Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

SemMedDB V43 update #8

Merged
merged 15 commits into from
Jan 11, 2023
Merged

SemMedDB V43 update #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
27d8134
format the code
erikyao Nov 29, 2022
468ea76
tiny refactor to eliminate pandas dependency
erikyao Nov 29, 2022
bbb64f6
major refactor: rename variables and functions; simply object CUI for…
erikyao Dec 5, 2022
2531bb2
resort to RE filter again with a simplified pattern; use pd.Series-wi…
erikyao Dec 6, 2022
377ddaf
tiny refactor: rename variables and simplify if conditions
erikyao Dec 6, 2022
ec678ee
restructure the parser; add functions about MRCUI data
erikyao Dec 6, 2022
20669dd
add filter on novelty scores for SemMed data
erikyao Dec 6, 2022
f86216b
major refactor: preprocess all predications in Pandas
erikyao Dec 30, 2022
856268c
add two marker columns, IS_SUBJECT_PIPED and IS_OBJECT_PIPED; change …
erikyao Dec 31, 2022
37f78ee
add functions to locate and delete equivalent NCBIGene IDs for piped …
erikyao Jan 4, 2023
7dd09da
add cache reading/writing for Node Normalizer queries; revise equival…
erikyao Jan 10, 2023
facb3b8
add comments
erikyao Jan 10, 2023
b21e641
revise function delete_equivalent_ncbigene_ids to reduce peak memory …
erikyao Jan 10, 2023
1d04d49
change the version number
erikyao Jan 10, 2023
279888e
change dumper file links in the manifest; update README
erikyao Jan 11, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 33 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1,33 @@
# SEMMED API parser 08/2021
# SemMedDB Predication Parser

## Source Data Files

There are four files required by this parser:

1. The _PREDICATION_ CSV file.
- Version: `semmedVER43_R`
- Download page: https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR/SemMedDB_download.html
- Direct download link: https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/SemRep_SemMedDB_SKR/semmedVER43_2022_R_PREDICATION.csv.gz
- Filename: `semmedVER43_2022_R_PREDICATION.csv.gz`
2. The _Semantic Type Mappings_ file.
- Version: `2018AB` (UMLS release version number, as shown in [UMLS Release File Archives](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html))
- Download page: https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/documentation/SemanticTypesAndGroups.html
- Direct download link: https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/Docs/SemanticTypes_2018AB.txt
- Filenname: `SemanticTypes_2018AB.txt`
3. The _Retired CUI Mapping_ file.
- Version: `2022AA` (UMLS release version number, as shown in [UMLS Release File Archives](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html))
- Download page: this file is part of the [_2022AA UMLS Metathesaurus Full Subset_](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html); no direct download link is available.
- Description: https://www.ncbi.nlm.nih.gov/books/NBK9685/table/ch03.T.retired_cui_mapping_file_mrcui_rr/
- Filename: `MRCUI.RRF`
4. The _Preferred CUI Names & Semtypes_ file.
- Github Repo: https://github.com/erikyao/UMLS_CUI_Semtype
- How to Generate:
- Source data files:
- The _Retired CUI Mapping_ file, `MRCUI.RRF` (see above).
- The _Concept Names and Sources_ file, `MRCONSO.RRF`.
- Version: `2022AA`
- Download page: https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html
- Description: https://www.ncbi.nlm.nih.gov/books/NBK9685/table/ch03.T.concept_names_and_sources_file_mr/
- The _Semantic Type Mappings_ file, `SemanticTypes_2018AB.txt` (see above).
- Script: [parser.py](https://github.com/erikyao/UMLS_CUI_Semtype/blob/main/parser.py)
- Filename: `UMLS_CUI_Semtype.tsv`, as shown [here](https://github.com/erikyao/UMLS_CUI_Semtype/blob/main/parser.py#L188)
17 changes: 10 additions & 7 deletions manifest.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,14 +1,17 @@
{
"version": "0.1",
"requires" : "pyyaml",
"version": "0.2",
"__metadata__" : {
"license_url" : "https://skr3.nlm.nih.gov/SemMedDB/",
"licence" : "CC BY 4.0",
"url" : "https://skr3.nlm.nih.gov/SemMedDB/"
"license_url" : "https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR.html",
"licence" : "UMLS Metathesaurus License",
"url" : "https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR.html"
},
"dumper" : {
"data_url" : ["https://dl.dropboxusercontent.com/s/im2ru5epalfr9lt/semmed_source.tar.gz",
"https://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt"],
"data_url" : [
"https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/SemRep_SemMedDB_SKR/semmedVER43_2022_R_PREDICATION.csv.gz",
"https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/Docs/SemanticTypes_2018AB.txt",
"http://localhost:8080/dataupload/mysrc/semmeddb/MRCUI.RRF",
"http://localhost:8080/dataupload/mysrc/semmeddb/UMLS_CUI_Semtype.tsv"
],
"uncompress" : true,
"release" : "version:get_release"
},
Expand Down
Loading