UMLS/NCImt/NCIt tools

This is a set of tools for working with the UMLS RRF format, NCI Metathesaurus and NCI Thesaurus.

umls-rrf-scala

A very basic library for parsing files in the UMLS RRF format.

This program expects the META directory from the NLM UMLS download to be in the directory where the program is executed. The --rrf-dir command line argument can also be used to point to the META directory in another directory. Output is produced in the SSSOM format.

$ sbt "run --from-source SNOMEDCT_US --to-source NCI -o mappings.tsv"
[info] Loading settings for project global-plugins from metals.sbt ...
[info] Loading global plugins from /Users/gaurav/.sbt/1.0/plugins
[info] Loading settings for project umls-rrf-scala-build from plugins.sbt ...
[info] Loading project definition from /Users/gaurav/Development/umls-rrf-scala/project
[info] Loading settings for project umls-rrf-scala from build.sbt ...
[info] Set current project to umls-rrf (in build file:/Users/gaurav/Development/umls-rrf-scala/)
[info] Compiling 1 Scala source to /Users/gaurav/Development/umls-rrf-scala/target/scala-2.13/classes ...
[info] running (fork) org.renci.umls.CodeMapper --from-source SNOMEDCT_US --to-source NCI -o mappings.txt
[info] 15:32:38.794 [main] INFO  org.renci.umls.CodeMapper$ - Loaded directory for release: # Release Metadata
[info] #Tue Oct 02 03:11:52 EDT 2018
[info] umls.release.date=20180801
[info] umls.release.name=201808
[info] mmsys.build.date=2018_09_17_23_18_10
[info] mmsys.version=MMSYS-2016AA-20160329
[info] nlm.build.date=2018_10_01_14_48_01
[info] umls.release.description=Base Release for 201808
[info] 15:32:38.802 [main] INFO  org.renci.umls.CodeMapper$ - Using SQLite backend: org.apache.commons.dbcp2.DriverManagerConnectionFactory@434a63ab
[info] 15:32:43.298 [main] INFO  org.renci.umls.db.DbConcepts - Concept table MRCONSO_bda810d0c047e368385a441642703331581153cd7fe728fdc256a3e3960f1c40 has 6857637 rows.
[info] 15:32:43.725 [main] INFO  org.renci.umls.db.DbConcepts - Loading halfmaps for SNOMEDCT_US
[info] 15:32:44.930 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 100000 halfmaps.
[info] 15:32:45.664 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 200000 halfmaps.
[info] 15:32:46.638 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 300000 halfmaps.
[info] 15:32:47.398 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 400000 halfmaps.
[info] 15:32:48.055 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 500000 halfmaps.
[info] 15:32:49.106 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 600000 halfmaps.
[info] 15:32:49.803 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 700000 halfmaps.
[info] 15:32:51.134 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 800000 halfmaps.
[info] 15:32:51.602 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 900000 halfmaps.
[info] 15:32:51.742 [main] INFO  org.renci.umls.db.DbConcepts - 914827 halfmaps loaded.
[info] 15:32:51.748 [main] INFO  org.renci.umls.db.DbConcepts - Loading halfmaps for NCI
[info] 15:32:53.637 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 100000 halfmaps.
[info] 15:32:54.506 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 200000 halfmaps.
[info] 15:32:55.204 [main] INFO  org.renci.umls.db.DbConcepts - Loaded 300000 halfmaps.
[info] 15:32:55.473 [main] INFO  org.renci.umls.db.DbConcepts - 343103 halfmaps loaded.
[success] Total time: 26 s, completed Apr 15, 2020, 3:32:58 PM

Filler

Filler takes in a set of mappings in the SSSOM format and attempts to fill in missing mappings based on its command line arguments.

$ JAVA_OPTS="-Xmx16G" sbt "runMain org.renci.sssom.Filler --input-file matched-with-ols-lbo.tsv --output-file matched-with-ols-lbo-hp-chebi.tsv --fill-predicate-id 'skos:narrowMatch' --from-ontology ontologies/hp.owl --from-ontology ontologies/chebi.owl"
[info] Loading settings for project global-plugins from metals.sbt ...
[info] Loading global plugins from /Users/gaurav/.sbt/1.0/plugins
[info] Loading settings for project umls-rrf-scala-build from plugins.sbt ...
[info] Loading project definition from /Users/gaurav/Development/umls-rrf-scala/project
[info] Loading settings for project umls-rrf-scala from build.sbt ...
[info] Set current project to umls-rrf (in build file:/Users/gaurav/Development/umls-rrf-scala/)
[warn] Multiple main classes detected.  Run 'show discoveredMainClasses' to see the list
[info] running (fork) org.renci.sssom.Filler --input-file matched-with-ols-lbo.tsv --output-file matched-with-ols-lbo-hp-chebi.tsv --fill-predicate-id 'skos:narrowMatch' --from-ontology ontologies/hp.owl --from-ontology ontologies/chebi.owl
[error] SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
[error] SLF4J: Defaulting to no-operation (NOP) logger implementation
[error] SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[info] 2020.09.16 21:14:28 [INFO] org.renci.sssom.ontologies.OntologyFiller:24:14 - Loaded ontology ontologies/hp.owl containing 953183 triples.
[info] 2020.09.16 21:15:03 [INFO] org.renci.sssom.ontologies.OntologyFiller:24:14 - Loaded ontology ontologies/chebi.owl containing 4924892 triples.
[info] 2020.09.16 21:15:03 [INFO] org.renci.sssom.Filler:63:14 - Active row fillers: OntologyFiller(ontologies/hp.owl), OntologyFiller(ontologies/chebi.owl)
[info] 2020.09.16 21:15:04 [INFO] org.renci.sssom.Filler.<local Filler>:95:20 - Filled subject ID SNOMEDCT_US:8836009 with ArraySeq(HashMap(predicate_label -> gallocyanin, predicate_id -> http://purl.obolibrary.org/obo/CHEBI_90106, comment -> Ontology ontologies/chebi.owl contains triple asserting http://purl.obolibrary.org/obo/CHEBI_90106 @http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym "Gallocyanine", mapping_set_version -> , subject_label -> Gallocyanine stain (substance)|Gallocyanine|Gallocyanine stain, subject_id -> SNOMEDCT_US:8836009, mapping_set_id -> , object_label -> , match_type -> , object_id -> ))
[info] 2020.09.16 21:15:04 [INFO] org.renci.sssom.Filler.<local Filler>:95:20 - Filled subject ID SNOMEDCT_US:11780008 with ArraySeq(HashMap(predicate_label -> Sirius red 4B, predicate_id -> http://purl.obolibrary.org/obo/CHEBI_88191, comment -> Ontology ontologies/chebi.owl contains triple asserting http://purl.obolibrary.org/obo/CHEBI_88191 @http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym "Chlorantine fast red 5B", mapping_set_version -> , subject_label -> Chlorantine fast red 5B|Durazol red stain|Chlorantine fast red|Durazol red stain (substance)|Durazol red, subject_id -> SNOMEDCT_US:11780008, mapping_set_id -> , object_label -> , match_type -> , object_id -> ))
[info] 2020.09.16 21:15:04 [INFO] org.renci.sssom.Filler.<local Filler>:95:20 - Filled subject ID SNOMEDCT_US:38707008 with ArraySeq(HashMap(predicate_label -> Celestin blue B, predicate_id -> http://purl.obolibrary.org/obo/CHEBI_88183, comment -> Ontology ontologies/chebi.owl contains triple asserting http://purl.obolibrary.org/obo/CHEBI_88183 @http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym "Mordant blue 14", mapping_set_version -> , subject_label -> Coelestine blue|Coelestine blue B stain|Celestine blue B stain (substance)|Celestine blue|Celestine blue B stain|Mordant blue 14, subject_id -> SNOMEDCT_US:38707008, mapping_set_id -> , object_label -> , match_type -> , object_id -> ))
[...]
[info] 2020.09.16 21:15:04 [INFO] org.renci.sssom.Filler.<local Filler>:95:20 - Filled subject ID SNOMEDCT_US:406969006 with ArraySeq(HashMap(predicate_label -> thionine, predicate_id -> http://purl.obolibrary.org/obo/CHEBI_52295, comment -> Ontology ontologies/chebi.owl contains triple asserting http://purl.obolibrary.org/obo/CHEBI_52295 @http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym "Thionin", mapping_set_version -> , subject_label -> Thionin|Thionin stain|Thionin stain (substance), subject_id -> SNOMEDCT_US:406969006, mapping_set_id -> , object_label -> , match_type -> , object_id -> ))
[info] 2020.09.16 21:15:04 [INFO] org.renci.sssom.Filler.<local Filler>:95:20 - Filled subject ID SNOMEDCT_US:406990003 with ArraySeq(HashMap(predicate_label -> methyl blue free acid, predicate_id -> http://purl.obolibrary.org/obo/CHEBI_87477, comment -> Ontology ontologies/chebi.owl contains triple asserting http://purl.obolibrary.org/obo/CHEBI_87477 @http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym "Aniline blue", mapping_set_version -> , subject_label -> Aniline blue stain (substance)|Aniline blue stain|Aniline blue, subject_id -> SNOMEDCT_US:406990003, mapping_set_id -> , object_label -> , match_type -> , object_id -> ))
[info] 2020.09.16 21:15:04 [INFO] org.renci.sssom.Filler:110:14 - Out of 7980 rows:
[info]   - 5546 rows (69.50%) have existing terms.
[info]   - 2426 rows (30.40%) could not be matched.
[info]   - 8 rows (0.10%) could be matched.
[success] Total time: 44 s, completed Sep 16, 2020, 9:15:05 PM