congenital, Hereditary, and Neonatal Diseases and Abnormalities","Input":"d003634","PubMedIDs":"31682807"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Congenital abnormality|Endocrine system disease|Urogenital disease (male)","DiseaseID":"MESH:D003456","DiseaseName":"Cryptorchidism","Input":"d003634","PubMedIDs":"16835070"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder","DiseaseID":"MESH:D003866","DiseaseName":"Depressive Disorder","Input":"d003634","PubMedIDs":"28263910"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Endocrine system disease|Metabolic disease","DiseaseID":"MESH:D003920","DiseaseName":"Diabetes Mellitus","Input":"d003634","PubMedIDs":"31746186"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseID":"MESH:D064420","DiseaseName":"Drug-Related Side Effects and Adverse Reactions","Input":"d003634","PubMedIDs":"2370251"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Respiratory tract disease|Signs and symptoms","DiseaseID":"MESH:D004417","DiseaseName":"Dyspnea","Input":"d003634","PubMedIDs":"16487989"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Immune system disease|Occupational disease|Respiratory tract disease","DiseaseID":"MESH:D005203","DiseaseName":"Farmer's Lung","Input":"d003634","PubMedIDs":"17182642"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease","DiseaseID":"MESH:D005234","DiseaseName":"Fatty Liver","Input":"d003634","PubMedIDs":"31746186"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Fetal disease|Pathology (process)|Pregnancy complication","DiseaseID":"MESH:D005317","DiseaseName":"Fetal Growth Retardation","Input":"d003634","PubMedIDs":"22310945"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Signs and symptoms","DiseaseID":"MESH:D005334","DiseaseName":"Fever","Input":"d003634","PubMedIDs":"3088650"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease","DiseaseID":"MESH:D006505","DiseaseName":"Hepatitis","Input":"d003634","PubMedIDs":"16487989"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease|Pathology (anatomical condition)","DiseaseID":"MESH:D006529","DiseaseName":"Hepatomegaly","Input":"d003634","PubMedIDs":"11272408|23684557|2387028"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cardiovascular disease","DiseaseID":"MESH:D006973","DiseaseName":"Hypertension","Input":"d003634","PubMedIDs":"27325568"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Endocrine system disease","DiseaseID":"MESH:D007037","DiseaseName":"Hypothyroidism","Input":"d003634","PubMedIDs":"20061368|24064777"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Infant-newborn disease","DiseaseID":"MESH:D007232","DiseaseName":"Infant, Newborn, Diseases","Input":"d003634","PubMedIDs":"31682807"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Urogenital disease (male)","DiseaseID":"MESH:D007248","DiseaseName":"Infertility, Male","Input":"d003634","PubMedIDs":"17157474|17192596|19303595"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Metabolic disease","DiseaseID":"MESH:D007333","DiseaseName":"Insulin Resistance","Input":"d003634","PubMedIDs":"31746186"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Urogenital disease (female)|Urogenital disease (male)","DiseaseID":"MESH:D007674","DiseaseName":"Kidney Diseases","Input":"d003634","PubMedIDs":"31682807"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Mental disorder|Nervous system disease|Signs and symptoms","DiseaseID":"MESH:D007859","DiseaseName":"Learning Disabilities","Input":"d003634","PubMedIDs":"7589230"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease|Pathology (process)","DiseaseID":"MESH:D008103","DiseaseName":"Liver Cirrhosis","Input":"d003634","PubMedIDs":"32508177"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Digestive system disease","DiseaseID":"MESH:D008107","DiseaseName":"Liver Diseases","Input":"d003634","PubMedIDs":"15729006"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D008113","DiseaseName":"Liver Neoplasms","Input":"d003634","PubMedIDs":"11948501|15975961|2431762|3621148"},{"CasRN":"50-29-3","ChemicalID":"D003634","ChemicalName":"DDT","DirectEvidence":"marker/mechanism|therapeutic","DiseaseCategories":"Cancer|Digestive system disease","DiseaseID":"MESH:D008114","DiseaseName":"Liver Neoplasms, 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+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Urogenital disease (female)|Urogenital disease (male)",
+    "DiseaseID": "MESH:D007674",
+    "DiseaseName": "Kidney Diseases",
+    "Input": "mercury",
+    "PubMedIDs": "11090055|17068093|17934191|18540850|21206114"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Mental disorder|Nervous system disease|Signs and symptoms",
+    "DiseaseID": "MESH:D007859",
+    "DiseaseName": "Learning Disabilities",
+    "Input": "mercury",
+    "PubMedIDs": "23742082"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Skin disease",
+    "DiseaseID": "MESH:D017512",
+    "DiseaseName": "Lichenoid Eruptions",
+    "Input": "mercury",
+    "PubMedIDs": "18393961"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Immune system disease|Lymphatic disease",
+    "DiseaseID": "MESH:D008232",
+    "DiseaseName": "Lymphoproliferative Disorders",
+    "Input": "mercury",
+    "PubMedIDs": "18314309"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease|Signs and symptoms",
+    "DiseaseID": "MESH:D008569",
+    "DiseaseName": "Memory Disorders",
+    "Input": "mercury",
+    "PubMedIDs": "23742082"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseID": "MESH:D008630",
+    "DiseaseName": "Mercury Poisoning",
+    "Input": "mercury",
+    "PubMedIDs": "16891999|18155151|18329067|18365070|18501191|18594997|19039081|19040355|21206114|21821123|22018916|22174729|23330093|24319713|24522097|26678598"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease",
+    "DiseaseID": "MESH:D020262",
+    "DiseaseName": "Mercury Poisoning, Nervous System",
+    "Input": "mercury",
+    "PubMedIDs": "18226494|18950830|21984480|30076900|7781173"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Metabolic disease",
+    "DiseaseID": "MESH:D024821",
+    "DiseaseName": "Metabolic Syndrome",
+    "Input": "mercury",
+    "PubMedIDs": "19221698|23824410|25053396|27420091|32176304"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Pathology (process)",
+    "DiseaseID": "MESH:D048629",
+    "DiseaseName": "Micronuclei, Chromosome-Defective",
+    "Input": "mercury",
+    "PubMedIDs": "17456398"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Metabolic disease",
+    "DiseaseID": "MESH:D028361",
+    "DiseaseName": "Mitochondrial Diseases",
+    "Input": "mercury",
+    "PubMedIDs": "21146384"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Signs and symptoms",
+    "DiseaseID": "MESH:D051346",
+    "DiseaseName": "Mobility Limitation",
+    "Input": "mercury",
+    "PubMedIDs": "25056781"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease",
+    "DiseaseID": "MESH:D009069",
+    "DiseaseName": "Movement Disorders",
+    "Input": "mercury",
+    "PubMedIDs": "19628251"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Urogenital disease (female)|Urogenital disease (male)",
+    "DiseaseID": "MESH:D009395",
+    "DiseaseName": "Nephritis, Interstitial",
+    "Input": "mercury",
+    "PubMedIDs": "10820171"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Urogenital disease (female)|Urogenital disease (male)",
+    "DiseaseID": "MESH:D009402",
+    "DiseaseName": "Nephrosis, Lipoid",
+    "Input": "mercury",
+    "PubMedIDs": "2947217"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Urogenital disease (female)|Urogenital disease (male)",
+    "DiseaseID": "MESH:D009404",
+    "DiseaseName": "Nephrotic Syndrome",
+    "Input": "mercury",
+    "PubMedIDs": "2947217"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Pathology (process)",
+    "DiseaseID": "MESH:D009410",
+    "DiseaseName": "Nerve Degeneration",
+    "Input": "mercury",
+    "PubMedIDs": "19288233"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease",
+    "DiseaseID": "MESH:D009422",
+    "DiseaseName": "Nervous System Diseases",
+    "Input": "mercury",
+    "PubMedIDs": "20929057"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease|Signs and symptoms",
+    "DiseaseID": "MESH:D019954",
+    "DiseaseName": "Neurobehavioral Manifestations",
+    "Input": "mercury",
+    "PubMedIDs": "21124968|23827881|25056781|25109824|25748564"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Mental disorder",
+    "DiseaseID": "MESH:D065886",
+    "DiseaseName": "Neurodevelopmental Disorders",
+    "Input": "mercury",
+    "PubMedIDs": "27262785"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease|Signs and symptoms",
+    "DiseaseID": "MESH:D009461",
+    "DiseaseName": "Neurologic Manifestations",
+    "Input": "mercury",
+    "PubMedIDs": "22184584"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease",
+    "DiseaseID": "MESH:D020258",
+    "DiseaseName": "Neurotoxicity Syndromes",
+    "Input": "mercury",
+    "PubMedIDs": "20222982|20226812"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nutrition disorder|Signs and symptoms",
+    "DiseaseID": "MESH:D009765",
+    "DiseaseName": "Obesity",
+    "Input": "mercury",
+    "PubMedIDs": "23824410|28029015"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease|Signs and symptoms",
+    "DiseaseID": "MESH:D010468",
+    "DiseaseName": "Perceptual Disorders",
+    "Input": "mercury",
+    "PubMedIDs": "26658153"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Nervous system disease",
+    "DiseaseID": "MESH:D010523",
+    "DiseaseName": "Peripheral Nervous System Diseases",
+    "Input": "mercury",
+    "PubMedIDs": "21998611"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Endocrine system disease|Metabolic disease",
+    "DiseaseID": "MESH:D011236",
+    "DiseaseName": "Prediabetic State",
+    "Input": "mercury",
+    "PubMedIDs": "26497629"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Pregnancy complication",
+    "DiseaseID": "MESH:D047928",
+    "DiseaseName": "Premature Birth",
+    "Input": "mercury",
+    "PubMedIDs": "32575788"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Pregnancy complication",
+    "DiseaseID": "MESH:D011297",
+    "DiseaseName": "Prenatal Exposure Delayed Effects",
+    "Input": "mercury",
+    "PubMedIDs": "20194072|23603214|25748564|27262785|31421448|32176304"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Pregnancy complication",
+    "DiseaseID": "MESH:D049188",
+    "DiseaseName": "Prenatal Injuries",
+    "Input": "mercury",
+    "PubMedIDs": "18501191"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Signs and symptoms|Urogenital disease (female)|Urogenital disease (male)",
+    "DiseaseID": "MESH:D011507",
+    "DiseaseName": "Proteinuria",
+    "Input": "mercury",
+    "PubMedIDs": "10820171|2947217"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Respiratory tract disease",
+    "DiseaseID": "MESH:D012128",
+    "DiseaseName": "Respiratory Distress Syndrome",
+    "Input": "mercury",
+    "PubMedIDs": "26678598"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Signs and symptoms",
+    "DiseaseID": "MESH:D012816",
+    "DiseaseName": "Signs and Symptoms",
+    "Input": "mercury",
+    "PubMedIDs": "25404430"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Pathology (anatomical condition)",
+    "DiseaseID": "MESH:D013163",
+    "DiseaseName": "Splenomegaly",
+    "Input": "mercury",
+    "PubMedIDs": "12928768|25237059"
+  },
+  {
+    "CasRN": "7439-97-6",
+    "ChemicalID": "D008628",
+    "ChemicalName": "Mercury",
+    "DirectEvidence": "marker/mechanism",
+    "DiseaseCategories": "Signs and symptoms",
+    "DiseaseID": "MESH:D015431",
+    "DiseaseName": "Weight Loss",
+    "Input": "mercury",
+    "PubMedIDs": "12928768|30103553"
+  }
+]
diff --git a/__test__/data/ebi_protein/edge.json b/__test__/data/ebi_protein/edge.json
index 4d6ff30..a83799b 100644
--- a/__test__/data/ebi_protein/edge.json
+++ b/__test__/data/ebi_protein/edge.json
@@ -1,51 +1,40 @@
 {
-    "input": "Q93099",
-    "query_operation": {
-        "params": {
-            "accession": "{inputs[0]}"
-        },
-        "path": "/proteins/{accession}",
-        "path_params": [
-            "accession"
-        ],
-        "method": "get",
-        "server": "https://www.ebi.ac.uk/proteins/api",
-        "tags": [
-            "anatomy",
-            "disease",
-            "gene",
-            "phenotype",
-            "pathway",
-            "annotation",
-            "query",
-            "translator"
-        ],
-        "supportBatch": false
+  "input": "Q93099",
+  "query_operation": {
+    "params": {
+      "accession": "{inputs[0]}"
     },
-    "association": {
-        "input_id": "UniProtKB",
-        "input_type": "Protein",
-        "output_id": "RHEA",
-        "output_type": "MolecularActivity",
-        "predicate": "related_to",
-        "api_name": "EBI Proteins API",
-        "smartapi": {
-            "id": "d22b657426375a5295e7da8a303b9893",
-            "meta": {
-                "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d",
-                "github_username": "newgene",
-                "timestamp": "2020-05-28T00:02:40.483712",
-                "uptime_status": "good",
-                "uptime_ts": "2020-06-11T00:05:38.030503",
-                "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml"
-            }
-        }
-    },
-    "response_mapping": {
-        "related_to": {
-            "RHEA": "comments.reaction.dbReferences.id",
-            "name": "comments.reaction.name"
-        }
-    },
-    "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
-}
\ No newline at end of file
+    "path": "/proteins/{accession}",
+    "path_params": ["accession"],
+    "method": "get",
+    "server": "https://www.ebi.ac.uk/proteins/api",
+    "tags": ["anatomy", "disease", "gene", "phenotype", "pathway", "annotation", "query", "translator"],
+    "supportBatch": false
+  },
+  "association": {
+    "input_id": "UniProtKB",
+    "input_type": "Protein",
+    "output_id": "RHEA",
+    "output_type": "MolecularActivity",
+    "predicate": "related_to",
+    "api_name": "EBI Proteins API",
+    "smartapi": {
+      "id": "d22b657426375a5295e7da8a303b9893",
+      "meta": {
+        "ETag": "62f25b12c5457f6924db7929d91e7d5a2e70de291e7672aebf06fa08d1526d9d",
+        "github_username": "newgene",
+        "timestamp": "2020-05-28T00:02:40.483712",
+        "uptime_status": "good",
+        "uptime_ts": "2020-06-11T00:05:38.030503",
+        "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biolink/openapi.yml"
+      }
+    }
+  },
+  "response_mapping": {
+    "related_to": {
+      "RHEA": "comments.reaction.dbReferences.id",
+      "name": "comments.reaction.name"
+    }
+  },
+  "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
+}
diff --git a/__test__/data/ebi_protein/response.json b/__test__/data/ebi_protein/response.json
index 5dd49a9..2905521 100644
--- a/__test__/data/ebi_protein/response.json
+++ b/__test__/data/ebi_protein/response.json
@@ -1,4743 +1,4650 @@
 {
-    "accession": "Q93099",
-    "id": "HGD_HUMAN",
-    "proteinExistence": "Evidence at protein level",
-    "info": {
-        "type": "Swiss-Prot",
-        "created": "1997-11-01",
-        "modified": "2021-04-07",
-        "version": 192
-    },
-    "organism": {
-        "taxonomy": 9606,
-        "names": [
-            {
-                "type": "scientific",
-                "value": "Homo sapiens"
-            },
-            {
-                "type": "common",
-                "value": "Human"
-            }
+  "accession": "Q93099",
+  "id": "HGD_HUMAN",
+  "proteinExistence": "Evidence at protein level",
+  "info": {
+    "type": "Swiss-Prot",
+    "created": "1997-11-01",
+    "modified": "2021-04-07",
+    "version": 192
+  },
+  "organism": {
+    "taxonomy": 9606,
+    "names": [
+      {
+        "type": "scientific",
+        "value": "Homo sapiens"
+      },
+      {
+        "type": "common",
+        "value": "Human"
+      }
+    ],
+    "lineage": [
+      "Eukaryota",
+      "Metazoa",
+      "Chordata",
+      "Craniata",
+      "Vertebrata",
+      "Euteleostomi",
+      "Mammalia",
+      "Eutheria",
+      "Euarchontoglires",
+      "Primates",
+      "Haplorrhini",
+      "Catarrhini",
+      "Hominidae",
+      "Homo"
+    ]
+  },
+  "secondaryAccession": ["A8K417", "B2R8Z0"],
+  "protein": {
+    "recommendedName": {
+      "fullName": {
+        "value": "Homogentisate 1,2-dioxygenase"
+      },
+      "ecNumber": [
+        {
+          "value": "1.13.11.5"
+        }
+      ]
+    },
+    "alternativeName": [
+      {
+        "fullName": {
+          "value": "Homogentisate oxygenase"
+        }
+      },
+      {
+        "fullName": {
+          "value": "Homogentisic acid oxidase"
+        }
+      },
+      {
+        "fullName": {
+          "value": "Homogentisicase"
+        }
+      }
+    ]
+  },
+  "gene": [
+    {
+      "name": {
+        "value": "HGD"
+      },
+      "synonyms": [
+        {
+          "value": "HGO"
+        }
+      ]
+    }
+  ],
+  "comments": [
+    {
+      "type": "CATALYTIC_ACTIVITY",
+      "reaction": {
+        "name": "homogentisate + O2 = 4-maleylacetoacetate + H(+)",
+        "dbReferences": [
+          {
+            "type": "Rhea",
+            "id": "RHEA:15449"
+          },
+          {
+            "type": "ChEBI",
+            "id": "CHEBI:15378"
+          },
+          {
+            "type": "ChEBI",
+            "id": "CHEBI:15379"
+          },
+          {
+            "type": "ChEBI",
+            "id": "CHEBI:16169"
+          },
+          {
+            "type": "ChEBI",
+            "id": "CHEBI:17105"
+          }
         ],
-        "lineage": [
-            "Eukaryota",
-            "Metazoa",
-            "Chordata",
-            "Craniata",
-            "Vertebrata",
-            "Euteleostomi",
-            "Mammalia",
-            "Eutheria",
-            "Euarchontoglires",
-            "Primates",
-            "Haplorrhini",
-            "Catarrhini",
-            "Hominidae",
-            "Homo"
-        ]
+        "ecNumber": "1.13.11.5"
+      }
     },
-    "secondaryAccession": [
-        "A8K417",
-        "B2R8Z0"
-    ],
-    "protein": {
-        "recommendedName": {
-            "fullName": {
-                "value": "Homogentisate 1,2-dioxygenase"
-            },
-            "ecNumber": [
-                {
-                    "value": "1.13.11.5"
-                }
-            ]
-        },
-        "alternativeName": [
-            {
-                "fullName": {
-                    "value": "Homogentisate oxygenase"
-                }
-            },
-            {
-                "fullName": {
-                    "value": "Homogentisic acid oxidase"
-                }
-            },
+    {
+      "type": "COFACTOR",
+      "cofactors": [
+        {
+          "name": "Fe cation",
+          "dbReference": {
+            "type": "CHEBI",
+            "id": "CHEBI:24875"
+          }
+        }
+      ]
+    },
+    {
+      "type": "PATHWAY",
+      "text": [
+        {
+          "value": "Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6"
+        }
+      ]
+    },
+    {
+      "type": "SUBUNIT",
+      "text": [
+        {
+          "value": "Homohexamer arranged as a dimer of trimers",
+          "evidences": [
             {
-                "fullName": {
-                    "value": "Homogentisicase"
-                }
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+                "id": "10876237",
+                "url": "http://www.ncbi.nlm.nih.gov/pubmed/10876237",
+                "alternativeUrl": "https://europepmc.org/abstract/MED/10876237"
+              }
             }
-        ]
+          ]
+        }
+      ]
     },
-    "gene": [
+    {
+      "type": "INTERACTION",
+      "interactions": [
+        {
+          "accession1": "Q93099",
+          "accession2": "Q93099",
+          "gene": "HGD",
+          "interactor1": "EBI-3907760",
+          "interactor2": "EBI-3907760",
+          "organismDiffer": false,
+          "experiments": 4
+        },
+        {
+          "accession1": "Q93099",
+          "accession2": "Q96HA8",
+          "gene": "NTAQ1",
+          "interactor1": "EBI-3907760",
+          "interactor2": "EBI-741158",
+          "organismDiffer": false,
+          "experiments": 3
+        },
+        {
+          "accession1": "Q93099",
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+          "interactor1": "EBI-3907760",
+          "interactor2": "EBI-710997",
+          "organismDiffer": false,
+          "experiments": 2
+        }
+      ]
+    },
+    {
+      "type": "TISSUE_SPECIFICITY",
+      "text": [
         {
-            "name": {
-                "value": "HGD"
-            },
-            "synonyms": [
-                {
-                    "value": "HGO"
-                }
-            ]
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         }
-    ],
-    "comments": [
-        {
-            "type": "CATALYTIC_ACTIVITY",
-            "reaction": {
-                "name": "homogentisate + O2 = 4-maleylacetoacetate + H(+)",
-                "dbReferences": [
-                    {
-                        "type": "Rhea",
-                        "id": "RHEA:15449"
-                    },
-                    {
-                        "type": "ChEBI",
-                        "id": "CHEBI:15378"
-                    },
-                    {
-                        "type": "ChEBI",
-                        "id": "CHEBI:15379"
-                    },
-                    {
-                        "type": "ChEBI",
-                        "id": "CHEBI:16169"
-                    },
-                    {
-                        "type": "ChEBI",
-                        "id": "CHEBI:17105"
-                    }
-                ],
-                "ecNumber": "1.13.11.5"
+      ]
+    },
+    {
+      "type": "DISEASE",
+      "diseaseId": "Alkaptonuria",
+      "acronym": "AKU",
+      "dbReference": {
+        "type": "MIM",
+        "id": "203500"
+      },
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+        "value": "An autosomal recessive error of metabolism characterized by an increase in the level of homogentisic acid. The clinical manifestations are urine that turns dark on standing and alkalinization, black ochronotic pigmentation of cartilage and collagenous tissues, and spine arthritis.",
+        "evidences": [
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+            "code": "ECO:0000269",
+            "source": {
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             }
-        },
-        {
-            "type": "COFACTOR",
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-                {
-                    "name": "Fe cation",
-                    "dbReference": {
-                        "type": "CHEBI",
-                        "id": "CHEBI:24875"
-                    }
-                }
-            ]
-        },
-        {
-            "type": "PATHWAY",
-            "text": [
-                {
-                    "value": "Amino-acid degradation; L-phenylalanine degradation; acetoacetate and fumarate from L-phenylalanine: step 4/6"
-                }
-            ]
-        },
-        {
-            "type": "SUBUNIT",
-            "text": [
-                {
-                    "value": "Homohexamer arranged as a dimer of trimers",
-                    "evidences": [
-                        {
-                            "code": "ECO:0000269",
-                            "source": {
-                                "name": "PubMed",
-                                "id": "10876237",
-                                "url": "http://www.ncbi.nlm.nih.gov/pubmed/10876237",
-                                "alternativeUrl": "https://europepmc.org/abstract/MED/10876237"
-                            }
-                        }
-                    ]
-                }
-            ]
-        },
-        {
-            "type": "INTERACTION",
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-                {
-                    "accession1": "Q93099",
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-                    "interactor1": "EBI-3907760",
-                    "interactor2": "EBI-3907760",
-                    "organismDiffer": false,
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-                },
-                {
-                    "accession1": "Q93099",
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-                    "interactor1": "EBI-3907760",
-                    "interactor2": "EBI-741158",
-                    "organismDiffer": false,
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-                },
-                {
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-                    "interactor2": "EBI-710997",
-                    "organismDiffer": false,
-                    "experiments": 2
-                }
-            ]
-        },
-        {
-            "type": "TISSUE_SPECIFICITY",
-            "text": [
-                {
-                    "value": "Highest expression in the prostate, small intestine, colon, kidney and liver"
-                }
-            ]
-        },
-        {
-            "type": "DISEASE",
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-            },
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-                "evidences": [
-                    {
-                        "code": "ECO:0000269",
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-                            "name": "PubMed",
-                            "id": "10205262",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/10205262",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/10205262"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
-                            "name": "PubMed",
-                            "id": "10340975",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/10340975",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/10340975"
-                        }
-                    },
-                    {
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-                            "name": "PubMed",
-                            "id": "10482952",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/10482952",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/10482952"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
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-                            "id": "10594001",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/10594001",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/10594001"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
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-                            "name": "PubMed",
-                            "id": "19862842",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/19862842",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/19862842"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
-                            "name": "PubMed",
-                            "id": "21437689",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/21437689",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/21437689"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
-                            "name": "PubMed",
-                            "id": "23353776",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/23353776",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/23353776"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
-                            "name": "PubMed",
-                            "id": "23430897",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/23430897",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/23430897"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
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-                            "id": "25681086",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/25681086",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/25681086"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
-                            "name": "PubMed",
-                            "id": "8782815",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/8782815",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/8782815"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
-                            "name": "PubMed",
-                            "id": "9154114",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/9154114",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/9154114"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
-                        "source": {
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-                            "id": "9529363",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/9529363",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/9529363"
-                        }
-                    },
-                    {
-                        "code": "ECO:0000269",
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-                            "name": "PubMed",
-                            "id": "9630082",
-                            "url": "http://www.ncbi.nlm.nih.gov/pubmed/9630082",
-                            "alternativeUrl": "https://europepmc.org/abstract/MED/9630082"
-                        }
-                    }
-                ]
-            },
-            "text": [
-                {
-                    "value": "The disease is caused by variants affecting the gene represented in this entry"
-                }
-            ]
-        },
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "10340975",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/10340975",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/10340975"
+            }
+          },
+          {
+            "code": "ECO:0000269",
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+              "id": "10482952",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/10482952",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/10482952"
+            }
+          },
+          {
+            "code": "ECO:0000269",
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+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/10594001",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/10594001"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
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+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/19862842",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/19862842"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "21437689",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/21437689",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/21437689"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "23353776",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/23353776",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/23353776"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "23430897",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/23430897",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/23430897"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "25681086",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/25681086",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/25681086"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "8782815",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/8782815",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/8782815"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "9154114",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/9154114",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/9154114"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "9529363",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/9529363",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/9529363"
+            }
+          },
+          {
+            "code": "ECO:0000269",
+            "source": {
+              "name": "PubMed",
+              "id": "9630082",
+              "url": "http://www.ncbi.nlm.nih.gov/pubmed/9630082",
+              "alternativeUrl": "https://europepmc.org/abstract/MED/9630082"
+            }
+          }
+        ]
+      },
+      "text": [
         {
-            "type": "SIMILARITY",
-            "text": [
-                {
-                    "value": "Belongs to the homogentisate dioxygenase family",
-                    "evidences": [
-                        {
-                            "code": "ECO:0000305"
-                        }
-                    ]
-                }
-            ]
+          "value": "The disease is caused by variants affecting the gene represented in this entry"
         }
-    ],
-    "features": [
-        {
-            "type": "CHAIN",
-            "category": "MOLECULE_PROCESSING",
-            "ftId": "PRO_0000220240",
-            "description": "Homogentisate 1,2-dioxygenase",
-            "begin": "1",
-            "end": "445",
-            "molecule": ""
-        },
-        {
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-            "category": "DOMAINS_AND_SITES",
-            "description": "Iron",
-            "begin": "335",
-            "end": "335",
-            "molecule": ""
-        },
-        {
-            "type": "METAL",
-            "category": "DOMAINS_AND_SITES",
-            "description": "Iron",
-            "begin": "341",
-            "end": "341",
-            "molecule": ""
-        },
-        {
-            "type": "METAL",
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-            "description": "Iron",
-            "begin": "371",
-            "end": "371",
-            "molecule": ""
-        },
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-            "category": "PTM",
-            "description": "N6-acetyllysine",
-            "begin": "98",
-            "end": "98",
-            "molecule": "",
-            "evidences": [
-                {
-                    "code": "ECO:0007744",
-                    "source": {
-                        "name": "PubMed",
-                        "id": "19608861",
-                        "url": "http://www.ncbi.nlm.nih.gov/pubmed/19608861",
-                        "alternativeUrl": "https://europepmc.org/abstract/MED/19608861"
-                    }
-                }
-            ]
-        },
-        {
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-            "category": "PTM",
-            "description": "N6-succinyllysine",
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-            "end": "414",
-            "molecule": "",
-            "evidences": [
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-                    "code": "ECO:0000250",
-                    "source": {
-                        "name": "UniProtKB",
-                        "id": "O09173",
-                        "url": "https://www.uniprot.org/uniprot/O09173"
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-                }
-            ]
-        },
-        {
-            "type": "VARIANT",
-            "category": "VARIANTS",
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-            "description": "in AKU; dbSNP:rs200412910",
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-                    "code": "ECO:0000269",
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-                        "alternativeUrl": "https://europepmc.org/abstract/MED/19862842"
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-                }
-            ]
-        },
-        {
-            "type": "VARIANT",
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-                }
-            ]
-        },
-        {
-            "type": "VARIANT",
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-                }
-            ]
-        },
-        {
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-            ]
-        },
-        {
-            "type": "VARIANT",
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-                    "Kumar C.",
-                    "Gnad F.",
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-                    "Beltran-Valero de Bernabe D.",
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-                "publicationDate": "1998",
-                "title": "A novel point mutation associated with alkaptonuria.",
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-                    "Higashino K.",
-                    "Liu W.",
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-                    "Fukui K.",
-                    "Ohno M.",
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-                    "Mutsch Y.",
-                    "Grehn F.",
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-                "authors": [
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-                    "Zhao R.",
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-                    "Tu M.",
-                    "He X.Y.",
-                    "Wu L.Q.",
-                    "Zhu Y.M."
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-                    "Huang J.",
-                    "Sun D.",
-                    "Wang L.",
-                    "Ye M.",
-                    "Zou H."
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+    },
+    {
+      "type": "EMBL",
+      "id": "AK313563",
+      "properties": {
+        "molecule type": "mRNA",
+        "protein sequence ID": "BAG36337.1"
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+    },
+    {
+      "type": "EMBL",
+      "id": "AC126182",
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+        "status": "NOT_ANNOTATED_CDS"
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+    },
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+      "type": "EMBL",
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+        "molecule type": "Genomic_DNA",
+        "status": "NOT_ANNOTATED_CDS"
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+    },
+    {
+      "type": "EMBL",
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+        "protein sequence ID": "EAW79524.1"
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+      "type": "EMBL",
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+      "type": "RefSeq",
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+        "nucleotide sequence ID": "NM_000187.3"
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+      "type": "PDB",
+      "id": "1EY2",
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+      "type": "BioGRID",
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+      "id": "9606.ENSP00000283871"
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+      "type": "iPTMnet",
+      "id": "Q93099"
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+      "type": "PhosphoSitePlus",
+      "id": "Q93099"
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+    {
+      "type": "BioMuta",
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+    {
+      "type": "jPOST",
+      "id": "Q93099"
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+      "type": "MassIVE",
+      "id": "Q93099"
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+    {
+      "type": "MaxQB",
+      "id": "Q93099"
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+    {
+      "type": "PaxDb",
+      "id": "Q93099"
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+    {
+      "type": "PeptideAtlas",
+      "id": "Q93099"
+    },
+    {
+      "type": "PRIDE",
+      "id": "Q93099"
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+      "type": "ProteomicsDB",
+      "id": "75725"
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+      "type": "Antibodypedia",
+      "id": "32802",
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+    },
+    {
+      "type": "DNASU",
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+    {
+      "type": "Ensembl",
+      "id": "ENST00000283871",
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+        "protein sequence ID": "ENSP00000283871"
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+    },
+    {
+      "type": "GeneID",
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+    {
+      "type": "KEGG",
+      "id": "hsa:3081"
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+    {
+      "type": "UCSC",
+      "id": "uc003edw.4",
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+    },
+    {
+      "type": "CTD",
+      "id": "3081"
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+      "id": "3081"
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+    {
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+      "type": "HGNC",
+      "id": "HGNC:4892",
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+      "type": "HPA",
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+    },
+    {
+      "type": "MalaCards",
+      "id": "HGD"
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+    {
+      "type": "MIM",
+      "id": "203500",
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+    },
+    {
+      "type": "MIM",
+      "id": "607474",
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+    {
+      "type": "neXtProt",
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+    {
+      "type": "OpenTargets",
+      "id": "ENSG00000113924"
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+      "type": "Orphanet",
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+      }
+    },
+    {
+      "type": "PharmGKB",
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+    {
+      "type": "eggNOG",
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+    },
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+      "type": "GeneTree",
+      "id": "ENSGT00390000004601"
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+      "id": "CLU_027174_0_0_1"
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+    {
+      "type": "InParanoid",
+      "id": "Q93099"
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+    {
+      "type": "OMA",
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+    {
+      "type": "OrthoDB",
+      "id": "795654at2759"
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+      "type": "PhylomeDB",
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+    {
+      "type": "TreeFam",
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+    {
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+      "type": "Reactome",
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+        }
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+    {
+      "type": "GO",
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+      "type": "GO",
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+          "code": "ECO:0000269",
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+            "alternativeUrl": "https://europepmc.org/abstract/MED/23533145"
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+        }
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+    {
+      "type": "GO",
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+          "code": "ECO:0000269",
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+        }
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+    },
+    {
+      "type": "GO",
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+      "evidences": [
+        {
+          "code": "ECO:0000269",
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+            "name": "PubMed",
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+        {
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+            "alternativeUrl": "https://europepmc.org/abstract/MED/32296183"
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+        }
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+    },
+    {
+      "type": "GO",
+      "id": "GO:0046872",
+      "properties": {
+        "term": "F:metal ion binding",
+        "source": "IEA:UniProtKB-KW"
+      }
+    },
+    {
+      "type": "GO",
+      "id": "GO:0006559",
+      "properties": {
+        "term": "P:L-phenylalanine catabolic process",
+        "source": "IBA:GO_Central"
+      },
+      "evidences": [
+        {
+          "code": "ECO:0000269",
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+            "name": "PubMed",
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+            "alternativeUrl": "https://europepmc.org/abstract/MED/21873635"
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+        }
+      ]
+    },
+    {
+      "type": "GO",
+      "id": "GO:0006572",
+      "properties": {
+        "term": "P:tyrosine catabolic process",
+        "source": "TAS:Reactome"
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+    },
+    {
+      "type": "Gene3D",
+      "id": "2.60.120.10",
+      "properties": {
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+    },
+    {
+      "type": "InterPro",
+      "id": "IPR005708",
+      "properties": {
+        "entry name": "Homogentis_dOase"
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+    },
+    {
+      "type": "InterPro",
+      "id": "IPR014710",
+      "properties": {
+        "entry name": "RmlC-like_jellyroll"
+      }
+    },
+    {
+      "type": "InterPro",
+      "id": "IPR011051",
+      "properties": {
+        "entry name": "RmlC_Cupin_sf"
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+    },
+    {
+      "type": "PANTHER",
+      "id": "PTHR11056",
+      "properties": {
+        "match status": "1",
+        "entry name": "PTHR11056"
+      }
+    },
+    {
+      "type": "Pfam",
+      "id": "PF04209",
+      "properties": {
+        "match status": "1",
+        "entry name": "HgmA"
+      }
+    },
+    {
+      "type": "SUPFAM",
+      "id": "SSF51182",
+      "properties": {
+        "match status": "1",
+        "entry name": "SSF51182"
+      }
+    },
+    {
+      "type": "TIGRFAMs",
+      "id": "TIGR01015",
+      "properties": {
+        "match status": "1",
+        "entry name": "hmgA"
+      }
+    }
+  ],
+  "keywords": [
+    {
+      "value": "3D-structure"
+    },
+    {
+      "value": "Acetylation"
+    },
+    {
+      "value": "Dioxygenase"
+    },
+    {
+      "value": "Disease variant"
+    },
+    {
+      "value": "Iron"
+    },
+    {
+      "value": "Metal-binding"
+    },
+    {
+      "value": "Oxidoreductase"
+    },
+    {
+      "value": "Phenylalanine catabolism"
+    },
+    {
+      "value": "Reference proteome"
+    },
+    {
+      "value": "Tyrosine catabolism"
+    }
+  ],
+  "references": [
+    {
+      "citation": {
+        "type": "journal article",
+        "publicationDate": "1996",
+        "title": "The molecular basis of alkaptonuria.",
+        "authors": [
+          "Fernandez-Canon J.M.",
+          "Granadino B.",
+          "Beltran-Valero de Bernabe D.",
+          "Renedo M.",
+          "Fernandez-Ruiz E.",
+          "Penalva M.A.",
+          "Rodriguez de Cordoba S."
+        ],
+        "publication": {
+          "journalName": "Nat. Genet."
+        },
+        "location": {
+          "volume": "14",
+          "firstPage": "19",
+          "lastPage": "24"
+        },
+        "dbReferences": [
+          {
+            "type": "PubMed",
+            "id": "8782815"
+          },
+          {
+            "type": "DOI",
+            "id": "10.1038/ng0996-19"
+          }
+        ]
+      },
+      "scope": ["NUCLEOTIDE SEQUENCE [MRNA]", "VARIANTS HIS-80; AKU SER-230 AND GLY-300"]
+    },
+    {
+      "citation": {
+        "type": "submission",
+        "publicationDate": "SEP-1996",
+        "title": "Homogentisate 1,2-dioxygenase human cDNA sequence.",
+        "authors": ["Ramos S.", "Hernandez M.", "Rozes A.", "Larruga J.", "Gonzalez P.", "Cabrera V.M."],
+        "publication": {
+          "submissionDatabase": "EMBL/GenBank/DDBJ databases"
+        }
+      },
+      "source": {
+        "tissue": [
+          {
+            "value": "Liver"
+          }
+        ]
+      },
+      "scope": ["NUCLEOTIDE SEQUENCE [MRNA]", "VARIANT HIS-80"]
+    },
+    {
+      "citation": {
+        "type": "journal article",
+        "publicationDate": "1997",
+        "title": "The human homogentisate 1,2-dioxygenase (HGO) gene.",
+        "authors": [
+          "Granadino B.",
+          "Beltran-Valero de Bernabe D.",
+          "Fernandez-Canon J.M.",
+          "Penalva M.A.",
+          "Rodriguez de Cordoba S."
+        ],
+        "publication": {
+          "journalName": "Genomics"
+        },
+        "location": {
+          "volume": "43",
+          "firstPage": "115",
+          "lastPage": "122"
+        },
+        "dbReferences": [
+          {
+            "type": "PubMed",
+            "id": "9244427"
+          },
+          {
+            "type": "DOI",
+            "id": "10.1006/geno.1997.4805"
+          }
+        ]
+      },
+      "scope": ["NUCLEOTIDE SEQUENCE [GENOMIC DNA]", "VARIANT HIS-80"]
+    },
+    {
+      "citation": {
+        "type": "journal article",
+        "publicationDate": "2004",
+        "title": "Complete sequencing and characterization of 21,243 full-length human cDNAs.",
+        "authors": [
+          "Ota T.",
+          "Suzuki Y.",
+          "Nishikawa T.",
+          "Otsuki T.",
+          "Sugiyama T.",
+          "Irie R.",
+          "Wakamatsu A.",
+          "Hayashi K.",
+          "Sato H.",
+          "Nagai K.",
+          "Kimura K.",
+          "Makita H.",
+          "Sekine M.",
+          "Obayashi M.",
+          "Nishi T.",
+          "Shibahara T.",
+          "Tanaka T.",
+          "Ishii S.",
+          "Yamamoto J.",
+          "Saito K.",
+          "Kawai Y.",
+          "Isono Y.",
+          "Nakamura Y.",
+          "Nagahari K.",
+          "Murakami K.",
+          "Yasuda T.",
+          "Iwayanagi T.",
+          "Wagatsuma M.",
+          "Shiratori A.",
+          "Sudo H.",
+          "Hosoiri T.",
+          "Kaku Y.",
+          "Kodaira H.",
+          "Kondo H.",
+          "Sugawara M.",
+          "Takahashi M.",
+          "Kanda K.",
+          "Yokoi T.",
+          "Furuya T.",
+          "Kikkawa E.",
+          "Omura Y.",
+          "Abe K.",
+          "Kamihara K.",
+          "Katsuta N.",
+          "Sato K.",
+          "Tanikawa M.",
+          "Yamazaki M.",
+          "Ninomiya K.",
+          "Ishibashi T.",
+          "Yamashita H.",
+          "Murakawa K.",
+          "Fujimori K.",
+          "Tanai H.",
+          "Kimata M.",
+          "Watanabe M.",
+          "Hiraoka S.",
+          "Chiba Y.",
+          "Ishida S.",
+          "Ono Y.",
+          "Takiguchi S.",
+          "Watanabe S.",
+          "Yosida M.",
+          "Hotuta T.",
+          "Kusano J.",
+          "Kanehori K.",
+          "Takahashi-Fujii A.",
+          "Hara H.",
+          "Tanase T.-O.",
+          "Nomura Y.",
+          "Togiya S.",
+          "Komai F.",
+          "Hara R.",
+          "Takeuchi K.",
+          "Arita M.",
+          "Imose N.",
+          "Musashino K.",
+          "Yuuki H.",
+          "Oshima A.",
+          "Sasaki N.",
+          "Aotsuka S.",
+          "Yoshikawa Y.",
+          "Matsunawa H.",
+          "Ichihara T.",
+          "Shiohata N.",
+          "Sano S.",
+          "Moriya S.",
+          "Momiyama H.",
+          "Satoh N.",
+          "Takami S.",
+          "Terashima Y.",
+          "Suzuki O.",
+          "Nakagawa S.",
+          "Senoh A.",
+          "Mizoguchi H.",
+          "Goto Y.",
+          "Shimizu F.",
+          "Wakebe H.",
+          "Hishigaki H.",
+          "Watanabe T.",
+          "Sugiyama A.",
+          "Takemoto M.",
+          "Kawakami B.",
+          "Yamazaki M.",
+          "Watanabe K.",
+          "Kumagai A.",
+          "Itakura S.",
+          "Fukuzumi Y.",
+          "Fujimori Y.",
+          "Komiyama M.",
+          "Tashiro H.",
+          "Tanigami A.",
+          "Fujiwara T.",
+          "Ono T.",
+          "Yamada K.",
+          "Fujii Y.",
+          "Ozaki K.",
+          "Hirao M.",
+          "Ohmori Y.",
+          "Kawabata A.",
+          "Hikiji T.",
+          "Kobatake N.",
+          "Inagaki H.",
+          "Ikema Y.",
+          "Okamoto S.",
+          "Okitani R.",
+          "Kawakami T.",
+          "Noguchi S.",
+          "Itoh T.",
+          "Shigeta K.",
+          "Senba T.",
+          "Matsumura K.",
+          "Nakajima Y.",
+          "Mizuno T.",
+          "Morinaga M.",
+          "Sasaki M.",
+          "Togashi T.",
+          "Oyama M.",
+          "Hata H.",
+          "Watanabe M.",
+          "Komatsu T.",
+          "Mizushima-Sugano J.",
+          "Satoh T.",
+          "Shirai Y.",
+          "Takahashi Y.",
+          "Nakagawa K.",
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+      "scope": ["VARIANT [LARGE SCALE ANALYSIS] HIS-80", "IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]"]
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+          }
+        ]
+      },
+      "scope": [
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     }
-}
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+    "modified": "2010-05-18",
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+}
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diff --git a/__test__/data/ols/response.json b/__test__/data/ols/response.json
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index 876275e..0c95f12 100644
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+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "PERAMPANEL",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL1214124",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "PERAMPANEL",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL1214124",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "PERAMPANEL",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL1214124",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "PERAMPANEL",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL1214124",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    },
+    {
+      "drug": {
+        "molecule_name": "TOPIRAMATE",
+        "id": "http://identifiers.org/chembl.compound/CHEMBL220492",
+        "molecule_type": "Small molecule"
+      }
+    }
+  ],
+  "size": 100
+}
diff --git a/__test__/data/semmedgene/edge.json b/__test__/data/semmedgene/edge.json
index c62f6bd..a545b35 100644
--- a/__test__/data/semmedgene/edge.json
+++ b/__test__/data/semmedgene/edge.json
@@ -1,60 +1,49 @@
 {
-    "input": [
-        "C1332824",
-        "C1332823",
-        "123"
-    ],
-    "query_operation": {
-        "params": {
-            "fields": "positively_regulates"
-        },
-        "request_body": {
-            "body": {
-                "size": 5,
-                "q": "{inputs[0]}",
-                "scopes": "umls"
-            }
-        },
-        "path": "/query",
-        "path_params": [],
-        "method": "post",
-        "server": "https://biothings.ncats.io/semmedgene",
-        "tags": [
-            "disease",
-            "annotation",
-            "query",
-            "translator",
-            "biothings",
-            "semmed"
-        ],
-        "supportBatch": true,
-        "inputSeparator": ","
+  "input": ["C1332824", "C1332823", "123"],
+  "query_operation": {
+    "params": {
+      "fields": "positively_regulates"
     },
-    "association": {
-        "input_id": "UMLS",
-        "input_type": "Gene",
-        "output_id": "UMLS",
-        "output_type": "Gene",
-        "predicate": "positively_regulates",
-        "source": "SEMMED",
-        "api_name": "SEMMED Gene API",
-        "smartapi": {
-            "id": "81955d376a10505c1c69cd06dbda3047",
-            "meta": {
-                "ETag": "f94053bc78b3c2f0b97f7afd52d7de2fe083b655e56a53090ad73e12be83673b",
-                "github_username": "kevinxin90",
-                "timestamp": "2020-05-27T16:53:40.804575",
-                "uptime_status": "good",
-                "uptime_ts": "2020-06-12T00:04:31.404599",
-                "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml"
-            }
-        }
+    "request_body": {
+      "body": {
+        "size": 5,
+        "q": "{inputs[0]}",
+        "scopes": "umls"
+      }
     },
-    "response_mapping": {
-        "positively_regulates": {
-            "pmid": "positively_regulates.pmid",
-            "umls": "positively_regulates.umls"
-        }
-    },
-    "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
-}
\ No newline at end of file
+    "path": "/query",
+    "path_params": [],
+    "method": "post",
+    "server": "https://biothings.ncats.io/semmedgene",
+    "tags": ["disease", "annotation", "query", "translator", "biothings", "semmed"],
+    "supportBatch": true,
+    "inputSeparator": ","
+  },
+  "association": {
+    "input_id": "UMLS",
+    "input_type": "Gene",
+    "output_id": "UMLS",
+    "output_type": "Gene",
+    "predicate": "positively_regulates",
+    "source": "SEMMED",
+    "api_name": "SEMMED Gene API",
+    "smartapi": {
+      "id": "81955d376a10505c1c69cd06dbda3047",
+      "meta": {
+        "ETag": "f94053bc78b3c2f0b97f7afd52d7de2fe083b655e56a53090ad73e12be83673b",
+        "github_username": "kevinxin90",
+        "timestamp": "2020-05-27T16:53:40.804575",
+        "uptime_status": "good",
+        "uptime_ts": "2020-06-12T00:04:31.404599",
+        "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml"
+      }
+    }
+  },
+  "response_mapping": {
+    "positively_regulates": {
+      "pmid": "positively_regulates.pmid",
+      "umls": "positively_regulates.umls"
+    }
+  },
+  "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
+}
diff --git a/__test__/data/semmedgene/response.json b/__test__/data/semmedgene/response.json
index 9bd4dbc..5550d60 100644
--- a/__test__/data/semmedgene/response.json
+++ b/__test__/data/semmedgene/response.json
@@ -1 +1,435 @@
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+      { "@type": "Gene", "name": "FOXO3 gene", "pmid": ["22802411"], "umls": "C1333573" },
+      { "@type": "Gene", "name": "EPB41L3 gene", "pmid": ["26280082"], "umls": "C1414425" },
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+      { "@type": "Gene", "name": "FOS gene", "pmid": ["17550983"], "umls": "C0087140" },
+      { "@type": "Gene", "name": "TNPO3 gene", "pmid": ["27783955"], "umls": "C1424743" },
+      { "@type": "Gene", "name": "SH3BP4 gene", "pmid": ["24692066"], "umls": "C1420023" },
+      { "@type": "Gene", "name": "RASGRP3 gene", "pmid": ["23308188"], "umls": "C1422744" },
+      { "@type": "Gene", "name": "LMOD1 gene", "pmid": ["25145299"], "umls": "C1416886" },
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+      { "@type": "Gene", "name": "FLVCR1 gene", "pmid": ["18452560"], "umls": "C1836722" },
+      { "@type": "Gene", "name": "RHOD gene", "pmid": ["17056591"], "umls": "C1412517" },
+      { "@type": "Gene", "name": "ERVW-1 gene", "pmid": ["18818518"], "umls": "C1422036" },
+      { "@type": "Gene", "name": "ID1 wt Allele", "pmid": ["24256728"], "umls": "C3274850" },
+      { "@type": "Gene", "name": "IL2 gene", "pmid": ["9591715"], "umls": "C0879590" },
+      { "@type": "Gene", "name": "IL2RA gene", "pmid": ["9808188"], "umls": "C1334114" },
+      { "@type": "Gene", "name": "IL8RB wt Allele", "pmid": ["28481874"], "umls": "C1704986" },
+      { "@type": "Gene", "name": "ISG20 gene", "pmid": ["9808188"], "umls": "C1416478" },
+      { "@type": "Gene", "name": "ITIH4 gene", "pmid": ["11356952"], "umls": "C1416509" },
+      { "@type": "Gene", "name": "ITK wt Allele", "pmid": ["26190113", "24403602"], "umls": "C1706224" },
+      { "@type": "Gene", "name": "JAK2 wt Allele", "pmid": ["16990584", "28544312"], "umls": "C1708581" },
+      { "@type": "Gene", "name": "JUN wt Allele", "pmid": ["27697100"], "umls": "C1706384" },
+      { "@type": "Gene", "name": "KDR wt Allele", "pmid": ["27388534"], "umls": "C1705712" },
+      { "@type": "Gene", "name": "MMP1 gene", "pmid": ["20102637"], "umls": "C1417199" },
+      { "@type": "Gene", "name": "MMP9 wt Allele", "pmid": ["26679758"], "umls": "C1708832" },
+      { "@type": "Gene", "name": "MYC wt Allele", "pmid": ["21530075"], "umls": "C1708843" },
+      { "@type": "Gene", "name": "NEU1 gene", "pmid": ["16061624"], "umls": "C1417680" },
+      { "@type": "Gene", "name": "NFKB1 wt Allele", "pmid": ["28687617"], "umls": "C2986464" },
+      { "@type": "Gene", "name": "NOS3 wt Allele", "pmid": ["27243031"], "umls": "C1709136" },
+      { "@type": "Gene", "name": "NR4A2 gene", "pmid": ["24154522"], "umls": "C1417836" },
+      { "@type": "Gene", "name": "OPRK1 gene", "pmid": ["21447649"], "umls": "C1417963" },
+      { "@type": "Gene", "name": "ATP8A2 wt Allele", "pmid": ["27454381"], "umls": "C1705556" },
+      { "@type": "Gene", "name": "PI3 wt Allele", "pmid": ["23434321"], "umls": "C3537449" },
+      { "@type": "Gene", "name": "PIK3CA gene", "pmid": ["22337890"], "umls": "C1335212" },
+      { "@type": "Gene", "name": "PIK3CB gene", "pmid": ["22337890"], "umls": "C1335213" },
+      { "@type": "Gene", "name": "PIK3CD wt Allele", "pmid": ["22337890"], "umls": "C3714973" },
+      { "@type": "Gene", "name": "PIK3CG wt Allele", "pmid": ["22337890"], "umls": "C1705325" },
+      { "@type": "Gene", "name": "ROBO4 wt Allele", "pmid": ["21211783"], "umls": "C2698937" },
+      {
+        "@type": "Gene",
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+      { "@type": "Gene", "name": "RAC1 wt Allele", "pmid": ["22345572", "21172654"], "umls": "C3274857" },
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+      { "@type": "Gene", "name": "RHO gene", "pmid": ["17056591"], "umls": "C1419385" },
+      { "@type": "Gene", "name": "BCR wt Allele", "pmid": ["10224286"], "umls": "C1704799" },
+      { "@type": "Gene", "name": "CCL5 gene", "pmid": ["16107514"], "umls": "C1332691" },
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+      { "@type": "Gene", "name": "CCL20 gene", "pmid": ["19340288"], "umls": "C1366524" },
+      {
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+      { "@type": "Gene", "name": "BMP6 gene", "pmid": ["21636574"], "umls": "C1332427" },
+      { "@type": "Gene", "name": "SLC22A3 wt Allele", "pmid": ["26190113", "24403602"], "umls": "C3812262" },
+      { "@type": "Gene", "name": "SRC wt Allele", "pmid": ["17158356", "23192271"], "umls": "C1705997" },
+      {
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+      { "@type": "Gene", "name": "TRBV20OR9-2 gene", "pmid": ["10464166"], "umls": "C1421047" },
+      { "@type": "Gene", "name": "TNF gene", "pmid": ["15093715", "16288025", "24451118"], "umls": "C0812246" },
+      { "@type": "Gene", "name": "C3AR1 gene", "pmid": ["22901257"], "umls": "C1412995" },
+      { "@type": "Gene", "name": "CCR2 gene", "pmid": ["16455991"], "umls": "C1413188" },
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+      {
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+      { "@type": "Gene", "name": "CAMK2G gene", "pmid": ["18220750", "14630801"], "umls": "C1413102" },
+      { "@type": "Gene", "name": "CAMP gene", "pmid": ["16204315", "18765807", "10644702"], "umls": "C1413106" },
+      { "@type": "Gene", "name": "TNFRSF10B gene", "pmid": ["19247452"], "umls": "C1336644" },
+      { "@type": "Gene", "name": "USP14 wt Allele", "pmid": ["19106094"], "umls": "C4321338" },
+      { "@type": "Gene", "name": "NEURL1 gene", "pmid": ["16061624"], "umls": "C1334875" },
+      {
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+      { "@type": "Gene", "name": "CD8B wt Allele", "pmid": ["29232699", "12573587", "25647836"], "umls": "C1706438" },
+      { "@type": "Gene", "name": "GRAP2 gene", "pmid": ["15972662"], "umls": "C1415284" },
+      {
+        "@type": "Gene",
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+        "pmid": ["23167782", "21655289", "19034720", "11781237", "19454674"],
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+      { "@type": "Gene", "name": "CD38 wt Allele", "pmid": ["17199940"], "umls": "C2827387" },
+      { "@type": "Gene", "name": "CD40 gene", "pmid": ["28281555"], "umls": "C1539081" },
+      { "@type": "Gene", "name": "CD40LG wt Allele", "pmid": ["24269609"], "umls": "C1706005" },
+      { "@type": "Gene", "name": "CD44 gene", "pmid": ["22384257"], "umls": "C1332712" },
+      { "@type": "Gene", "name": "CD63 wt Allele", "pmid": ["21270405"], "umls": "C3811252" },
+      { "@type": "ChemicalSubstance", "name": "Ethanol", "pmid": ["23300006"], "umls": "C0001962" },
+      {
+        "@type": "ChemicalSubstance",
+        "name": "Angiogenesis Factor",
+        "pmid": ["24486002", "22917235"],
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+      },
+      { "@type": "ChemicalSubstance", "name": "Antigens", "pmid": ["19696965"], "umls": "C0003320" },
+      { "@type": "ChemicalSubstance", "name": "Binding Sites", "pmid": ["15078935"], "umls": "C0005456" },
+      {
+        "@type": "ChemicalSubstance",
+        "name": "Calcium",
+        "pmid": ["14982745", "12845769", "22157717", "9439607"],
+        "umls": "C0006675"
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+      { "@type": "Gene", "name": "Cyclic AMP-Dependent Protein Kinases", "pmid": ["18765807"], "umls": "C0010531" },
+      { "@type": "ChemicalSubstance", "name": "Dinoprostone", "pmid": ["16204315"], "umls": "C0012472" },
+      { "@type": "ChemicalSubstance", "name": "Elements", "pmid": ["17878524"], "umls": "C0013879" },
+      { "@type": "Gene", "name": "Genes", "pmid": ["26413813", "24632620"], "umls": "C0017337" },
+      { "@type": "Gene", "name": "Guanosine Triphosphate Phosphohydrolases", "pmid": ["18632858"], "umls": "C0018296" },
+      {
+        "@type": "ChemicalSubstance",
+        "name": "Lipopolysaccharides",
+        "pmid": ["12072369", "22219610"],
+        "umls": "C0023810"
+      },
+      { "@type": "Gene", "name": "Phosphotransferases", "pmid": ["10542964", "24912431"], "umls": "C0031727" },
+      { "@type": "Gene", "name": "Protein Kinase C", "pmid": ["27127886", "25784988"], "umls": "C0033634" },
+      { "@type": "Gene", "name": "Protein Kinases", "pmid": ["11157475"], "umls": "C0033640" },
+      { "@type": "ChemicalSubstance", "name": "RNA, Messenger", "pmid": ["23815460"], "umls": "C0035696" },
+      { "@type": "ChemicalSubstance", "name": "Superoxides", "pmid": ["15509740"], "umls": "C0038836" },
+      { "@type": "ChemicalSubstance", "name": "Tetrodotoxin", "pmid": ["16476083"], "umls": "C0039705" },
+      {
+        "@type": "Gene",
+        "name": "1-Phosphatidylinositol 3-Kinase",
+        "pmid": ["20038597", "24632620", "23434321", "11157475"],
+        "umls": "C0044602"
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+      { "@type": "Gene", "name": "c-myc Genes", "pmid": ["21530075"], "umls": "C0079068" },
+      { "@type": "ChemicalSubstance", "name": "Ecstasy - drug", "pmid": ["11390582"], "umls": "C0115471" },
+      { "@type": "Gene", "name": "Interstitial Collagenase", "pmid": ["20102637"], "umls": "C0127082" },
+      { "@type": "ChemicalSubstance", "name": "prostratin", "pmid": ["15457682"], "umls": "C0138750" },
+      { "@type": "Gene", "name": "protein-tyrosine kinase c-src", "pmid": ["23192271"], "umls": "C0138965" },
+      { "@type": "ChemicalSubstance", "name": "Reactive Oxygen Species", "pmid": ["23315288"], "umls": "C0162772" },
+      {
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+        "pmid": ["22793053", "21306303", "26261552", "26679758"],
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+      { "@type": "Gene", "name": "Mitogen Activated Protein Kinase 1", "pmid": ["20956518"], "umls": "C0170168" },
+      { "@type": "Gene", "name": "Matrix Metalloproteinase 2", "pmid": ["22345572"], "umls": "C0172537" },
+      { "@type": "Gene", "name": "Genes, Reporter", "pmid": ["15210854"], "umls": "C0206414" },
+      { "@type": "ChemicalSubstance", "name": "Opioids", "pmid": ["25175863"], "umls": "C0242402" },
+      { "@type": "ChemicalSubstance", "name": "agonists", "pmid": ["28626925", "28186979"], "umls": "C0243192" },
+      { "@type": "ChemicalSubstance", "name": "docetaxel", "pmid": ["25359780"], "umls": "C0246415" },
+      {
+        "@type": "Gene",
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+        "pmid": ["18220750", "14630801"],
+        "umls": "C0248868"
+      },
+      { "@type": "Gene", "name": "src-Family Kinases", "pmid": ["17158356"], "umls": "C0282625" },
+      {
+        "@type": "Gene",
+        "name": "RAC-Alpha Serine/Threonine Kinase",
+        "pmid": ["20829512", "14630801", "18840710"],
+        "umls": "C0285558"
+      },
+      { "@type": "Gene", "name": "LIM Domain Kinase 1", "pmid": ["25359780"], "umls": "C0294209" },
+      { "@type": "Gene", "name": "ran-binding protein 2", "pmid": ["28100513"], "umls": "C0299456" },
+      {
+        "@type": "Gene",
+        "name": "Extracellular Signal Regulated Kinases",
+        "pmid": ["17550983", "9453574", "12444153", "17904532", "10651866", "25121739"],
+        "umls": "C0600388"
+      },
+      { "@type": "ChemicalSubstance", "name": "Response Elements", "pmid": ["20007689"], "umls": "C0600508" },
+      { "@type": "ChemicalSubstance", "name": "AMD 3100", "pmid": ["18384792", "17878755"], "umls": "C0662900" },
+      { "@type": "Gene", "name": "NOS3 protein, human", "pmid": ["27243031"], "umls": "C0669365" },
+      {
+        "@type": "Gene",
+        "name": "Mitogen-Activated Protein Kinases",
+        "pmid": ["18481208", "10997882", "23308188", "28687617"],
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+      },
+      { "@type": "Gene", "name": "BCR gene", "pmid": ["10224286"], "umls": "C0812385" },
+      { "@type": "Gene", "name": "C-KIT Gene", "pmid": ["23894420"], "umls": "C0920288" },
+      { "@type": "ChemicalSubstance", "name": "MicroRNAs", "pmid": ["25536052"], "umls": "C1101610" },
+      { "@type": "Gene", "name": "mitogen-activated protein kinase p38", "pmid": ["15972662"], "umls": "C1120843" },
+      { "@type": "ChemicalSubstance", "name": "Microbicides", "pmid": ["18765807"], "umls": "C1136254" },
+      { "@type": "Gene", "name": "BMP2 gene", "pmid": ["27725318"], "umls": "C1332424" },
+      { "@type": "Gene", "name": "CXCR2 gene", "pmid": ["28481874"], "umls": "C1334126" },
+      { "@type": "Gene", "name": "JAK2 gene", "pmid": ["16990584"], "umls": "C1334291" },
+      { "@type": "Gene", "name": "KDR gene", "pmid": ["27388534"], "umls": "C1334306" },
+      { "@type": "Gene", "name": "CXCL13 gene", "pmid": ["23773523"], "umls": "C1366572" },
+      { "@type": "Gene", "name": "CD8B1 gene", "pmid": ["29232699", "12573587", "25647836"], "umls": "C1367471" },
+      { "@type": "Gene", "name": "EGF gene", "pmid": ["17714434"], "umls": "C1367721" },
+      { "@type": "Gene", "name": "MAPK8 gene", "pmid": ["18481208", "28584306", "25121739"], "umls": "C1367731" },
+      { "@type": "Gene", "name": "MAPK14 protein, human", "pmid": ["24170200"], "umls": "C1456380" },
+      { "@type": "ChemicalSubstance", "name": "AMD3451", "pmid": ["15542651"], "umls": "C1529450" }
+    ],
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+  },
+  {
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+    "name": "CXCR6 gene",
+    "positively_regulates": [
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+      { "@type": "Gene", "name": "AKT1 gene", "pmid": ["20848509"], "umls": "C0812228" },
+      { "@type": "Gene", "name": "FLVCR1 gene", "pmid": ["18452560"], "umls": "C1836722" },
+      { "@type": "Gene", "name": "CXCL16 wt Allele", "pmid": ["18452560"], "umls": "C3538864" },
+      { "@type": "Gene", "name": "CXCL12 wt Allele", "pmid": ["18452560"], "umls": "C1704964" },
+      { "@type": "Gene", "name": "CCR2 gene", "pmid": ["12480562"], "umls": "C1413188" },
+      { "@type": "Gene", "name": "CD69 gene", "pmid": ["12914753"], "umls": "C1413235" },
+      { "@type": "ChemicalSubstance", "name": "Haptens", "pmid": ["20972432"], "umls": "C0018593" },
+      { "@type": "Gene", "name": "Proto-Oncogene Proteins c-akt", "pmid": ["20848509"], "umls": "C0164786" },
+      { "@type": "Gene", "name": "Mitogen-Activated Protein Kinases", "pmid": ["20848509"], "umls": "C0752312" }
+    ],
+    "umls": "C1332824"
+  },
+  { "query": "123", "notfound": true }
+]
diff --git a/__test__/ebi_protein_transformer.test.ts b/__test__/ebi_protein_transformer.test.ts
index f3bc9a6..e0f7952 100644
--- a/__test__/ebi_protein_transformer.test.ts
+++ b/__test__/ebi_protein_transformer.test.ts
@@ -19,7 +19,7 @@ describe("test EBI Protein transformer", () => {
   });
 
   test("test ebi wrapper", async () => {
-    let tf = new jq_tf(input, {type: "ebi"});
+    let tf = new jq_tf(input, { type: "ebi" });
     let res = await tf.wrap(response);
     expect(res.comments[0].reaction.dbReferences).toHaveLength(1);
   });
diff --git a/__test__/opentarget_transformer.test.ts b/__test__/opentarget_transformer.test.ts
index 470316f..c14f409 100644
--- a/__test__/opentarget_transformer.test.ts
+++ b/__test__/opentarget_transformer.test.ts
@@ -1,46 +1,44 @@
-import {describe, expect, test} from '@jest/globals';
+import { describe, expect, test } from "@jest/globals";
 import jq_tf from "../built/transformers/jq_transformer";
 import fs from "fs";
 import path from "path";
 
 describe("test opentarget transformer", () => {
+  let response;
+  let input;
 
-    let response;
-    let input;
+  beforeEach(() => {
+    const response_path = path.resolve(__dirname, "./data/opentarget/response.json");
+    response = JSON.parse(fs.readFileSync(response_path, { encoding: "utf8" }));
+    const edge_path = path.resolve(__dirname, "./data/opentarget/edge.json");
+    const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+    input = {
+      response,
+      edge,
+    };
+  });
 
-    beforeEach(() => {
-        const response_path = path.resolve(__dirname, './data/opentarget/response.json');
-        response = JSON.parse(fs.readFileSync(response_path, { encoding: 'utf8' }));
-        const edge_path = path.resolve(__dirname, './data/opentarget/edge.json');
-        const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-        input = {
-            response,
-            edge
-        }
-    })
+  // skip these tests since we're not ingesting opentargets right now
+  test.skip("test opentarget wrapper", async () => {
+    let tf = new jq_tf(input, { type: "opentarget" });
+    let res = await tf.wrap(response);
+    expect(res).toHaveProperty("data");
+    expect(res.data[0].drug.id).toEqual("CHEMBL220492");
+  });
 
-// skip these tests since we're not ingesting opentargets right now
-    test.skip("test opentarget wrapper", async () => {
-        let tf = new jq_tf(input, { type: "opentarget" });
-        let res = await tf.wrap(response);
-        expect(res).toHaveProperty("data");
-        expect(res.data[0].drug.id).toEqual("CHEMBL220492");
-    })
-
-    test.skip("test opentarget wrapper if id field is not chembl", async () => {
-        let tf = new jq_tf(input, { type: "opentarget" });
-        const fake = {
-            data: [
-                {
-                    "drug": {
-                        id: "http://identifiers.org/drugbank/DB0001"
-                    }
-                }
-            ]
-        }
-        let res = await tf.wrap(fake);
-        expect(res).toHaveProperty("data");
-        expect(res.data[0].drug.id).toEqual("http://identifiers.org/drugbank/DB0001");
-    })
-
-})
+  test.skip("test opentarget wrapper if id field is not chembl", async () => {
+    let tf = new jq_tf(input, { type: "opentarget" });
+    const fake = {
+      data: [
+        {
+          drug: {
+            id: "http://identifiers.org/drugbank/DB0001",
+          },
+        },
+      ],
+    };
+    let res = await tf.wrap(fake);
+    expect(res).toHaveProperty("data");
+    expect(res.data[0].drug.id).toEqual("http://identifiers.org/drugbank/DB0001");
+  });
+});
diff --git a/__test__/record.test.ts b/__test__/record.test.ts
index c9c3c4a..608be90 100644
--- a/__test__/record.test.ts
+++ b/__test__/record.test.ts
@@ -1,81 +1,71 @@
-import {describe, expect, test} from '@jest/globals';
+import { describe, expect, test } from "@jest/globals";
 
-import { Record } from '../src/record';
+import { Record } from "../src/record";
 
 describe("test record class", () => {
-
   const testFrozenRecord = {
     subject: {
-      original:'originalThing0',
-      qNodeID: 'n0',
+      original: "originalThing0",
+      qNodeID: "n0",
       isSet: false,
-      curie: 'prefix:1',
-      UMLS: 'UMLSstring0',
-      semanticType: 'gene',
-      label: 'someLabel0',
-      names: [
-        'someName0'
-      ],
-      attributes: {}
+      curie: "prefix:1",
+      UMLS: "UMLSstring0",
+      semanticType: "gene",
+      label: "someLabel0",
+      names: ["someName0"],
+      attributes: {},
     },
     object: {
-      original:'originalThing1',
-      qNodeID: 'n1',
+      original: "originalThing1",
+      qNodeID: "n1",
       isSet: false,
-      curie: 'prefix:2',
-      UMLS: 'UMLSstring1',
-      semanticType: 'gene',
-      label: 'someLabel1',
-      names: [
-        'someName1'
-      ],
-      attributes: {}
+      curie: "prefix:2",
+      UMLS: "UMLSstring1",
+      semanticType: "gene",
+      label: "someLabel1",
+      names: ["someName1"],
+      attributes: {},
     },
-    predicate: 'somePredicate',
-    publications: [
-      'PMID:nopenotreal'
-    ],
+    predicate: "somePredicate",
+    publications: ["PMID:nopenotreal"],
     mappedResponse: {
       edgeAttributes: [
         {
-          attribute_source: 'someSource',
-          attribute_type_id: 'someID',
+          attribute_source: "someSource",
+          attribute_type_id: "someID",
           value: false,
-          value_type_id: 'boolean',
-        }
+          value_type_id: "boolean",
+        },
       ],
     },
-    api: 'someAPI',
-    apiInforesCurie: 'infores:something',
-    metaEdgeSource: 'infores:somethingElse'
-  }
+    api: "someAPI",
+    apiInforesCurie: "infores:something",
+    metaEdgeSource: "infores:somethingElse",
+  };
 
   const testRecord = new Record(testFrozenRecord);
   describe("test initialization, record behavior", () => {
-
     test("Record produces fake association", () => {
-      expect(testRecord.association.predicate).toEqual(testFrozenRecord.predicate)
-      expect(testRecord.association.api_name).toEqual(testFrozenRecord.api)
-      expect(testRecord.association.source).toEqual(testFrozenRecord.metaEdgeSource)
-      expect(testRecord.association['x-translator'].infores).toEqual(testFrozenRecord.apiInforesCurie);
+      expect(testRecord.association.predicate).toEqual(testFrozenRecord.predicate);
+      expect(testRecord.association.api_name).toEqual(testFrozenRecord.api);
+      expect(testRecord.association.source).toEqual(testFrozenRecord.metaEdgeSource);
+      expect(testRecord.association["x-translator"].infores).toEqual(testFrozenRecord.apiInforesCurie);
     });
+  });
 
-    });
-
-    test("Record produces fake qEdge", () => {
-      expect(testRecord.qEdge).toBeTruthy();
-      expect(testRecord.qEdge.getInputNode().getID()).toEqual(testFrozenRecord.subject.qNodeID);
-      expect(testRecord.qEdge.getInputNode().isSet()).toBeFalsy();
-      expect(testRecord.qEdge.getOutputNode().isSet()).toBeFalsy();
-      expect(testRecord.qEdge.getOutputNode().getID()).toEqual(testFrozenRecord.object.qNodeID);
-      expect(testRecord.qEdge.getHashedEdgeRepresentation()).toBeTruthy();
-
-    });
+  test("Record produces fake qEdge", () => {
+    expect(testRecord.qEdge).toBeTruthy();
+    expect(testRecord.qEdge.getInputNode().getID()).toEqual(testFrozenRecord.subject.qNodeID);
+    expect(testRecord.qEdge.getInputNode().isSet()).toBeFalsy();
+    expect(testRecord.qEdge.getOutputNode().isSet()).toBeFalsy();
+    expect(testRecord.qEdge.getOutputNode().getID()).toEqual(testFrozenRecord.object.qNodeID);
+    expect(testRecord.qEdge.getHashedEdgeRepresentation()).toBeTruthy();
+  });
 
-    test("Record produces fake qNodes", () => {
-      expect(testRecord.object.qNodeID).toEqual(testFrozenRecord.object.qNodeID);
-      expect(testRecord.subject.normalizedInfo).toBeTruthy();
-    });
+  test("Record produces fake qNodes", () => {
+    expect(testRecord.object.qNodeID).toEqual(testFrozenRecord.object.qNodeID);
+    expect(testRecord.subject.normalizedInfo).toBeTruthy();
+  });
 
   describe("test freeze/unfreeze", () => {
     test("frozenRecord return format", () => {
@@ -84,5 +74,4 @@ describe("test record class", () => {
       expect(Record.unfreezeRecords(Record.freezeRecords([testRecord]))[0].recordHash).toEqual(testRecord.recordHash);
     });
   });
-
 });
diff --git a/__test__/semmed_transformer.test.ts b/__test__/semmed_transformer.test.ts
index aad097f..8e3df18 100644
--- a/__test__/semmed_transformer.test.ts
+++ b/__test__/semmed_transformer.test.ts
@@ -3,59 +3,57 @@ import path from "path";
 import semmed_tf from "../src/transformers/semmed_transformer";
 
 describe("test semmed transformer", () => {
-
-    let response, input;
-
-    beforeEach(() => {
-        const response_path = path.resolve(__dirname, './data/semmedgene/response.json');
-        response = JSON.parse(fs.readFileSync(response_path, { encoding: 'utf8' }));
-        const edge_path = path.resolve(__dirname, './data/semmedgene/edge.json');
-        const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: 'utf8' }));
-        input = {
-            response,
-            edge
-        }
-    })
-
-    test("test semmed pairCurieWithAPIResponse", async () => {
-        let tf = new semmed_tf(input, {});
-        let res = await tf.pairCurieWithAPIResponse();
-        expect(res["UMLS:C1332823"][0]['umls']).toBe("C1332823");
-        expect(res).toHaveProperty('UMLS:C1332823');
-        expect(res["UMLS:123"]).toBeUndefined();
-    });
-
-    test("test wrapper", () => {
-        let tf = new semmed_tf(input, {});
-        let res = tf.wrap(input.response[0]);
-        expect(res).toHaveProperty("positively_regulates");
-    });
-
-    test("test json transform", () => {
-        let tf = new semmed_tf(input, {});
-        let res = tf.jsonTransform(input.response[0]);
-        expect(res).toEqual(input.response[0]);
-    });
-
-    test("add edge info", async () => {
-        let tf = new semmed_tf(input, {});
-        let res = await tf.pairCurieWithAPIResponse();
-        let rec = res["UMLS:C1332823"][0];
-        rec = tf.wrap(rec);
-        let result = await tf.formatRecords("UMLS:C1332823", rec["positively_regulates"][0]);
-        expect(result[0]).toHaveProperty("association");
-        expect(result[0].api).toBe("SEMMED Gene API")
-    });
-
-    test("test main function transform", async () => {
-        let tf = new semmed_tf(input, {});
-        let res = await tf.transform();
-        expect(res[0]).not.toHaveProperty('UMLS');
-        expect(res[0]).not.toHaveProperty('@type');
-        expect(res[0]).toHaveProperty("association");
-        expect(res[0]).toHaveProperty("subject");
-        expect(res.slice(-1)[0]).toHaveProperty("subject");
-        expect(res.length).toBeGreaterThan(30);
-    })
-
-})
\ No newline at end of file
+  let response, input;
+
+  beforeEach(() => {
+    const response_path = path.resolve(__dirname, "./data/semmedgene/response.json");
+    response = JSON.parse(fs.readFileSync(response_path, { encoding: "utf8" }));
+    const edge_path = path.resolve(__dirname, "./data/semmedgene/edge.json");
+    const edge = JSON.parse(fs.readFileSync(edge_path, { encoding: "utf8" }));
+    input = {
+      response,
+      edge,
+    };
+  });
+
+  test("test semmed pairCurieWithAPIResponse", async () => {
+    let tf = new semmed_tf(input, {});
+    let res = await tf.pairCurieWithAPIResponse();
+    expect(res["UMLS:C1332823"][0]["umls"]).toBe("C1332823");
+    expect(res).toHaveProperty("UMLS:C1332823");
+    expect(res["UMLS:123"]).toBeUndefined();
+  });
+
+  test("test wrapper", () => {
+    let tf = new semmed_tf(input, {});
+    let res = tf.wrap(input.response[0]);
+    expect(res).toHaveProperty("positively_regulates");
+  });
+
+  test("test json transform", () => {
+    let tf = new semmed_tf(input, {});
+    let res = tf.jsonTransform(input.response[0]);
+    expect(res).toEqual(input.response[0]);
+  });
+
+  test("add edge info", async () => {
+    let tf = new semmed_tf(input, {});
+    let res = await tf.pairCurieWithAPIResponse();
+    let rec = res["UMLS:C1332823"][0];
+    rec = tf.wrap(rec);
+    let result = await tf.formatRecords("UMLS:C1332823", rec["positively_regulates"][0]);
+    expect(result[0]).toHaveProperty("association");
+    expect(result[0].api).toBe("SEMMED Gene API");
+  });
+
+  test("test main function transform", async () => {
+    let tf = new semmed_tf(input, {});
+    let res = await tf.transform();
+    expect(res[0]).not.toHaveProperty("UMLS");
+    expect(res[0]).not.toHaveProperty("@type");
+    expect(res[0]).toHaveProperty("association");
+    expect(res[0]).toHaveProperty("subject");
+    expect(res.slice(-1)[0]).toHaveProperty("subject");
+    expect(res.length).toBeGreaterThan(30);
+  });
+});
diff --git a/__test__/transformers.test.ts b/__test__/transformers.test.ts
index 789ab7c..ca91723 100644
--- a/__test__/transformers.test.ts
+++ b/__test__/transformers.test.ts
@@ -10,8 +10,8 @@ import axios, { AxiosStatic } from "axios";
 import path from "path";
 import fs from "fs/promises";
 
-const og_axios = jest.requireActual('axios')
-jest.mock('axios')
+const og_axios = jest.requireActual("axios");
+jest.mock("axios");
 
 // not ingesting opentargets right now; no need for this test; this api is no longer there
 // describe("test opentarget transformer", () => {
@@ -43,137 +43,127 @@ jest.mock('axios')
 //     })
 // })
 
-
 describe("test ctd transformer", () => {
+  let api_response;
 
-    let api_response;
-
-    beforeAll(async () => {
-        (axios.get as jest.MockedFunction<AxiosStatic>).mockImplementation(async (url) => {
-          const data_path = path.resolve(__dirname, "./data/ctd/response2.json")
-          const data = JSON.parse(await fs.readFile(data_path, 'utf-8'))
-          return {data, status: 200, statusText: "OK", headers: undefined, config: {}}
-        })
-        let res = await axios.get("http://ctdbase.org/tools/batchQuery.go?inputType=chem&inputTerms=D003634|mercury&report=diseases_curated&format=json");
-        api_response = res.data;
+  beforeAll(async () => {
+    (axios.get as jest.MockedFunction<AxiosStatic>).mockImplementation(async url => {
+      const data_path = path.resolve(__dirname, "./data/ctd/response2.json");
+      const data = JSON.parse(await fs.readFile(data_path, "utf-8"));
+      return { data, status: 200, statusText: "OK", headers: undefined, config: {} };
     });
-
-    test("test ctd wrapper", () => {
-        let input = {
-            response: api_response,
-            edge: {
-                input: "238",
-                association: {
-                    output_type: "Gene",
-                    input_type: "",
-                    predicate: "",
-                },
-                response_mapping: {
-                    sookie: "kevin"
-                }
-            }
-        }
-        let tf = new ctd_tf(input, {});
-        let res = tf.wrap(api_response);
-        expect(res.data[0]['DiseaseID']).toBe("D000022");
-        expect(res.data[0]['PubMedIDs']).toContain("16120699");
-    })
-})
-
+    let res = await axios.get(
+      "http://ctdbase.org/tools/batchQuery.go?inputType=chem&inputTerms=D003634|mercury&report=diseases_curated&format=json",
+    );
+    api_response = res.data;
+  });
+
+  test("test ctd wrapper", () => {
+    let input = {
+      response: api_response,
+      edge: {
+        input: "238",
+        association: {
+          output_type: "Gene",
+          input_type: "",
+          predicate: "",
+        },
+        response_mapping: {
+          sookie: "kevin",
+        },
+      },
+    };
+    let tf = new ctd_tf(input, {});
+    let res = tf.wrap(api_response);
+    expect(res.data[0]["DiseaseID"]).toBe("D000022");
+    expect(res.data[0]["PubMedIDs"]).toContain("16120699");
+  });
+});
 
 describe("test biothings transformer", () => {
-
-    let api_response;
-    let input;
-
-    beforeAll(async () => {
-        (axios as jest.MockedFunction<AxiosStatic>).mockImplementation(async (q) => {
-          const data_path = path.resolve(__dirname, "./data/semmedgene/response.json")
-          const data = JSON.parse(await fs.readFile(data_path, 'utf-8'))
-          return {data, status: 200, statusText: "OK", headers: undefined, config: {}}
-        })
-        let res = await axios({
-            method: 'post',
-            url: 'https://biothings.ncats.io/semmedgene/query',
-            data: 'q=C1332823, C1332824, 123&scopes=umls',
-            params: {
-                fields: 'name,umls,positively_regulates',
-                size: '5'
-            }
-        })
-        api_response = res.data;
-        input = {
-            response: api_response,
-            edge: {
-                "input": ["C1332824", "C1332823", "123"],
-                "query_operation": {
-                    "params": {
-                        "fields": "positively_regulates"
-                    },
-                    "request_body": {
-                        "body": {
-                            "q": "{inputs[0]}",
-                            "scopes": "umls"
-                        }
-                    },
-                    "path": "/query",
-                    "path_params": [],
-                    "method": "post",
-                    "server": "https://biothings.ncats.io/semmedgene",
-                    "tags": [
-                        "disease",
-                        "annotation",
-                        "query",
-                        "translator",
-                        "biothings",
-                        "semmed"
-                    ],
-                    "supportBatch": true,
-                    "inputSeparator": ","
-                },
-                "association": {
-                    "input_id": "UMLS",
-                    "input_type": "Gene",
-                    "output_id": "UMLS",
-                    "output_type": "Gene",
-                    "predicate": "positively_regulates",
-                    "source": "SEMMED",
-                    "api_name": "SEMMED Gene API",
-                    "smartapi": {
-                        "id": "81955d376a10505c1c69cd06dbda3047",
-                        "meta": {
-                            "ETag": "f94053bc78b3c2f0b97f7afd52d7de2fe083b655e56a53090ad73e12be83673b",
-                            "github_username": "kevinxin90",
-                            "timestamp": "2020-05-27T16:53:40.804575",
-                            "uptime_status": "good",
-                            "uptime_ts": "2020-06-12T00:04:31.404599",
-                            "url": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml"
-                        }
-                    }
-                },
-                "response_mapping": {
-                    "positively_regulates": {
-                        "pmid": "positively_regulates.pmid",
-                        "umls": "positively_regulates.umls"
-                    }
-                },
-                "id": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"
-            }
-        }
+  let api_response;
+  let input;
+
+  beforeAll(async () => {
+    (axios as jest.MockedFunction<AxiosStatic>).mockImplementation(async q => {
+      const data_path = path.resolve(__dirname, "./data/semmedgene/response.json");
+      const data = JSON.parse(await fs.readFile(data_path, "utf-8"));
+      return { data, status: 200, statusText: "OK", headers: undefined, config: {} };
     });
-
-    test("test biothings pairCurieWithAPIResponse", async () => {
-        let tf = new biothings_tf(input, {});
-        let res = await tf.pairCurieWithAPIResponse();
-        expect(res["UMLS:C1332823"][0]['umls']).toBe("C1332823");
-        expect(res).toHaveProperty('UMLS:C1332823');
-        expect(res["123"]).toBeUndefined();
+    let res = await axios({
+      method: "post",
+      url: "https://biothings.ncats.io/semmedgene/query",
+      data: "q=C1332823, C1332824, 123&scopes=umls",
+      params: {
+        fields: "name,umls,positively_regulates",
+        size: "5",
+      },
     });
-
-    test("test wrapper", () => {
-        let tf = new biothings_tf(input, {});
-        let res = tf.wrap(input.response[0]);
-        expect(res).toHaveProperty("query");
-    });
-
-})
+    api_response = res.data;
+    input = {
+      response: api_response,
+      edge: {
+        input: ["C1332824", "C1332823", "123"],
+        query_operation: {
+          params: {
+            fields: "positively_regulates",
+          },
+          request_body: {
+            body: {
+              q: "{inputs[0]}",
+              scopes: "umls",
+            },
+          },
+          path: "/query",
+          path_params: [],
+          method: "post",
+          server: "https://biothings.ncats.io/semmedgene",
+          tags: ["disease", "annotation", "query", "translator", "biothings", "semmed"],
+          supportBatch: true,
+          inputSeparator: ",",
+        },
+        association: {
+          input_id: "UMLS",
+          input_type: "Gene",
+          output_id: "UMLS",
+          output_type: "Gene",
+          predicate: "positively_regulates",
+          source: "SEMMED",
+          api_name: "SEMMED Gene API",
+          smartapi: {
+            id: "81955d376a10505c1c69cd06dbda3047",
+            meta: {
+              ETag: "f94053bc78b3c2f0b97f7afd52d7de2fe083b655e56a53090ad73e12be83673b",
+              github_username: "kevinxin90",
+              timestamp: "2020-05-27T16:53:40.804575",
+              uptime_status: "good",
+              uptime_ts: "2020-06-12T00:04:31.404599",
+              url: "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/semmed/semmed_gene.yaml",
+            },
+          },
+        },
+        response_mapping: {
+          positively_regulates: {
+            pmid: "positively_regulates.pmid",
+            umls: "positively_regulates.umls",
+          },
+        },
+        id: "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b",
+      },
+    };
+  });
+
+  test("test biothings pairCurieWithAPIResponse", async () => {
+    let tf = new biothings_tf(input, {});
+    let res = await tf.pairCurieWithAPIResponse();
+    expect(res["UMLS:C1332823"][0]["umls"]).toBe("C1332823");
+    expect(res).toHaveProperty("UMLS:C1332823");
+    expect(res["123"]).toBeUndefined();
+  });
+
+  test("test wrapper", () => {
+    let tf = new biothings_tf(input, {});
+    let res = tf.wrap(input.response[0]);
+    expect(res).toHaveProperty("query");
+  });
+});
diff --git a/__test__/utils.test.ts b/__test__/utils.test.ts
index 629ad53..8d8272b 100644
--- a/__test__/utils.test.ts
+++ b/__test__/utils.test.ts
@@ -5,41 +5,37 @@
 import { generateCurie, toArray } from "../src/utils";
 
 describe("test utils module", () => {
-
-    describe("test generateCurie function", () => {
-        test("test if id is a list", () => {
-            const inputIDs = ["1017", "1018"];
-            const res = generateCurie("NCBIGene", inputIDs);
-            expect(res).toEqual("NCBIGene:1017")
-        })
-
-        test("test if id is not a list", () => {
-            const inputIDs = "1017";
-            const res = generateCurie("NCBIGene", inputIDs);
-            expect(res).toEqual("NCBIGene:1017")
-        })
-
-        test("test if id is already curied", () => {
-            const inputIDs = "NCBIGene1:1017";
-            const res = generateCurie("NCBIGene", inputIDs);
-            expect(res).toEqual("NCBIGene:1017")
-        })
-
-    })
-
-    describe("Test toArray function", () => {
-        test("test if input is already an array", () => {
-            const input = [1];
-            const res = toArray(input);
-            expect(res).toEqual(input);
-        })
-
-        test("test if input is not an array", () => {
-            const input = 1;
-            const res = toArray(input);
-            expect(res).toEqual([1]);
-        })
-    })
-
-
-})
+  describe("test generateCurie function", () => {
+    test("test if id is a list", () => {
+      const inputIDs = ["1017", "1018"];
+      const res = generateCurie("NCBIGene", inputIDs);
+      expect(res).toEqual("NCBIGene:1017");
+    });
+
+    test("test if id is not a list", () => {
+      const inputIDs = "1017";
+      const res = generateCurie("NCBIGene", inputIDs);
+      expect(res).toEqual("NCBIGene:1017");
+    });
+
+    test("test if id is already curied", () => {
+      const inputIDs = "NCBIGene1:1017";
+      const res = generateCurie("NCBIGene", inputIDs);
+      expect(res).toEqual("NCBIGene:1017");
+    });
+  });
+
+  describe("Test toArray function", () => {
+    test("test if input is already an array", () => {
+      const input = [1];
+      const res = toArray(input);
+      expect(res).toEqual(input);
+    });
+
+    test("test if input is not an array", () => {
+      const input = 1;
+      const res = toArray(input);
+      expect(res).toEqual([1]);
+    });
+  });
+});
diff --git a/src/json_transform/index.ts b/src/json_transform/index.ts
index adc89ed..609b5a4 100644
--- a/src/json_transform/index.ts
+++ b/src/json_transform/index.ts
@@ -1,18 +1,18 @@
-import { separateSimpleAnComplexPaths, transformComplexObject, transformSimpleObject } from './utils';
-import { JSONDoc, UserInputTemplate, BaseTemplate, ComplexTemplate } from './types';
+import { separateSimpleAnComplexPaths, transformComplexObject, transformSimpleObject } from "./utils";
+import { JSONDoc, UserInputTemplate, BaseTemplate, ComplexTemplate } from "./types";
 
 export const transform = (json_doc: JSONDoc | JSONDoc[], template: UserInputTemplate) => {
-    let transformed_json_doc;
-    let simple_path_template: BaseTemplate;
-    let complex_path_template: ComplexTemplate;
-    ({ simple_path_template, complex_path_template } = separateSimpleAnComplexPaths(template));
-    transformed_json_doc = transformSimpleObject(json_doc, simple_path_template);
-    for (let [key, value] of Object.entries(complex_path_template)) {
-        if (Array.isArray(value)) {
-            transformed_json_doc[key] = value.map((tmpl) => transformComplexObject(json_doc, tmpl));
-        } else {
-            transformed_json_doc[key] = transformComplexObject(json_doc, value);
-        }
+  let transformed_json_doc;
+  let simple_path_template: BaseTemplate;
+  let complex_path_template: ComplexTemplate;
+  ({ simple_path_template, complex_path_template } = separateSimpleAnComplexPaths(template));
+  transformed_json_doc = transformSimpleObject(json_doc, simple_path_template);
+  for (let [key, value] of Object.entries(complex_path_template)) {
+    if (Array.isArray(value)) {
+      transformed_json_doc[key] = value.map(tmpl => transformComplexObject(json_doc, tmpl));
+    } else {
+      transformed_json_doc[key] = transformComplexObject(json_doc, value);
     }
-    return transformed_json_doc;
-}
+  }
+  return transformed_json_doc;
+};
diff --git a/src/json_transform/types.ts b/src/json_transform/types.ts
index bf5fe2e..79c17ab 100644
--- a/src/json_transform/types.ts
+++ b/src/json_transform/types.ts
@@ -1,24 +1,24 @@
 export interface BaseTemplate {
-    [key: string]: string | string[];
+  [key: string]: string | string[];
 }
 
 export interface ComplexTemplate {
-    [key: string]: BaseTemplate;
+  [key: string]: BaseTemplate;
 }
 
 export interface UserInputTemplate {
-    [key: string]: string | string[] | BaseTemplate;
+  [key: string]: string | string[] | BaseTemplate;
 }
 
 export interface BaseTransformedObject {
-    [key: string]: any;
+  [key: string]: any;
 }
 
 export interface JSONDoc {
-    [key1: string]: any;
-    [key2: number]: any;
+  [key1: string]: any;
+  [key2: number]: any;
 }
 
 export interface PairedResponse {
-    [curie: string]: JSONDoc[]
-}
\ No newline at end of file
+  [curie: string]: JSONDoc[];
+}
diff --git a/src/json_transform/utils.ts b/src/json_transform/utils.ts
index a31ca8a..5b55da0 100644
--- a/src/json_transform/utils.ts
+++ b/src/json_transform/utils.ts
@@ -1,23 +1,23 @@
-import jsonata from 'jsonata';
-import _ from 'lodash';
-import commonpath from 'common-path-prefix';
-import { BaseTemplate, ComplexTemplate, UserInputTemplate, BaseTransformedObject, JSONDoc } from './types'
+import jsonata from "jsonata";
+import _ from "lodash";
+import commonpath from "common-path-prefix";
+import { BaseTemplate, ComplexTemplate, UserInputTemplate, BaseTransformedObject, JSONDoc } from "./types";
 /**
  * Extract all paths from a template object
  * @param {object} template - part of the template
  * @returns {object} - an array of paths
  */
 export const extractPathsFromTemplate = (template: BaseTemplate): string[] => {
-    let paths: string[] = [];
-    Object.values(template).map(val => {
-        if (typeof val === "string") {
-            paths.push(val);
-        } else {
-            paths = [...paths, ...val];
-        }
-    })
-    return paths;
-}
+  let paths: string[] = [];
+  Object.values(template).map(val => {
+    if (typeof val === "string") {
+      paths.push(val);
+    } else {
+      paths = [...paths, ...val];
+    }
+  });
+  return paths;
+};
 
 /**
  * find the longest common path given an array of paths
@@ -25,15 +25,15 @@ export const extractPathsFromTemplate = (template: BaseTemplate): string[] => {
  * @returns - the longest common path(separated by dot)
  */
 export const findLongestCommonPath = (paths: string[]): string => {
-    if (paths.length === 0) {
-        return undefined;
-    }
-    if (paths.length === 1) {
-        return paths[0];
-    }
-    const common_path = commonpath(paths, '.');
-    return (common_path.endsWith('.')) ? common_path.slice(0, -1) : undefined;
-}
+  if (paths.length === 0) {
+    return undefined;
+  }
+  if (paths.length === 1) {
+    return paths[0];
+  }
+  const common_path = commonpath(paths, ".");
+  return common_path.endsWith(".") ? common_path.slice(0, -1) : undefined;
+};
 
 /**
  * Transform a simple JSON object based on the template
@@ -42,26 +42,26 @@ export const findLongestCommonPath = (paths: string[]): string => {
  * @returns {object} - the transformed json object
  */
 export const transformSimpleObject = (json_doc: JSONDoc, template: BaseTemplate): BaseTransformedObject => {
-    const new_doc = {} as BaseTransformedObject;
-    let val;
-    let expression;
-    if (Object.keys(json_doc).length === 0) {
-        return new_doc;
-    }
-    for (let [key, value] of Object.entries(template)) {
-        if (typeof value === "string") {
-            expression = jsonata(value);
-            val = [expression.evaluate(json_doc)];
-        } else {
-            val = value.map(element => jsonata(element).evaluate(json_doc));
-        }
-        val = val.filter(item => !(typeof item === "undefined"));
-        if (val.length === 0) continue;
-        if (val.length === 1) val = val[0];
-        new_doc[key] = val;
-    }
+  const new_doc = {} as BaseTransformedObject;
+  let val;
+  let expression;
+  if (Object.keys(json_doc).length === 0) {
     return new_doc;
-}
+  }
+  for (let [key, value] of Object.entries(template)) {
+    if (typeof value === "string") {
+      expression = jsonata(value);
+      val = [expression.evaluate(json_doc)];
+    } else {
+      val = value.map(element => jsonata(element).evaluate(json_doc));
+    }
+    val = val.filter(item => !(typeof item === "undefined"));
+    if (val.length === 0) continue;
+    if (val.length === 1) val = val[0];
+    new_doc[key] = val;
+  }
+  return new_doc;
+};
 
 /**
  * Transform an array of simple JSON object based on the template
@@ -69,12 +69,15 @@ export const transformSimpleObject = (json_doc: JSONDoc, template: BaseTemplate)
  * @param {object} template - the template on which the transform is based
  * @returns {array} - the transformed json object
  */
-export const transformArrayOfSimpleObject = (json_doc: JSONDoc | JSONDoc[], template: BaseTemplate): BaseTransformedObject | BaseTransformedObject[] => {
-    if (Array.isArray(json_doc)) {
-        return json_doc.map((_doc) => transformSimpleObject(_doc, template))
-    }
-    return json_doc;
-}
+export const transformArrayOfSimpleObject = (
+  json_doc: JSONDoc | JSONDoc[],
+  template: BaseTemplate,
+): BaseTransformedObject | BaseTransformedObject[] => {
+  if (Array.isArray(json_doc)) {
+    return json_doc.map(_doc => transformSimpleObject(_doc, template));
+  }
+  return json_doc;
+};
 
 /**
  * Transform a complex JSON object based on the template
@@ -83,31 +86,31 @@ export const transformArrayOfSimpleObject = (json_doc: JSONDoc | JSONDoc[], temp
  * @returns {object} - the transformed json object
  */
 export const transformComplexObject = (json_doc: JSONDoc, template: BaseTemplate) => {
-    let new_doc = {};
-    let trimmed_json_doc;
-    let trimmed_template;
-    const paths = extractPathsFromTemplate(template);
-    const common_path = findLongestCommonPath(paths);
-    if (paths.length === 1 && paths[0] === common_path) {
-        return transformSimpleObject(json_doc, template)
-    }
-    if (common_path) {
-        trimmed_json_doc = jsonata(common_path).evaluate(json_doc);
-        trimmed_template = removeCommonPathFromTemplate(template, common_path);
-    } else {
-        trimmed_json_doc = json_doc;
-        trimmed_template = template;
-    }
-    if (typeof trimmed_json_doc === "undefined") {
-        return {}
-    }
-    if (Array.isArray(trimmed_json_doc)) {
-        new_doc = transformArrayOfSimpleObject(trimmed_json_doc, trimmed_template)
-    } else {
-        new_doc = transformSimpleObject(trimmed_json_doc, trimmed_template);
-    }
-    return new_doc;
-}
+  let new_doc = {};
+  let trimmed_json_doc;
+  let trimmed_template;
+  const paths = extractPathsFromTemplate(template);
+  const common_path = findLongestCommonPath(paths);
+  if (paths.length === 1 && paths[0] === common_path) {
+    return transformSimpleObject(json_doc, template);
+  }
+  if (common_path) {
+    trimmed_json_doc = jsonata(common_path).evaluate(json_doc);
+    trimmed_template = removeCommonPathFromTemplate(template, common_path);
+  } else {
+    trimmed_json_doc = json_doc;
+    trimmed_template = template;
+  }
+  if (typeof trimmed_json_doc === "undefined") {
+    return {};
+  }
+  if (Array.isArray(trimmed_json_doc)) {
+    new_doc = transformArrayOfSimpleObject(trimmed_json_doc, trimmed_template);
+  } else {
+    new_doc = transformSimpleObject(trimmed_json_doc, trimmed_template);
+  }
+  return new_doc;
+};
 
 /**
  * Remove common prefix from template
@@ -116,43 +119,43 @@ export const transformComplexObject = (json_doc: JSONDoc, template: BaseTemplate
  * @returns {object} - new template of which the common path has been removed
  */
 export const removeCommonPathFromTemplate = (template: BaseTemplate, common_path: string): BaseTemplate => {
-    if (typeof common_path !== "string") {
-        return template
-    }
-    common_path = common_path + '.';
-    const new_template = {} as BaseTemplate;
-    for (let [key, value] of Object.entries(template)) {
-        if (typeof value === 'string') {
-            new_template[key] = (value.startsWith(common_path)) ? value.substring(common_path.length,) : value;
-        } else {
-            const new_value = [] as string[];
-            value.map(path => {
-                const trimmed_path = (path.startsWith(common_path)) ? path.substring(common_path.length,) : path;
-                new_value.push(trimmed_path);
-            })
-            new_template[key] = new_value;
-        }
+  if (typeof common_path !== "string") {
+    return template;
+  }
+  common_path = common_path + ".";
+  const new_template = {} as BaseTemplate;
+  for (let [key, value] of Object.entries(template)) {
+    if (typeof value === "string") {
+      new_template[key] = value.startsWith(common_path) ? value.substring(common_path.length) : value;
+    } else {
+      const new_value = [] as string[];
+      value.map(path => {
+        const trimmed_path = path.startsWith(common_path) ? path.substring(common_path.length) : path;
+        new_value.push(trimmed_path);
+      });
+      new_template[key] = new_value;
     }
-    return new_template;
-}
+  }
+  return new_template;
+};
 
 const isArrayOfString = (input: string | string[] | BaseTemplate): input is string[] => {
-    return Array.isArray(input) && input.every(i => (typeof i === "string"));
-}
+  return Array.isArray(input) && input.every(i => typeof i === "string");
+};
 
 /**
  * distinguish simple paths and complex paths from template
  * @param {object} template - the template which transformation is based on
  */
 export const separateSimpleAnComplexPaths = (template: UserInputTemplate) => {
-    const simple_path_template = {} as BaseTemplate;
-    const complex_path_template = {} as ComplexTemplate;
-    for (let [key, value] of Object.entries(template)) {
-        if (typeof value === "string" || isArrayOfString(value)) {
-            simple_path_template[key] = value;
-        } else {
-            complex_path_template[key] = value;
-        }
+  const simple_path_template = {} as BaseTemplate;
+  const complex_path_template = {} as ComplexTemplate;
+  for (let [key, value] of Object.entries(template)) {
+    if (typeof value === "string" || isArrayOfString(value)) {
+      simple_path_template[key] = value;
+    } else {
+      complex_path_template[key] = value;
     }
-    return { simple_path_template, complex_path_template };
-}
\ No newline at end of file
+  }
+  return { simple_path_template, complex_path_template };
+};
diff --git a/src/transformers/biolink_transformer.ts b/src/transformers/biolink_transformer.ts
index d1d6b12..6108c16 100644
--- a/src/transformers/biolink_transformer.ts
+++ b/src/transformers/biolink_transformer.ts
@@ -1,38 +1,38 @@
 import BaseTransformer from "./transformer";
 
 export default class BiolinkTransformer extends BaseTransformer {
-    wrap(res) {
-        //super.wrap();
-        const PREFIXES = ['HGNC', 'NCBIGene', 'REACT'];
-        if ("associations" in res) {
-            for (let rec of res.associations) {
-                if (rec.object && 'id' in rec.object) {
-                    let prefix, value;
-                    [prefix, value] = rec.object.id.split(":");
-                    if (PREFIXES.includes(prefix)) {
-                        rec['object'][prefix] = value;
-                    } else {
-                        rec['object'][prefix] = rec.object.id;
-                    }
-                }
-                if (rec.publications === undefined || rec.publications.length === 0) {
-                    delete rec.publications
-                } else {
-                    const oldPublications = rec.publications;
-                    rec.publications = [];
-                    for (let oldPub of oldPublications) {
-                        if (!oldPub?.id?.startsWith?.("PMID:")) {
-                            continue;
-                        }
-
-                        rec.publications.push({ id: oldPub.id.split(':').slice(-1)[0] });
-                    }
-                }
-                if (!("provided_by" in rec)) {
-                    delete rec.provided_by
-                }
+  wrap(res) {
+    //super.wrap();
+    const PREFIXES = ["HGNC", "NCBIGene", "REACT"];
+    if ("associations" in res) {
+      for (let rec of res.associations) {
+        if (rec.object && "id" in rec.object) {
+          let prefix, value;
+          [prefix, value] = rec.object.id.split(":");
+          if (PREFIXES.includes(prefix)) {
+            rec["object"][prefix] = value;
+          } else {
+            rec["object"][prefix] = rec.object.id;
+          }
+        }
+        if (rec.publications === undefined || rec.publications.length === 0) {
+          delete rec.publications;
+        } else {
+          const oldPublications = rec.publications;
+          rec.publications = [];
+          for (let oldPub of oldPublications) {
+            if (!oldPub?.id?.startsWith?.("PMID:")) {
+              continue;
             }
-        };
-        return res;
+
+            rec.publications.push({ id: oldPub.id.split(":").slice(-1)[0] });
+          }
+        }
+        if (!("provided_by" in rec)) {
+          delete rec.provided_by;
+        }
+      }
     }
-}
\ No newline at end of file
+    return res;
+  }
+}
diff --git a/src/transformers/biothings_transformer.ts b/src/transformers/biothings_transformer.ts
index cec7629..8676dbc 100644
--- a/src/transformers/biothings_transformer.ts
+++ b/src/transformers/biothings_transformer.ts
@@ -1,33 +1,32 @@
 import BaseTransformer from "./transformer";
-import { generateCurie } from '../utils';
+import { generateCurie } from "../utils";
 
 export default class BioThingsTransformer extends BaseTransformer {
-    async pairCurieWithAPIResponse() {
-        if (this.edge.query_operation.method === "post") {
-            let res = {};
-            const mapper = item => {
-                // for input not found, BioThings API returns an entry with a key "notfound" equal to true
-                if (!('notfound' in item)) {
-                    let input = generateCurie(this.edge.association.input_id, item.query);
-                    if (input in res) {
-                        res[input].push(item);
-                    } else {
-                        res[input] = [item]
-                    }
-                }
-            }
-
-            if (this.data.response.hasOwnProperty("hits")) {
-                // @ts-ignore
-                this.data.response.hits.map(mapper);
-            } else {
-                // @ts-ignore
-                this.data.response.map(mapper);
-            }
-            return res;
-        } else {
-            return super.pairCurieWithAPIResponse();
+  async pairCurieWithAPIResponse() {
+    if (this.edge.query_operation.method === "post") {
+      let res = {};
+      const mapper = item => {
+        // for input not found, BioThings API returns an entry with a key "notfound" equal to true
+        if (!("notfound" in item)) {
+          let input = generateCurie(this.edge.association.input_id, item.query);
+          if (input in res) {
+            res[input].push(item);
+          } else {
+            res[input] = [item];
+          }
         }
+      };
 
+      if (this.data.response.hasOwnProperty("hits")) {
+        // @ts-ignore
+        this.data.response.hits.map(mapper);
+      } else {
+        // @ts-ignore
+        this.data.response.map(mapper);
+      }
+      return res;
+    } else {
+      return super.pairCurieWithAPIResponse();
     }
+  }
 }
diff --git a/src/transformers/cord_transformer.ts b/src/transformers/cord_transformer.ts
index 1f70958..2090456 100644
--- a/src/transformers/cord_transformer.ts
+++ b/src/transformers/cord_transformer.ts
@@ -2,33 +2,35 @@ import BioThingsTransformer from "./biothings_transformer";
 
 // deprecated
 export default class CordTransformer extends BioThingsTransformer {
-
-    wrap(res) {
-        const PREFIXES = ['pr', 'go', 'mop', 'hgnc', 'uberon', 'so', 'cl', 'doid', 'chebi'];
-        let result = {};
-        for (let predicate of Object.keys(res)) {
-            let tmp = [];
-            if (Array.isArray(res[predicate]) && res[predicate].length > 0) {
-                res[predicate].map(item => {
-                    if (item["@type"] === this.edge.association.output_type || (item["@type"] === "DiseaseOrPhenotypicFeature" && this.edge.association.output_type === 'Disease')) {
-                        for (let key of Object.keys(item)) {
-                            if (PREFIXES.includes(key)) {
-                                item[key.toUpperCase()] = item[key];
-                                delete item[key];
-                            }
-                        };
-                        tmp.push(item);
-                    }
-                })
-            };
-            if (tmp.length > 0) {
-                result["related_to"] = tmp;
+  wrap(res) {
+    const PREFIXES = ["pr", "go", "mop", "hgnc", "uberon", "so", "cl", "doid", "chebi"];
+    let result = {};
+    for (let predicate of Object.keys(res)) {
+      let tmp = [];
+      if (Array.isArray(res[predicate]) && res[predicate].length > 0) {
+        res[predicate].map(item => {
+          if (
+            item["@type"] === this.edge.association.output_type ||
+            (item["@type"] === "DiseaseOrPhenotypicFeature" && this.edge.association.output_type === "Disease")
+          ) {
+            for (let key of Object.keys(item)) {
+              if (PREFIXES.includes(key)) {
+                item[key.toUpperCase()] = item[key];
+                delete item[key];
+              }
             }
-        };
-        return result;
+            tmp.push(item);
+          }
+        });
+      }
+      if (tmp.length > 0) {
+        result["related_to"] = tmp;
+      }
     }
+    return result;
+  }
 
-    jsonTransform(res) {
-        return res;
-    }
+  jsonTransform(res) {
+    return res;
+  }
 }
diff --git a/src/transformers/ctd_transformer.ts b/src/transformers/ctd_transformer.ts
index e639e80..43f7d5e 100644
--- a/src/transformers/ctd_transformer.ts
+++ b/src/transformers/ctd_transformer.ts
@@ -1,23 +1,22 @@
 import BaseTransformer from "./transformer";
 
-
 export default class CTDTransformer extends BaseTransformer {
-    wrap(res) {
-        res = res.map(item => {
-            if (typeof item.PubMedIDs === "string") {
-                item.PubMedIDs = item.PubMedIDs.split('|');
-            }
-            if (typeof item.PubMedIds === "string") {
-                item.PubMedIds = item.PubMedIds.split('|');
-            }
-            if (typeof item.DiseaseID === "string") {
-                item.DiseaseID = item.DiseaseID.split(':').slice(-1)[0];
-            }
-            if (typeof item.DiseaseId === "string") {
-                item.DiseaseId = item.DiseaseId.split(':').slice(-1)[0];
-            }
-            return item;
-        });
-        return { data: res };
-    }
-}
\ No newline at end of file
+  wrap(res) {
+    res = res.map(item => {
+      if (typeof item.PubMedIDs === "string") {
+        item.PubMedIDs = item.PubMedIDs.split("|");
+      }
+      if (typeof item.PubMedIds === "string") {
+        item.PubMedIds = item.PubMedIds.split("|");
+      }
+      if (typeof item.DiseaseID === "string") {
+        item.DiseaseID = item.DiseaseID.split(":").slice(-1)[0];
+      }
+      if (typeof item.DiseaseId === "string") {
+        item.DiseaseId = item.DiseaseId.split(":").slice(-1)[0];
+      }
+      return item;
+    });
+    return { data: res };
+  }
+}
diff --git a/src/transformers/ebi_protein_transformer.ts b/src/transformers/ebi_protein_transformer.ts
index 65867dc..a65903f 100644
--- a/src/transformers/ebi_protein_transformer.ts
+++ b/src/transformers/ebi_protein_transformer.ts
@@ -1,18 +1,17 @@
 import BaseTransformer from "./transformer";
 
-
 export default class EBIProteinTransformer extends BaseTransformer {
-    wrap(res) {
-        const new_comments = [];
-        if (res && "comments" in res) {
-            res.comments.map(comment => {
-                if ("reaction" in comment) {
-                    comment.reaction.dbReferences = comment.reaction.dbReferences.filter(item => item.type === "Rhea")
-                }
-                new_comments.push(comment);
-            })
+  wrap(res) {
+    const new_comments = [];
+    if (res && "comments" in res) {
+      res.comments.map(comment => {
+        if ("reaction" in comment) {
+          comment.reaction.dbReferences = comment.reaction.dbReferences.filter(item => item.type === "Rhea");
         }
-        res.comments = new_comments;
-        return res;
+        new_comments.push(comment);
+      });
     }
-}
\ No newline at end of file
+    res.comments = new_comments;
+    return res;
+  }
+}
diff --git a/src/transformers/opentarget_transformer.ts b/src/transformers/opentarget_transformer.ts
index 69e13a9..7f1a605 100644
--- a/src/transformers/opentarget_transformer.ts
+++ b/src/transformers/opentarget_transformer.ts
@@ -2,8 +2,9 @@ import BaseTransformer from "./transformer";
 import jq from "node-jq";
 
 export default class OpenTargetTransformer extends BaseTransformer {
-    async wrap(res) {
-        const filterString = '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)';
-        return await jq.run(filterString, res);
-    }
-}
\ No newline at end of file
+  async wrap(res) {
+    const filterString =
+      '(.data | .[] | select(.drug.id != null) | select(.drug.id | contains("CHEMBL")) | .drug.id) |= (split("/") | last)';
+    return await jq.run(filterString, res);
+  }
+}
diff --git a/src/transformers/semmed_transformer.ts b/src/transformers/semmed_transformer.ts
index 0766e01..7154cc2 100644
--- a/src/transformers/semmed_transformer.ts
+++ b/src/transformers/semmed_transformer.ts
@@ -1,30 +1,32 @@
-import BioThingsTransformer from './biothings_transformer';
+import BioThingsTransformer from "./biothings_transformer";
 
 export default class SemmedTransformer extends BioThingsTransformer {
-
-    wrap(res) {
-        let result = {};
-        for (let predicate of Object.keys(res)) {
-            let tmp = [];
-            if (Array.isArray(res[predicate]) && res[predicate].length > 0) {
-                res[predicate].map(item => {
-                    if (item["@type"] === this.edge.association.output_type || (item["@type"] === "DiseaseOrPhenotypicFeature" && this.edge.association.output_type === 'Disease')) {
-                        item['UMLS'] = item['umls'];
-                        item['pubmed'] = item['pmid'];
-                        delete item['umls'];
-                        delete item['pmid'];
-                        tmp.push(item);
-                    }
-                })
-            };
-            if (tmp.length > 0) {
-                result[predicate] = tmp;
-            }
-        };
-        return result;
+  wrap(res) {
+    let result = {};
+    for (let predicate of Object.keys(res)) {
+      let tmp = [];
+      if (Array.isArray(res[predicate]) && res[predicate].length > 0) {
+        res[predicate].map(item => {
+          if (
+            item["@type"] === this.edge.association.output_type ||
+            (item["@type"] === "DiseaseOrPhenotypicFeature" && this.edge.association.output_type === "Disease")
+          ) {
+            item["UMLS"] = item["umls"];
+            item["pubmed"] = item["pmid"];
+            delete item["umls"];
+            delete item["pmid"];
+            tmp.push(item);
+          }
+        });
+      }
+      if (tmp.length > 0) {
+        result[predicate] = tmp;
+      }
     }
+    return result;
+  }
 
-    jsonTransform(res) {
-        return res;
-    }
-}
\ No newline at end of file
+  jsonTransform(res) {
+    return res;
+  }
+}
diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts
index 68d22ae..7f5906d 100644
--- a/src/transformers/transformer.ts
+++ b/src/transformers/transformer.ts
@@ -10,30 +10,30 @@ import async from "async";
 const debug = Debug("bte:api-response-transform:transformer");
 
 export default class BaseTransformer {
-    protected edge: BTEKGOperationObject;
-    protected data: BTEQueryObject;
-    public config: any;
+  protected edge: BTEKGOperationObject;
+  protected data: BTEQueryObject;
+  public config: any;
 
-    constructor(data: BTEQueryObject, config: any) {
-        this.data = data;
-        this.edge = data.edge;
-        this.config = config;
-    }
+  constructor(data: BTEQueryObject, config: any) {
+    this.data = data;
+    this.edge = data.edge;
+    this.config = config;
+  }
 
-    /**
-     * Create an object with key representing input, and value representing the output of API
-     */
-    async pairCurieWithAPIResponse() {
-        let input = generateCurie(
-            this.edge.association.input_id,
-            this.edge.input.hasOwnProperty('queryInputs') ? this.edge.input["queryInputs"] : this.edge.input as string
-        );
-        return {
-            [input]: [this.data.response],
-        };
-    }
+  /**
+   * Create an object with key representing input, and value representing the output of API
+   */
+  async pairCurieWithAPIResponse() {
+    let input = generateCurie(
+      this.edge.association.input_id,
+      this.edge.input.hasOwnProperty("queryInputs") ? this.edge.input["queryInputs"] : (this.edge.input as string),
+    );
+    return {
+      [input]: [this.data.response],
+    };
+  }
 
-    /*
+  /*
       if $edge.input | keys | contains(["queryInputs"]) then
         {[generateCurie($edge.association.input_id, $edge.input.queryInputs)]: .response}
       else
@@ -41,223 +41,244 @@ export default class BaseTransformer {
       end
     */
 
-    /**
-     * Wrapper functions to transform API response before passing to JSON Transformer
-     * @return {Object} - key is curie representing input, value is an array of outputs.
-     */
-    wrap(res) {
-        if (Array.isArray(res)) {
-            res = { data: res };
-        }
-        return res;
+  /**
+   * Wrapper functions to transform API response before passing to JSON Transformer
+   * @return {Object} - key is curie representing input, value is an array of outputs.
+   */
+  wrap(res) {
+    if (Array.isArray(res)) {
+      res = { data: res };
     }
+    return res;
+  }
 
-    /**
-     * Transform Individual JSON response into Biolink compatible format
-     * @param {Object} res - JSON response representing an output.
-     */
-    jsonTransform(res: JSONDoc | JSONDoc[]) {
-        res = transform(res, this.edge.response_mapping);
-        return res;
-    }
-
-    _updatePublications(mappedResponse: any) {
-        if (!Array.isArray(mappedResponse.publications)) {
-            mappedResponse.publications = [];
-        }
-
-        const publicationTypes = [
-            {prop: "ref_pmid", prefix: "PMID:", urls: ["http://www.ncbi.nlm.nih.gov/pubmed/", "http://europepmc.org/abstract/MED/", "https://www.ncbi.nlm.nih.gov/pubmed/"]},
-            {prop: "ref_pmcid", prefix: "PMCID:", urls: ["http://www.ncbi.nlm.nih.gov/pmc/articles/", "http://europepmc.org/articles/"]},
-            {prop: "ref_clinicaltrials", prefix: "clinicaltrials:", urls: ["https://clinicaltrials.gov/ct2/show/", "https://www.clinicaltrials.gov/ct2/show/"]},
-            {prop: "ref_doi", prefix: "doi:", urls: ["https://doi.org/", "http://www.nejm.org/doi/full/", "https://www.tandfonline.com/doi/abs/", "http://onlinelibrary.wiley.com/doi/"]},
-            {prop: "ref_isbn", prefix: "isbn:", urls: ["https://www.isbn-international.org/identifier/"]}
-        ]
+  /**
+   * Transform Individual JSON response into Biolink compatible format
+   * @param {Object} res - JSON response representing an output.
+   */
+  jsonTransform(res: JSONDoc | JSONDoc[]) {
+    res = transform(res, this.edge.response_mapping);
+    return res;
+  }
 
-        // handle URLs (which could be CURIEs)
-        if ("ref_url" in mappedResponse) {
-            for (let publication of toArray(mappedResponse.ref_url)) {
-                if (typeof publication !== "string" || publication.length === 0) {
-                    continue;
-                }
-
-                let isCurie = false;
-                for (let publicationType of publicationTypes) {
-                    for (let url of publicationType.urls) {
-                        if (publication.startsWith(url)) {
-                            isCurie = true;
-    
-                            if (!mappedResponse[publicationType.prop]) {
-                                mappedResponse[publicationType.prop] = [];
-                            }
-                            else if (!Array.isArray(mappedResponse[publicationType.prop])) {
-                                mappedResponse[publicationType.prop] = toArray(mappedResponse[publicationType.prop]);
-                            }
-                            
-                            mappedResponse[publicationType.prop].push(publication.slice(url.length));
-                            
-                            break;
-                        }
-                    }
+  _updatePublications(mappedResponse: any) {
+    if (!Array.isArray(mappedResponse.publications)) {
+      mappedResponse.publications = [];
+    }
 
-                    if (isCurie) {
-                        break;
-                    }
-                }
+    const publicationTypes = [
+      {
+        prop: "ref_pmid",
+        prefix: "PMID:",
+        urls: [
+          "http://www.ncbi.nlm.nih.gov/pubmed/",
+          "http://europepmc.org/abstract/MED/",
+          "https://www.ncbi.nlm.nih.gov/pubmed/",
+        ],
+      },
+      {
+        prop: "ref_pmcid",
+        prefix: "PMCID:",
+        urls: ["http://www.ncbi.nlm.nih.gov/pmc/articles/", "http://europepmc.org/articles/"],
+      },
+      {
+        prop: "ref_clinicaltrials",
+        prefix: "clinicaltrials:",
+        urls: ["https://clinicaltrials.gov/ct2/show/", "https://www.clinicaltrials.gov/ct2/show/"],
+      },
+      {
+        prop: "ref_doi",
+        prefix: "doi:",
+        urls: [
+          "https://doi.org/",
+          "http://www.nejm.org/doi/full/",
+          "https://www.tandfonline.com/doi/abs/",
+          "http://onlinelibrary.wiley.com/doi/",
+        ],
+      },
+      { prop: "ref_isbn", prefix: "isbn:", urls: ["https://www.isbn-international.org/identifier/"] },
+    ];
 
-                if (!isCurie) {
-                    mappedResponse.publications.push(publication);
-                }
-            }
+    // handle URLs (which could be CURIEs)
+    if ("ref_url" in mappedResponse) {
+      for (let publication of toArray(mappedResponse.ref_url)) {
+        if (typeof publication !== "string" || publication.length === 0) {
+          continue;
         }
-        delete mappedResponse.ref_url;
 
+        let isCurie = false;
         for (let publicationType of publicationTypes) {
-            if (publicationType.prop in mappedResponse) {
-                for (let publication of toArray(mappedResponse[publicationType.prop])) {
-                    // handle numbers
-                    if (typeof publication === "number") {
-                        publication = publication.toString();
-                    }
+          for (let url of publicationType.urls) {
+            if (publication.startsWith(url)) {
+              isCurie = true;
 
-                    if (typeof publication !== "string" || publication.length === 0) {
-                        continue;
-                    }
+              if (!mappedResponse[publicationType.prop]) {
+                mappedResponse[publicationType.prop] = [];
+              } else if (!Array.isArray(mappedResponse[publicationType.prop])) {
+                mappedResponse[publicationType.prop] = toArray(mappedResponse[publicationType.prop]);
+              }
 
-                    if (publication.toUpperCase().startsWith(publicationType.prefix.toUpperCase())) {
-                        mappedResponse.publications.push(publicationType.prefix + publication.slice(publicationType.prefix.length));
-                    }
-                    else {
-                        mappedResponse.publications.push(publicationType.prefix + publication);
-                    }
-                }
+              mappedResponse[publicationType.prop].push(publication.slice(url.length));
 
-                delete mappedResponse[publicationType.prop];
+              break;
             }
-        }
-    
-        if (mappedResponse.publications.length === 0) {
-            delete mappedResponse.publications;
+          }
+
+          if (isCurie) {
+            break;
+          }
         }
 
-        return mappedResponse;
+        if (!isCurie) {
+          mappedResponse.publications.push(publication);
+        }
+      }
     }
+    delete mappedResponse.ref_url;
 
-    // _updateEdgeMetadata(res) {
-    //     res.$edge_metadata = {
-    //         ...this.edge.association,
-    //         trapi_qEdge_obj: this.edge.reasoner_edge,
-    //         filter: this.edge.filter,
-    //     };
-    //     return res;
-    // }
+    for (let publicationType of publicationTypes) {
+      if (publicationType.prop in mappedResponse) {
+        for (let publication of toArray(mappedResponse[publicationType.prop])) {
+          // handle numbers
+          if (typeof publication === "number") {
+            publication = publication.toString();
+          }
 
-    _getSubject(subjectCurie: any) {
+          if (typeof publication !== "string" || publication.length === 0) {
+            continue;
+          }
 
-        //debug(`input: ${input}`);
-        let subject = {
-            original: typeof this.edge.original_input === "undefined" ? undefined : this.edge.original_input[subjectCurie],
-            // normalizedInfo:
-            //     typeof this.edge.input_resolved_identifiers === "undefined" || typeof this.edge.original_input === "undefined"
-            //     ? undefined
-            //     : this.edge.input_resolved_identifiers[this.edge.original_input[subjectCurie]],
+          if (publication.toUpperCase().startsWith(publicationType.prefix.toUpperCase())) {
+            mappedResponse.publications.push(publicationType.prefix + publication.slice(publicationType.prefix.length));
+          } else {
+            mappedResponse.publications.push(publicationType.prefix + publication);
+          }
         }
-        if (this.edge.input_resolved_identifiers && subject.original === undefined) {
-            //try to find an equivalent ids object if the original input doesn't match (for ICEES)
-            for (let curie of Object.keys(this.edge.input_resolved_identifiers)) {
-                if (this.edge.input_resolved_identifiers[curie].equivalentIDs.includes(subjectCurie)) {
-                    subject = {
-                        original: curie,
-                        // normalizedInfo: this.edge.input_resolved_identifiers[curie],
-                    };
-                    break;
-                }
-            }
-        }
-        return subject;
+
+        delete mappedResponse[publicationType.prop];
+      }
     }
 
-    _removeNonEdgeData(mappedResponse: any) {
-        delete mappedResponse["@type"];
-        delete mappedResponse[this.edge.association.output_id];
-        delete mappedResponse["input_name"];
-        delete mappedResponse["output_name"];
-        return mappedResponse;
+    if (mappedResponse.publications.length === 0) {
+      delete mappedResponse.publications;
     }
 
-    /**
-     * Add edge information into individual output JSON.
-     * @param {Object} mappedResponse - JSON response representing an output.
-     */
-    async formatRecords(subjectCurie: string, mappedResponse: any) {
-        if (mappedResponse === undefined || Object.keys(mappedResponse).length === 0) {
-            return [];
-        }
+    return mappedResponse;
+  }
 
-        // mappedResponse = this._updateEdgeMetadata(mappedResponse);
-        const objectIDs = this.extractObjectIDs(mappedResponse);
-        const outputName = mappedResponse.output_name;
-        const inputName = mappedResponse.input_name; 
-        mappedResponse = this._removeNonEdgeData(mappedResponse);
-        mappedResponse = this._updatePublications(mappedResponse);
+  // _updateEdgeMetadata(res) {
+  //     res.$edge_metadata = {
+  //         ...this.edge.association,
+  //         trapi_qEdge_obj: this.edge.reasoner_edge,
+  //         filter: this.edge.filter,
+  //     };
+  //     return res;
+  // }
 
-        const frozenRecord = {
-            subject: {...this._getSubject(subjectCurie), apiLabel: inputName},
-            association: {...this.edge.association},
-            qEdge: this.edge.reasoner_edge,
-            mappedResponse: {...mappedResponse},
+  _getSubject(subjectCurie: any) {
+    //debug(`input: ${input}`);
+    let subject = {
+      original: typeof this.edge.original_input === "undefined" ? undefined : this.edge.original_input[subjectCurie],
+      // normalizedInfo:
+      //     typeof this.edge.input_resolved_identifiers === "undefined" || typeof this.edge.original_input === "undefined"
+      //     ? undefined
+      //     : this.edge.input_resolved_identifiers[this.edge.original_input[subjectCurie]],
+    };
+    if (this.edge.input_resolved_identifiers && subject.original === undefined) {
+      //try to find an equivalent ids object if the original input doesn't match (for ICEES)
+      for (let curie of Object.keys(this.edge.input_resolved_identifiers)) {
+        if (this.edge.input_resolved_identifiers[curie].equivalentIDs.includes(subjectCurie)) {
+          subject = {
+            original: curie,
+            // normalizedInfo: this.edge.input_resolved_identifiers[curie],
+          };
+          break;
         }
+      }
+    }
+    return subject;
+  }
 
-        let transformedRecords = await async.mapSeries(objectIDs, async (curie: string) => {
+  _removeNonEdgeData(mappedResponse: any) {
+    delete mappedResponse["@type"];
+    delete mappedResponse[this.edge.association.output_id];
+    delete mappedResponse["input_name"];
+    delete mappedResponse["output_name"];
+    return mappedResponse;
+  }
 
-            let copyRecord = {
-                ...frozenRecord,
-                 object: {
-                     original: curie,
-                     apiLabel: outputName
-                 }
-            };
-            return new Record(copyRecord, this.config, this.edge.association, this.edge.reasoner_edge);
-        });
-        return transformedRecords;
+  /**
+   * Add edge information into individual output JSON.
+   * @param {Object} mappedResponse - JSON response representing an output.
+   */
+  async formatRecords(subjectCurie: string, mappedResponse: any) {
+    if (mappedResponse === undefined || Object.keys(mappedResponse).length === 0) {
+      return [];
     }
 
-    /**
-     * Main function to transform API response
-     */
-    async transform() {
-        let transformedRecords = [];
-        let responses = await this.pairCurieWithAPIResponse();
+    // mappedResponse = this._updateEdgeMetadata(mappedResponse);
+    const objectIDs = this.extractObjectIDs(mappedResponse);
+    const outputName = mappedResponse.output_name;
+    const inputName = mappedResponse.input_name;
+    mappedResponse = this._removeNonEdgeData(mappedResponse);
+    mappedResponse = this._updatePublications(mappedResponse);
 
-        await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
-            if (Array.isArray(curieResponses) && curieResponses.length > 0) {
-                await async.eachSeries(curieResponses, async response => {
-                    const predicateResponse = this.jsonTransform(await this.wrap(response));
-                    await async.eachSeries(Object.entries(predicateResponse), async ([predicate, mappedResponses]) => {
-                        if (Array.isArray(mappedResponses) && mappedResponses.length > 0) {
-                            await async.eachSeries(mappedResponses, async (mappedResponse: any[]) => {
-                                transformedRecords.push(...(await this.formatRecords(curie, mappedResponse)));
-                            });
-                        } else {
-                            transformedRecords.push(...(await this.formatRecords(curie, mappedResponses)));
-                        }
-                    });
-                });
+    const frozenRecord = {
+      subject: { ...this._getSubject(subjectCurie), apiLabel: inputName },
+      association: { ...this.edge.association },
+      qEdge: this.edge.reasoner_edge,
+      mappedResponse: { ...mappedResponse },
+    };
+
+    let transformedRecords = await async.mapSeries(objectIDs, async (curie: string) => {
+      let copyRecord = {
+        ...frozenRecord,
+        object: {
+          original: curie,
+          apiLabel: outputName,
+        },
+      };
+      return new Record(copyRecord, this.config, this.edge.association, this.edge.reasoner_edge);
+    });
+    return transformedRecords;
+  }
+
+  /**
+   * Main function to transform API response
+   */
+  async transform() {
+    let transformedRecords = [];
+    let responses = await this.pairCurieWithAPIResponse();
+
+    await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
+      if (Array.isArray(curieResponses) && curieResponses.length > 0) {
+        await async.eachSeries(curieResponses, async response => {
+          const predicateResponse = this.jsonTransform(await this.wrap(response));
+          await async.eachSeries(Object.entries(predicateResponse), async ([predicate, mappedResponses]) => {
+            if (Array.isArray(mappedResponses) && mappedResponses.length > 0) {
+              await async.eachSeries(mappedResponses, async (mappedResponse: any[]) => {
+                transformedRecords.push(...(await this.formatRecords(curie, mappedResponse)));
+              });
+            } else {
+              transformedRecords.push(...(await this.formatRecords(curie, mappedResponses)));
             }
-        })
-        return transformedRecords;
-    }
+          });
+        });
+      }
+    });
+    return transformedRecords;
+  }
 
-    /**
-     * Retrieve all output IDs.
-     * @param {Object} mappedResponse - JSON response representing an output.
-     */
-    extractObjectIDs(mappedResponse: object) {
-        const output_id_type = this.edge.association.output_id;
-        if (!(output_id_type in mappedResponse)) {
-            return [];
-        }
-        mappedResponse[output_id_type] = toArray(mappedResponse[output_id_type]);
-        return mappedResponse[output_id_type].map((id: string) => generateCurie(output_id_type, id));
+  /**
+   * Retrieve all output IDs.
+   * @param {Object} mappedResponse - JSON response representing an output.
+   */
+  extractObjectIDs(mappedResponse: object) {
+    const output_id_type = this.edge.association.output_id;
+    if (!(output_id_type in mappedResponse)) {
+      return [];
     }
+    mappedResponse[output_id_type] = toArray(mappedResponse[output_id_type]);
+    return mappedResponse[output_id_type].map((id: string) => generateCurie(output_id_type, id));
+  }
 }
diff --git a/src/transformers/trapi_transformer.ts b/src/transformers/trapi_transformer.ts
index 402f848..8abdda8 100644
--- a/src/transformers/trapi_transformer.ts
+++ b/src/transformers/trapi_transformer.ts
@@ -15,7 +15,9 @@ export default class TRAPITransformer extends BaseTransformer {
           analysis?.edge_bindings?.e01?.forEach(binding => {
             const edgeID = binding?.id;
             const edge =
-              "message" in this.data.response && edgeID ? this.data.response.message.knowledge_graph.edges[edgeID] : undefined;
+              "message" in this.data.response && edgeID
+                ? this.data.response.message.knowledge_graph.edges[edgeID]
+                : undefined;
             const edgeHasSupportGraph = edge.attributes.some(attribute => {
               if (attribute.attribute_type_id === "biolink:support_graphs" && attribute.value?.length) {
                 return true;
@@ -23,10 +25,14 @@ export default class TRAPITransformer extends BaseTransformer {
             });
             if (edgeHasSupportGraph || !edgeID) return;
             edges[edgeID] = {
-              subject: (this.data.response as JSONDoc).message.knowledge_graph.edges[edgeID].subject ?? result.node_bindings.n0[0].id,
-              object: (this.data.response as JSONDoc).message.knowledge_graph.edges[edgeID].object ?? result.node_bindings.n1[0].id,
+              subject:
+                (this.data.response as JSONDoc).message.knowledge_graph.edges[edgeID].subject ??
+                result.node_bindings.n0[0].id,
+              object:
+                (this.data.response as JSONDoc).message.knowledge_graph.edges[edgeID].object ??
+                result.node_bindings.n1[0].id,
             };
-          })
+          });
         });
       });
     }
@@ -62,7 +68,7 @@ export default class TRAPITransformer extends BaseTransformer {
       qEdge: this.edge.reasoner_edge,
       mappedResponse: {
         "edge-attributes": [...edge.attributes],
-        trapi_sources: edge.sources
+        trapi_sources: edge.sources,
       },
     };
     if (frozenRecord.subject.original) {
diff --git a/src/utils.ts b/src/utils.ts
index d6c0c3f..ffa9b24 100644
--- a/src/utils.ts
+++ b/src/utils.ts
@@ -1,16 +1,16 @@
 export function generateCurie(idType: string, id: string | string[]) {
-    if (Array.isArray(id)) {
-        id = id[0];
-    }
-    if (typeof id === "string" && id.includes(':')) {
-        id = id.split(':').slice(-1)[0];
-    }
-    return idType + ':' + id;
+  if (Array.isArray(id)) {
+    id = id[0];
+  }
+  if (typeof id === "string" && id.includes(":")) {
+    id = id.split(":").slice(-1)[0];
+  }
+  return idType + ":" + id;
 }
 
 export function toArray(item) {
-    if (!(Array.isArray(item))) {
-        return [item];
-    }
-    return item;
-}
\ No newline at end of file
+  if (!Array.isArray(item)) {
+    return [item];
+  }
+  return item;
+}