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Babel 1.15 #620

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e5cd96e
Added UMLS:C0011847 to MONDO:0005148 type 2 diabetes mellitus.
gaurav Dec 4, 2025
891341e
Updated versions.
gaurav Dec 8, 2025
fc2df24
Fixed disease manual concords.
gaurav Dec 9, 2025
abc0c45
Remove synonyms/Publication.txt once it has been generated.
gaurav Dec 12, 2025
cfa49cf
Added newline to end of file.
gaurav Dec 16, 2025
520c1fa
Merge branch 'master' into babel-1.15
gaurav Dec 18, 2025
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8 changes: 4 additions & 4 deletions config.yaml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
# Build information. Currently unstructured -- you can use this to write down any notes on what is going on with
# this specific build of Babel.
build:
branch: babel-1.14
branch: babel-1.15

# Versions that need to be updated on every release.
biolink_version: "4.3.2"
umls_version: "2025AA"
rxnorm_version: "10062025"
biolink_version: "4.3.6"
umls_version: "2025AB"
rxnorm_version: "12012025"
drugbank_version: "5-1-13"

# Overall inputs and outputs.
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7 changes: 6 additions & 1 deletion input_data/manual_concords/disease.txt
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Expand Up @@ -123,4 +123,9 @@ EFO:1001390 oio:closeMatch UMLS:C2936258
HP:0040412 oio:closeMatch UMLS:C0587044
EFO:1001348 oio:closeMatch UMLS:C1136321
MONDO:0015517 oio:closeMatch DOID:12177
EFO:1001863 oio:closeMatch UMLS:C0042135
EFO:1001863 oio:closeMatch UMLS:C0042135

# Diabetes (UMLS:C0011847) is mapped to ICD10CM:E11, which is specifically
# type 2 diabetes mellitus. So we should combine it with the MONDO term.
UMLS:C0011847 oio:exactMatch MONDO:0005148

2 changes: 1 addition & 1 deletion input_data/manual_concords/drugchemical.tsv
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Expand Up @@ -30,4 +30,4 @@ CHEBI:136034 skos:relatedMatch HMDB:HMDB0254418 "Not sure why these aren’t com
CHEBI:59173 skos:relatedMatch PUBCHEM.COMPOUND:19797045 Conflating all the bivalirudin cliques into a single conflated clique https://github.com/TranslatorSRI/Babel/issues/346
CHEBI:59173 skos:relatedMatch PUBCHEM.COMPOUND:78357798 Conflating all the bivalirudin cliques into a single conflated clique https://github.com/TranslatorSRI/Babel/issues/346
MESH:D013668 skos:exactMatch CHEMBL.COMPOUND:CHEMBL1201522 Appears to be the same concept https://github.com/TranslatorSRI/NodeNormalization/issues/280
UNII:2S9ZZM9Q9V skos:exactMatch UMLS:C0796392 "UNII:2S9ZZM9Q9V includes UMLS:C0796392 as an identifier, but is also generated as its own clique by the protein module." https://github.com/NCATSTranslator/Feedback/issues/970
UNII:2S9ZZM9Q9V skos:exactMatch UMLS:C0796392 "UNII:2S9ZZM9Q9V includes UMLS:C0796392 as an identifier, but is also generated as its own clique by the protein module." https://github.com/NCATSTranslator/Feedback/issues/970
5 changes: 4 additions & 1 deletion src/snakefiles/publications.snakefile
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@@ -1,3 +1,5 @@
import os

import src.createcompendia.publications as publications
import src.assess_compendia as assessments
from src.snakefiles import util
Expand Down Expand Up @@ -65,10 +67,11 @@ rule generate_pubmed_compendia:
publications.generate_compendium(
[input.pmid_doi_concord_file], [input.metadata_yaml], [input.pmid_id_file], input.titles, output.publication_compendium, input.icrdf_filename
)
# generate_compendium() will generate an (empty) Publication.txt.gz file, but we need
# generate_compendium() will generate an (empty) Publication.txt file, but we need
# to compress it.
publication_synonyms = os.path.splitext(output.publication_synonyms_gz)[0]
util.gzip_files([publication_synonyms])
os.remove(publication_synonyms)


rule check_publications_completeness:
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