From f625975d17d72405aa2d480b60b97526c710e81b Mon Sep 17 00:00:00 2001 From: edgargaticaCU <88678635+edgargaticaCU@users.noreply.github.com> Date: Fri, 28 Apr 2023 16:10:06 -0500 Subject: [PATCH 1/2] Updating to TRAPI 1.4 provenance --- text_mining/smartapi.yaml | 62 +++++++++++++++++++++------------------ 1 file changed, 34 insertions(+), 28 deletions(-) diff --git a/text_mining/smartapi.yaml b/text_mining/smartapi.yaml index 627cf75a..6d568d10 100644 --- a/text_mining/smartapi.yaml +++ b/text_mining/smartapi.yaml @@ -628,7 +628,7 @@ components: "scopes": ["subject.DRUGBANK", "association.edge_label"] } parameters: - fields: object.MONDO,association.edge_attributes + fields: object.MONDO,association.edge_attributes,association.sources size: 1000 outputs: - id: MONDO @@ -655,7 +655,7 @@ components: "scopes": ["object.MONDO", "association.edge_label"] } parameters: - fields: subject.DRUGBANK,association.edge_attributes + fields: subject.DRUGBANK,association.edge_attributes,association.sources size: 1000 outputs: - id: DRUGBANK @@ -682,7 +682,7 @@ components: "scopes": ["subject.DRUGBANK", "association.edge_label"] } parameters: - fields: object.HP,association.edge_attributes + fields: object.HP,association.edge_attributes,association.sources size: 1000 outputs: - id: HP @@ -709,7 +709,7 @@ components: "scopes": ["object.HP", "association.edge_label"] } parameters: - fields: subject.DRUGBANK,association.edge_attributes + fields: subject.DRUGBANK,association.edge_attributes,association.sources size: 1000 outputs: - id: DRUGBANK @@ -735,7 +735,7 @@ components: "scopes": ["subject.DRUGBANK", "association.edge_label"] } parameters: - fields: object.UniProtKB,association.edge_attributes + fields: object.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -767,7 +767,7 @@ components: "scopes": ["object.UniProtKB", "association.edge_label"] } parameters: - fields: subject.DRUGBANK,association.edge_attributes + fields: subject.DRUGBANK,association.edge_attributes,association.sources size: 1000 outputs: - id: DRUGBANK @@ -798,7 +798,7 @@ components: "scopes": ["subject.DRUGBANK", "association.edge_label"] } parameters: - fields: object.UniProtKB,association.edge_attributes + fields: object.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -830,7 +830,7 @@ components: "scopes": ["object.UniProtKB", "association.edge_label"] } parameters: - fields: subject.DRUGBANK,association.edge_attributes + fields: subject.DRUGBANK,association.edge_attributes,association.sources size: 1000 outputs: - id: DRUGBANK @@ -861,7 +861,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.UniProtKB,association.edge_attributes + fields: object.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -891,7 +891,7 @@ components: "scopes": ["object.UniProtKB", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -921,7 +921,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.UniProtKB,association.edge_attributes + fields: object.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -951,7 +951,7 @@ components: "scopes": ["object.UniProtKB", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -981,7 +981,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.MONDO,association.edge_attributes + fields: object.MONDO,association.edge_attributes,association.sources size: 1000 outputs: - id: MONDO @@ -1008,7 +1008,7 @@ components: "scopes": ["object.MONDO", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -1034,7 +1034,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.HP,association.edge_attributes + fields: object.HP,association.edge_attributes,association.sources size: 1000 outputs: - id: HP @@ -1061,7 +1061,7 @@ components: "scopes": ["object.HP", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -1087,7 +1087,7 @@ components: "scopes": ["subject.DRUGBANK", "association.edge_label"] } parameters: - fields: object.HP,association.edge_attributes + fields: object.HP,association.edge_attributes,association.sources size: 1000 outputs: - id: HP @@ -1110,7 +1110,7 @@ components: "scopes": ["object.HP", "association.edge_label"] } parameters: - fields: subject.DRUGBANK,association.edge_attributes + fields: subject.DRUGBANK,association.edge_attributes,association.sources size: 1000 outputs: - id: DRUGBANK @@ -1133,7 +1133,7 @@ components: "scopes": ["subject.DRUGBANK", "association.edge_label"] } parameters: - fields: object.MONDO,association.edge_attributes + fields: object.MONDO,association.edge_attributes,association.sources size: 1000 outputs: - id: MONDO @@ -1156,7 +1156,7 @@ components: "scopes": ["object.MONDO", "association.edge_label"] } parameters: - fields: subject.DRUGBANK,association.edge_attributes + fields: subject.DRUGBANK,association.edge_attributes,association.sources size: 1000 outputs: - id: DRUGBANK @@ -1179,7 +1179,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.HP,association.edge_attributes + fields: object.HP,association.edge_attributes,association.sources size: 1000 outputs: - id: HP @@ -1208,7 +1208,7 @@ components: "scopes": ["object.HP", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -1237,7 +1237,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.MONDO,association.edge_attributes + fields: object.MONDO,association.edge_attributes,association.sources size: 1000 outputs: - id: MONDO @@ -1266,7 +1266,7 @@ components: "scopes": ["object.MONDO", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -1295,7 +1295,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.HP,association.edge_attributes + fields: object.HP,association.edge_attributes,association.sources size: 1000 outputs: - id: HP @@ -1324,7 +1324,7 @@ components: "scopes": ["object.HP", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -1353,7 +1353,7 @@ components: "scopes": ["subject.UniProtKB", "association.edge_label"] } parameters: - fields: object.MONDO,association.edge_attributes + fields: object.MONDO,association.edge_attributes,association.sources size: 1000 outputs: - id: MONDO @@ -1382,7 +1382,7 @@ components: "scopes": ["object.MONDO", "association.edge_label"] } parameters: - fields: subject.UniProtKB,association.edge_attributes + fields: subject.UniProtKB,association.edge_attributes,association.sources size: 1000 outputs: - id: UniProtKB @@ -1400,18 +1400,24 @@ components: mondo-object: MONDO: object.MONDO edge-attributes: association.edge_attributes + trapi_sources: association.sources chebi-subject: CHEBI: subject.CHEBI edge-attributes: association.edge_attributes + trapi_sources: association.sources hp-object: HP: object.HP edge-attributes: association.edge_attributes + trapi_sources: association.sources drugbank-subject: DRUGBANK: subject.DRUGBANK edge-attributes: association.edge_attributes + trapi_sources: association.sources uniprotkb-object: UniProtKB: object.UniProtKB edge-attributes: association.edge_attributes + trapi_sources: association.sources uniprotkb-subject: UniProtKB: subject.UniProtKB edge-attributes: association.edge_attributes + trapi_sources: association.sources From e4675fab54919dbfd599acf9e2cc6fdf6a99cf0c Mon Sep 17 00:00:00 2001 From: edgargaticaCU <88678635+edgargaticaCU@users.noreply.github.com> Date: Mon, 1 May 2023 13:08:25 -0500 Subject: [PATCH 2/2] Removing the last vestiges of CHEBI --- text_mining/smartapi.yaml | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/text_mining/smartapi.yaml b/text_mining/smartapi.yaml index 6d568d10..2ec440c9 100644 --- a/text_mining/smartapi.yaml +++ b/text_mining/smartapi.yaml @@ -414,7 +414,7 @@ components: If "fields=all", all available fields will be returned. - Note that it supports dot notation as well, e.g., you can pass "chebi.name". + Note that it supports dot notation as well, e.g., you can pass "mondo.name". Default: "fields=all". The parameter "filter" is an alias for this parameter. in: query @@ -604,12 +604,12 @@ components: ## - for reverse operations, some edge attributes may seem odd (reversed subj/obj) ## - don't use subject.type/object.type in q, that came from SRI ID resolver and differs a lot between IDs of same namespace ## - use heuristics to specify input / output type. BTE will handle any discrepancies w/ SRI ID resolver... - ## - CHEBI, DRUGBANK :SmallMolecule + ## - DRUGBANK :SmallMolecule ## - MONDO: Disease ## - HP: PhenotypicFeaure ## - UniProtKB: Gene ## - currently we can't express _exists_ with this kind of query: useful for setting the output - ## - currently, BTE handles prefix (CHEBI / MONDO / HP keep their prefixes, DRUGBANK / UniProtKB does not). + ## - currently, BTE handles prefix (MONDO / HP keep their prefixes, DRUGBANK / UniProtKB does not). ## in the future, could edit parser + queries to handle prefixes ## - joinSafe is only needed if the delimiter isn't a comma drugbank-treats-mondo: @@ -1401,10 +1401,6 @@ components: MONDO: object.MONDO edge-attributes: association.edge_attributes trapi_sources: association.sources - chebi-subject: - CHEBI: subject.CHEBI - edge-attributes: association.edge_attributes - trapi_sources: association.sources hp-object: HP: object.HP edge-attributes: association.edge_attributes