diff --git a/.gitignore b/.gitignore index e8c465f..47d9100 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ downloads/ generated_parquet/ - +*.parquet # project specific downloads/ generated_parquet/ diff --git a/.sqlfluffignore b/.sqlfluffignore new file mode 100644 index 0000000..344ba51 --- /dev/null +++ b/.sqlfluffignore @@ -0,0 +1 @@ +cumulus_library_umls/reference_sql \ No newline at end of file diff --git a/cumulus_library_umls/.DS_Store b/cumulus_library_umls/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/cumulus_library_umls/.DS_Store differ diff --git a/cumulus_library_umls/umls/manifest.toml b/cumulus_library_umls/manifest.toml similarity index 69% rename from cumulus_library_umls/umls/manifest.toml rename to cumulus_library_umls/manifest.toml index ef5a223..e038d2f 100644 --- a/cumulus_library_umls/umls/manifest.toml +++ b/cumulus_library_umls/manifest.toml @@ -2,7 +2,8 @@ study_prefix = "umls" [table_builder_config] file_names = [ - "umls_builder.py" + "umls_builder.py", + "static_builder.py" ] [advanced_options] diff --git a/cumulus_library_umls/reference_sql/static_builder.sql b/cumulus_library_umls/reference_sql/static_builder.sql new file mode 100644 index 0000000..dbe4fce --- /dev/null +++ b/cumulus_library_umls/reference_sql/static_builder.sql @@ -0,0 +1,69 @@ +-- noqa: disable=all +-- This sql was autogenerated as a reference example using the library +-- CLI. Its format is tied to the specific database it was run against, +-- and it may not be correct for all databases. Use the CLI's build +-- option to derive the best SQL for your dataset. + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__semantic_types` ( + abbrev STRING, + TUI STRING, + full_type_name STRING +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/SemanticTypes_2018AB' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__semantic_groups` ( + abbrev STRING, + group_name STRING, + TUI STRING, + full_type_name STRING +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/SemGroups_2018' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__rel_description` ( + REL STRING, + REL_STR STRING +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls_rel' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__rela_description` ( + RELA STRING, + RELA_STR STRING +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls_rela' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__tty_description` ( + TTY STRING, + TTY_STR STRING +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls_tty' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__tui_description` ( + STY STRING, + TUI STRING, + TUI_STR STRING +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls_tui' +tblproperties ("parquet.compression"="SNAPPY"); diff --git a/cumulus_library_umls/reference_sql/umls_builder.sql b/cumulus_library_umls/reference_sql/umls_builder.sql new file mode 100644 index 0000000..3a52586 --- /dev/null +++ b/cumulus_library_umls/reference_sql/umls_builder.sql @@ -0,0 +1,347 @@ +-- noqa: disable=all +-- This sql was autogenerated as a reference example using the library +-- CLI. Its format is tied to the specific database it was run against, +-- and it may not be correct for all databases. Use the CLI's build +-- option to derive the best SQL for your dataset. + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRHIST` ( + CUI String, + SOURCEUI String, + SAB String, + SVER String, + CHANGETYPE String, + CHANGEKEY String, + CHANGEVAL String, + REASON String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRHIST' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRCONSO` ( + CUI String, + LAT String, + TS String, + LUI String, + STT String, + SUI String, + ISPREF String, + AUI String, + SAUI String, + SCUI String, + SDUI String, + SAB String, + TTY String, + CODE String, + STR String, + SRL Integer, + SUPPRESS String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRCONSO' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRSTY` ( + CUI String, + TUI String, + STN String, + STY String, + ATUI String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRSTY' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRFILES` ( + FIL String, + DES String, + FMT String, + CLS Integer, + RWS Integer, + BTS Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRFILES' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRCOLS` ( + COL String, + DES String, + REF String, + MIN Integer, + AV Float, + MAX Integer, + FIL String, + DTY String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRCOLS' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRDOC` ( + DOCKEY String, + VALUE String, + TYPE String, + EXPL String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRDOC' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRREL` ( + CUI1 String, + AUI1 String, + STYPE1 String, + REL String, + CUI2 String, + AUI2 String, + STYPE2 String, + RELA String, + RUI String, + SRUI String, + SAB String, + SL String, + RG String, + DIR String, + SUPPRESS String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRREL' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRSAT` ( + CUI String, + LUI String, + SUI String, + METAUI String, + STYPE String, + CODE String, + ATUI String, + SATUI String, + ATN String, + SAB String, + ATV String, + SUPPRESS String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRSAT' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRRANK` ( + RANK Integer, + SAB String, + TTY String, + SUPPRESS String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRRANK' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRSAB` ( + VCUI String, + RCUI String, + VSAB String, + RSAB String, + SON String, + SF String, + SVER String, + VSTART String, + VEND String, + IMETA String, + RMETA String, + SLC String, + SCC String, + SRL Integer, + TFR Integer, + CFR Integer, + CXTY String, + TTYL String, + ATNL String, + LAT String, + CENC String, + CURVER String, + SABIN String, + SSN String, + SCIT String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRSAB' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRAUI` ( + AUI1 String, + CUI1 String, + VER String, + REL String, + RELA String, + MAPREASON String, + AUI2 String, + CUI2 String, + MAPIN String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRAUI' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRSMAP` ( + MAPSETCUI String, + MAPSETSAB String, + MAPID String, + MAPSID String, + FROMEXPR String, + FROMTYPE String, + REL String, + RELA String, + TOEXPR String, + TOTYPE String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRSMAP' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__AMBIGLUI` ( + LUI String, + CUI String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/AMBIGLUI' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRHIER` ( + CUI String, + AUI String, + CXN Integer, + PAUI String, + SAB String, + RELA String, + PTR String, + HCD String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRHIER' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRCUI` ( + CUI1 String, + VER String, + REL String, + RELA String, + MAPREASON String, + CUI2 String, + MAPIN String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRCUI' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRMAP` ( + MAPSETCUI String, + MAPSETSAB String, + MAPSUBSETID String, + MAPRANK Integer, + MAPID String, + MAPSID String, + FROMID String, + FROMSID String, + FROMEXPR String, + FROMTYPE String, + FROMRULE String, + FROMRES String, + REL String, + RELA String, + TOID String, + TOSID String, + TOEXPR String, + TOTYPE String, + TORULE String, + TORES String, + MAPRULE String, + MAPRES String, + MAPTYPE String, + MAPATN String, + MAPATV String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRMAP' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__MRDEF` ( + CUI String, + AUI String, + ATUI String, + SATUI String, + SAB String, + DEF String, + SUPPRESS String, + CVF Integer +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/MRDEF' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE EXTERNAL TABLE IF NOT EXISTS `umls`.`umls__AMBIGSUI` ( + SUI String, + CUI String +) +STORED AS PARQUET +LOCATION 's3://bucket/db_path/umls/AMBIGSUI' +tblproperties ("parquet.compression"="SNAPPY"); + +-- ########################################################### + +CREATE TABLE umls__mrrel_is_a AS +SELECT * FROM umls.mrrel +WHERE (REL = 'CHD' +OR RELA IN ('isa','tradename_of','has_tradename','has_basis_of_strength_substance')) +AND REL NOT IN ('RB', 'PAR') + +-- ########################################################### + +CREATE TABLE umls__mrconso_drugs AS +SELECT * FROM umls.mrconso +WHERE SAB IN ('ATC','CVX','DRUGBANK','GS','MED-RT','MMSL','MMX','MTHCMSFRF','MTHSPL', + 'NDDF','RXNORM','SNOMEDCT_US','USP','VANDF') diff --git a/cumulus_library_umls/static_builder.py b/cumulus_library_umls/static_builder.py new file mode 100644 index 0000000..c0f2207 --- /dev/null +++ b/cumulus_library_umls/static_builder.py @@ -0,0 +1,160 @@ +"""Builder for UMLS files that generally do not change over time""" +import dataclasses +import pathlib + +import pandas +from cumulus_library import base_table_builder, base_utils, study_manifest +from cumulus_library.template_sql import base_templates + + +@dataclasses.dataclass(kw_only=True) +class StaticTableConfig: + """Convenience class for holding params for configuring tables from flat files""" + + file_path: str + delimiter: str + table_name: str + headers: list[str] + dtypes: dict + parquet_types: list[str] + ignore_header: bool = False + + +class StaticBuilder(base_table_builder.BaseTableBuilder): + base_path = pathlib.Path(__file__).resolve().parent + display_text = "Building static UMLS tables..." + + def get_table_configs(self): + return [ + # https://lhncbc.nlm.nih.gov/ii/tools/MetaMap/documentation/SemanticTypesAndGroups.html + StaticTableConfig( + file_path=self.base_path / "./static_files/SemanticTypes_2018AB.txt", + delimiter="|", + table_name="semantic_types", + headers=["abbrev", "TUI", "full_type_name"], + dtypes={ + "type_abbrev": "str", + "TUI": "str", + "full_type_name": "str", + }, + parquet_types=["STRING", "STRING", "STRING"], + ), + StaticTableConfig( + file_path=self.base_path / "./static_files/SemGroups_2018.txt", + delimiter="|", + table_name="semantic_groups", + headers=["abbrev", "group_name", "TUI", "full_type_name"], + dtypes={ + "group_abbrev": "str", + "group_name": "str", + "TUI": "str", + "full_type_name": "str", + }, + parquet_types=["STRING", "STRING", "STRING", "STRING"], + ), + # https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html + StaticTableConfig( + file_path=self.base_path / "./static_files/umls_rel.tsv", + delimiter="\t", + table_name="rel_description", + headers=["REL", "REL_STR"], + dtypes={ + "REL": "str", + "REL_STR": "str", + }, + parquet_types=["STRING", "STRING"], + ignore_header=True, + ), + StaticTableConfig( + file_path=self.base_path / "./static_files/umls_rela.tsv", + delimiter="\t", + table_name="rela_description", + headers=["RELA", "RELA_STR"], + dtypes={ + "RELA": "str", + "RELA_STR": "str", + }, + parquet_types=["STRING", "STRING"], + ignore_header=True, + ), + StaticTableConfig( + file_path=self.base_path / "./static_files/umls_tty.tsv", + delimiter="\t", + table_name="tty_description", + headers=["TTY", "TTY_STR"], + dtypes={ + "TTY": "str", + "TTY_STR": "str", + }, + parquet_types=["STRING", "STRING"], + ignore_header=True, + ), + StaticTableConfig( + file_path=self.base_path / "./static_files/umls_tui.tsv", + delimiter="\t", + table_name="tui_description", + headers=["STY", "TUI", "TUI_STR"], + dtypes={ + "STY": "str", + "TUI": "str", + "TUI_STR": "str", + }, + parquet_types=["STRING", "STRING", "STRING"], + ignore_header=True, + ), + ] + + def prepare_queries( + self, + config: base_utils.StudyConfig, + manifest: study_manifest.StudyManifest, + *args, + **kwargs, + ): + # fetch and add vsac tables + self.tables = self.get_table_configs() + with base_utils.get_progress_bar() as progress: + task = progress.add_task( + "Uploading UMLS dictionary files...", total=len(self.tables) + ) + + for table in self.tables: + # Determine what we're using as a source file + path = self.base_path / table.file_path + parquet_path = ( + table.file_path.parent + / table.file_path.stem + / f"{table.file_path.stem}.parquet" + ) + parquet_path.parent.mkdir(parents=True, exist_ok=True) + # Read the file, using lots of the TableConfig params, and generate + # a parquet file + df = pandas.read_csv( + path, + delimiter=table.delimiter, + names=table.headers, + header=0 if table.ignore_header else None, + dtype=table.dtypes, + index_col=False, + na_values=["\\N"], + ) + df.to_parquet(parquet_path) + # Upload to S3 and create a table that reads from it + prefix = manifest.get_study_prefix() + remote_path = config.db.upload_file( + file=parquet_path, + study=prefix, + topic=parquet_path.stem, + force_upload=config.force_upload, + ) + self.queries.append( + base_templates.get_ctas_from_parquet_query( + schema_name=config.schema, + table_name=f"{prefix}__{table.table_name}", + local_location=parquet_path.parent, + remote_location=remote_path, + table_cols=table.headers, + remote_table_cols_types=table.parquet_types, + ) + ) + progress.advance(task) diff --git a/cumulus_library_umls/static_files/.DS_Store b/cumulus_library_umls/static_files/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/cumulus_library_umls/static_files/.DS_Store differ diff --git a/cumulus_library_umls/static_files/SemGroups_2018.txt b/cumulus_library_umls/static_files/SemGroups_2018.txt new file mode 100644 index 0000000..bfb61e6 --- /dev/null +++ b/cumulus_library_umls/static_files/SemGroups_2018.txt @@ -0,0 +1,127 @@ +ACTI|Activities & Behaviors|T052|Activity +ACTI|Activities & Behaviors|T053|Behavior +ACTI|Activities & Behaviors|T056|Daily or Recreational Activity +ACTI|Activities & Behaviors|T051|Event +ACTI|Activities & Behaviors|T064|Governmental or Regulatory Activity +ACTI|Activities & Behaviors|T055|Individual Behavior +ACTI|Activities & Behaviors|T066|Machine Activity +ACTI|Activities & Behaviors|T057|Occupational Activity +ACTI|Activities & Behaviors|T054|Social Behavior +ANAT|Anatomy|T017|Anatomical Structure +ANAT|Anatomy|T029|Body Location or Region +ANAT|Anatomy|T023|Body Part, Organ, or Organ Component +ANAT|Anatomy|T030|Body Space or Junction +ANAT|Anatomy|T031|Body Substance +ANAT|Anatomy|T022|Body System +ANAT|Anatomy|T025|Cell +ANAT|Anatomy|T026|Cell Component +ANAT|Anatomy|T018|Embryonic Structure +ANAT|Anatomy|T021|Fully Formed Anatomical Structure +ANAT|Anatomy|T024|Tissue +CHEM|Chemicals & Drugs|T116|Amino Acid, Peptide, or Protein +CHEM|Chemicals & Drugs|T195|Antibiotic +CHEM|Chemicals & Drugs|T123|Biologically Active Substance +CHEM|Chemicals & Drugs|T122|Biomedical or Dental Material +CHEM|Chemicals & Drugs|T103|Chemical +CHEM|Chemicals & Drugs|T120|Chemical Viewed Functionally +CHEM|Chemicals & Drugs|T104|Chemical Viewed Structurally +CHEM|Chemicals & Drugs|T200|Clinical Drug +CHEM|Chemicals & Drugs|T196|Element, Ion, or Isotope +CHEM|Chemicals & Drugs|T126|Enzyme +CHEM|Chemicals & Drugs|T131|Hazardous or Poisonous Substance +CHEM|Chemicals & Drugs|T125|Hormone +CHEM|Chemicals & Drugs|T129|Immunologic Factor +CHEM|Chemicals & Drugs|T130|Indicator, Reagent, or Diagnostic Aid +CHEM|Chemicals & Drugs|T197|Inorganic Chemical +CHEM|Chemicals & Drugs|T114|Nucleic Acid, Nucleoside, or Nucleotide +CHEM|Chemicals & Drugs|T109|Organic Chemical +CHEM|Chemicals & Drugs|T121|Pharmacologic Substance +CHEM|Chemicals & Drugs|T192|Receptor +CHEM|Chemicals & Drugs|T127|Vitamin +CONC|Concepts & Ideas|T185|Classification +CONC|Concepts & Ideas|T077|Conceptual Entity +CONC|Concepts & Ideas|T169|Functional Concept +CONC|Concepts & Ideas|T102|Group Attribute +CONC|Concepts & Ideas|T078|Idea or Concept +CONC|Concepts & Ideas|T170|Intellectual Product +CONC|Concepts & Ideas|T171|Language +CONC|Concepts & Ideas|T080|Qualitative Concept +CONC|Concepts & Ideas|T081|Quantitative Concept +CONC|Concepts & Ideas|T089|Regulation or Law +CONC|Concepts & Ideas|T082|Spatial Concept +CONC|Concepts & Ideas|T079|Temporal Concept +DEVI|Devices|T203|Drug Delivery Device +DEVI|Devices|T074|Medical Device +DEVI|Devices|T075|Research Device +DISO|Disorders|T020|Acquired Abnormality +DISO|Disorders|T190|Anatomical Abnormality +DISO|Disorders|T049|Cell or Molecular Dysfunction +DISO|Disorders|T019|Congenital Abnormality +DISO|Disorders|T047|Disease or Syndrome +DISO|Disorders|T050|Experimental Model of Disease +DISO|Disorders|T033|Finding +DISO|Disorders|T037|Injury or Poisoning +DISO|Disorders|T048|Mental or Behavioral Dysfunction +DISO|Disorders|T191|Neoplastic Process +DISO|Disorders|T046|Pathologic Function +DISO|Disorders|T184|Sign or Symptom +GENE|Genes & Molecular Sequences|T087|Amino Acid Sequence +GENE|Genes & Molecular Sequences|T088|Carbohydrate Sequence +GENE|Genes & Molecular Sequences|T028|Gene or Genome +GENE|Genes & Molecular Sequences|T085|Molecular Sequence +GENE|Genes & Molecular Sequences|T086|Nucleotide Sequence +GEOG|Geographic Areas|T083|Geographic Area +LIVB|Living Beings|T100|Age Group +LIVB|Living Beings|T011|Amphibian +LIVB|Living Beings|T008|Animal +LIVB|Living Beings|T194|Archaeon +LIVB|Living Beings|T007|Bacterium +LIVB|Living Beings|T012|Bird +LIVB|Living Beings|T204|Eukaryote +LIVB|Living Beings|T099|Family Group +LIVB|Living Beings|T013|Fish +LIVB|Living Beings|T004|Fungus +LIVB|Living Beings|T096|Group +LIVB|Living Beings|T016|Human +LIVB|Living Beings|T015|Mammal +LIVB|Living Beings|T001|Organism +LIVB|Living Beings|T101|Patient or Disabled Group +LIVB|Living Beings|T002|Plant +LIVB|Living Beings|T098|Population Group +LIVB|Living Beings|T097|Professional or Occupational Group +LIVB|Living Beings|T014|Reptile +LIVB|Living Beings|T010|Vertebrate +LIVB|Living Beings|T005|Virus +OBJC|Objects|T071|Entity +OBJC|Objects|T168|Food +OBJC|Objects|T073|Manufactured Object +OBJC|Objects|T072|Physical Object +OBJC|Objects|T167|Substance +OCCU|Occupations|T091|Biomedical Occupation or Discipline +OCCU|Occupations|T090|Occupation or Discipline +ORGA|Organizations|T093|Health Care Related Organization +ORGA|Organizations|T092|Organization +ORGA|Organizations|T094|Professional Society +ORGA|Organizations|T095|Self-help or Relief Organization +PHEN|Phenomena|T038|Biologic Function +PHEN|Phenomena|T069|Environmental Effect of Humans +PHEN|Phenomena|T068|Human-caused Phenomenon or Process +PHEN|Phenomena|T034|Laboratory or Test Result +PHEN|Phenomena|T070|Natural Phenomenon or Process +PHEN|Phenomena|T067|Phenomenon or Process +PHYS|Physiology|T043|Cell Function +PHYS|Physiology|T201|Clinical Attribute +PHYS|Physiology|T045|Genetic Function +PHYS|Physiology|T041|Mental Process +PHYS|Physiology|T044|Molecular Function +PHYS|Physiology|T032|Organism Attribute +PHYS|Physiology|T040|Organism Function +PHYS|Physiology|T042|Organ or Tissue Function +PHYS|Physiology|T039|Physiologic Function +PROC|Procedures|T060|Diagnostic Procedure +PROC|Procedures|T065|Educational Activity +PROC|Procedures|T058|Health Care Activity +PROC|Procedures|T059|Laboratory Procedure +PROC|Procedures|T063|Molecular Biology Research Technique +PROC|Procedures|T062|Research Activity +PROC|Procedures|T061|Therapeutic or Preventive Procedure diff --git a/cumulus_library_umls/static_files/SemanticTypes_2018AB.txt b/cumulus_library_umls/static_files/SemanticTypes_2018AB.txt new file mode 100644 index 0000000..d5d309e --- /dev/null +++ b/cumulus_library_umls/static_files/SemanticTypes_2018AB.txt @@ -0,0 +1,127 @@ +aapp|T116|Amino Acid, Peptide, or Protein +acab|T020|Acquired Abnormality +acty|T052|Activity +aggp|T100|Age Group +amas|T087|Amino Acid Sequence +amph|T011|Amphibian +anab|T190|Anatomical Abnormality +anim|T008|Animal +anst|T017|Anatomical Structure +antb|T195|Antibiotic +arch|T194|Archaeon +bacs|T123|Biologically Active Substance +bact|T007|Bacterium +bdsu|T031|Body Substance +bdsy|T022|Body System +bhvr|T053|Behavior +biof|T038|Biologic Function +bird|T012|Bird +blor|T029|Body Location or Region +bmod|T091|Biomedical Occupation or Discipline +bodm|T122|Biomedical or Dental Material +bpoc|T023|Body Part, Organ, or Organ Component +bsoj|T030|Body Space or Junction +celc|T026|Cell Component +celf|T043|Cell Function +cell|T025|Cell +cgab|T019|Congenital Abnormality +chem|T103|Chemical +chvf|T120|Chemical Viewed Functionally +chvs|T104|Chemical Viewed Structurally +clas|T185|Classification +clna|T201|Clinical Attribute +clnd|T200|Clinical Drug +cnce|T077|Conceptual Entity +comd|T049|Cell or Molecular Dysfunction +crbs|T088|Carbohydrate Sequence +diap|T060|Diagnostic Procedure +dora|T056|Daily or Recreational Activity +drdd|T203|Drug Delivery Device +dsyn|T047|Disease or Syndrome +edac|T065|Educational Activity +eehu|T069|Environmental Effect of Humans +elii|T196|Element, Ion, or Isotope +emod|T050|Experimental Model of Disease +emst|T018|Embryonic Structure +enty|T071|Entity +enzy|T126|Enzyme +euka|T204|Eukaryote +evnt|T051|Event +famg|T099|Family Group +ffas|T021|Fully Formed Anatomical Structure +fish|T013|Fish +fndg|T033|Finding +fngs|T004|Fungus +food|T168|Food +ftcn|T169|Functional Concept +genf|T045|Genetic Function +geoa|T083|Geographic Area +gngm|T028|Gene or Genome +gora|T064|Governmental or Regulatory Activity +grpa|T102|Group Attribute +grup|T096|Group +hcpp|T068|Human-caused Phenomenon or Process +hcro|T093|Health Care Related Organization +hlca|T058|Health Care Activity +hops|T131|Hazardous or Poisonous Substance +horm|T125|Hormone +humn|T016|Human +idcn|T078|Idea or Concept +imft|T129|Immunologic Factor +inbe|T055|Individual Behavior +inch|T197|Inorganic Chemical +inpo|T037|Injury or Poisoning +inpr|T170|Intellectual Product +irda|T130|Indicator, Reagent, or Diagnostic Aid +lang|T171|Language +lbpr|T059|Laboratory Procedure +lbtr|T034|Laboratory or Test Result +mamm|T015|Mammal +mbrt|T063|Molecular Biology Research Technique +mcha|T066|Machine Activity +medd|T074|Medical Device +menp|T041|Mental Process +mnob|T073|Manufactured Object +mobd|T048|Mental or Behavioral Dysfunction +moft|T044|Molecular Function +mosq|T085|Molecular Sequence +neop|T191|Neoplastic Process +nnon|T114|Nucleic Acid, Nucleoside, or Nucleotide +npop|T070|Natural Phenomenon or Process +nusq|T086|Nucleotide Sequence +ocac|T057|Occupational Activity +ocdi|T090|Occupation or Discipline +orch|T109|Organic Chemical +orga|T032|Organism Attribute +orgf|T040|Organism Function +orgm|T001|Organism +orgt|T092|Organization +ortf|T042|Organ or Tissue Function +patf|T046|Pathologic Function +phob|T072|Physical Object +phpr|T067|Phenomenon or Process +phsf|T039|Physiologic Function +phsu|T121|Pharmacologic Substance +plnt|T002|Plant +podg|T101|Patient or Disabled Group +popg|T098|Population Group +prog|T097|Professional or Occupational Group +pros|T094|Professional Society +qlco|T080|Qualitative Concept +qnco|T081|Quantitative Concept +rcpt|T192|Receptor +rept|T014|Reptile +resa|T062|Research Activity +resd|T075|Research Device +rnlw|T089|Regulation or Law +sbst|T167|Substance +shro|T095|Self-help or Relief Organization +socb|T054|Social Behavior +sosy|T184|Sign or Symptom +spco|T082|Spatial Concept +tisu|T024|Tissue +tmco|T079|Temporal Concept +topp|T061|Therapeutic or Preventive Procedure +virs|T005|Virus +vita|T127|Vitamin +vtbt|T010|Vertebrate diff --git a/cumulus_library_umls/static_files/umls_rel.tsv b/cumulus_library_umls/static_files/umls_rel.tsv new file mode 100644 index 0000000..de81f12 --- /dev/null +++ b/cumulus_library_umls/static_files/umls_rel.tsv @@ -0,0 +1,14 @@ +#REL (Relationship) REL Description +AQ Allowed qualifier +CHD has child relationship in a UMLS Metathesaurus +DEL Deleted concept +PAR has parent relationship in a UMLS Metathesaurus +QB can be qualified by. +RB has a broader relationship +RL similar or alike or synonymous or self-referential CUI1 = CUI2 +RN has a narrower relationship +RO has relationship other than synonymous, narrower, or broader +RQ related and possibly synonymous +RU Related, unspecified +SY source asserted synonymy. +XR Not related, no mapping diff --git a/cumulus_library_umls/static_files/umls_rela.tsv b/cumulus_library_umls/static_files/umls_rela.tsv new file mode 100644 index 0000000..e38de61 --- /dev/null +++ b/cumulus_library_umls/static_files/umls_rela.tsv @@ -0,0 +1,1024 @@ +#RELA (Relationship Attribute) RELA Description +abnormal_cell_affected_by_chemical_or_drug abnormal cell affected by chemical or drug +abnormality_associated_with_allele abnormality associated with allele +absorbability_of Absorbability of +access_device_used_by Access device used by +access_instrument_of Access instrument of +access_of Access of +acted_on_by_process Acted on by process +active_ingredient_of Active ingredient of +active_metabolites_of Active metabolites of +active_moiety_of Active Moiety of +activity_of_allele activity of allele +actual_outcome_of Actual outcome of +add_on_code_for Add on code for (Report with) +adheres_to Adheres to +adjacent_to Adjacent to +adjectival_form_of Adjectival form of +adjustment_of Adjustment of +afferent_to Afferent to +after After +alias_of Alias_of +allele_absent_from_wild-type_chromosomal_location allele absent from wild-type chromosomal location +allele_has_abnormality allele has abnormality +allele_has_activity allele has activity +allele_in_chromosomal_location allele in chromosomal location +allele_plays_altered_role_in_process allele plays altered role in process +allele_plays_role_in_metabolism_of_chemical_or_drug allele plays role in metabolism of chemical or drug +allelic_variant_of Allelic Variant of +alternative_of Alternative of +analyzed_by Analyzed by +analyzes Analyzes +anatomic_structure_has_location anatomic structure has location +anatomic_structure_is_physical_part_of anatomic structure is physical part of +anatomical_entity_observed_in anatomical entity observed in +anatomy_originated_from_biological_process anatomy originated from biological process +answer_to_is_sterile Answer to is sterile +answer_to answer to +anterior_to anterior to +anteroinferior_to anteroinferior to +anterolateral_to anterolateral to +anteromedial_to anteromedial to +anterosuperior_to anterosuperior to +approach_of_excluded Approach of excluded +approach_of_possibly_included Approach of possibly included +approach_of Approach of +archetype_of Archetype of +arterial_supply_of Arterial supply of +articulates_with Articulates with +associated_condition_of Associated condition of +associated_disease Associated disease +associated_etiologic_finding_of Associated etiologic finding of +associated_finding_of_excluded Associated finding of excluded +associated_finding_of_possibly_included Associated finding of possibly included +associated_finding_of Associated finding of +associated_function_of Associated function of +associated_genetic_condition Associated genetic condition +associated_morphology_of Associated morphology of +associated_observation_of Associated observation of +associated_procedure_of_excluded Associated procedure of excluded +associated_procedure_of_possibly_included Associated procedure of possibly included +associated_procedure_of Associated procedure of +associated_with_malfunction_of_gene_product associated with malfunction of gene product +associated_with Associated with +attaches_to Attaches to +away_from Away from +basic_dose_form_of Basic dose form of +basis_of_strength_substance_of Basis of strength substance of +before Before +biological_process_has_associated_location biological process has associated location +biological_process_has_initiator_chemical_or_drug biological process has initiator chemical or drug +biological_process_has_initiator_process biological process has initiator process +biological_process_has_result_anatomy biological process has result anatomy +biological_process_has_result_biological_process biological process has result biological process +biological_process_has_result_chemical_or_drug biological process has result chemical or drug +biological_process_involves_chemical_or_drug biological process involves chemical or drug +biological_process_involves_gene_product biological process involves gene product +biological_process_is_part_of_process biological process is part of process +biological_process_results_from_biological_process biological process results from biological process +biomarker_type_includes_gene_product biomarker type includes gene product +biomarker_type_includes_gene biomarker type includes gene +boss_of Basis of strength substance of +bounded_by Bounded by +bounds Bounds +branch_of Branch of +british_form_of British form of +causative_agent_of Causative agent of +cause_of Cause of +cell_type_is_associated_with_eo_disease cell type is associated with eo disease +cell_type_or_tissue_affected_by_chemical_or_drug cell type or tissue affected by chemical or drug +challenge_of Challenge of +characterized_by Characterized by +characterizes Characterizes +chemical_or_drug_affects_abnormal_cell chemical or drug affects abnormal cell +chemical_or_drug_affects_cell_type_or_tissue chemical or drug affects cell type or tissue +chemical_or_drug_affects_gene_product chemical or drug affects gene product +chemical_or_drug_has_mechanism_of_action chemical or drug has mechanism of action +chemical_or_drug_has_physiologic_effect chemical or drug has physiologic effect +chemical_or_drug_initiates_biological_process chemical or drug initiates biological process +chemical_or_drug_is_metabolized_by_enzyme chemical or drug is metabolized by enzyme +chemical_or_drug_is_product_of_biological_process chemical or drug is product of biological process +chemical_or_drug_metabolism_is_associated_with_allele chemical or drug metabolism is associated with allele +chemical_or_drug_plays_role_in_biological_process chemical or drug plays role in biological process +chemotherapy_regimen_has_component chemotherapy regimen has component +chromosomal_location_of_allele chromosomal location of allele +chromosomal_location_of_wild-type_gene chromosomal location of wild-type gene +chromosome_involved_in_cytogenetic_abnormality chromosome involved in cytogenetic abnormality +chromosome_mapped_to_disease chromosome mapped to disease +class_code_classified_by Class code classified by +class_of Class of +classified_as Classified as +classifies_class_code Classifies class code +classifies Classifies +clinical_course_of Clinical course of +clinically_associated_with Clinically associated with +clinically_similar Clinically similar +clinician_form_of Clinician form of +co-occurs_with Co-ocurrs with +coating_material_of Coating material of +common_name_of common name of +completely_excised_anatomy_has_procedure completely excised anatomy has procedure +completely_excised_anatomy_may_have_procedure Completely excised anatomy may have procedure +complex_has_physical_part complex has physical part +component_of_excluded Component of excluded +component_of_possibly_included Component of possibly included +component_of Component of +compositional_material_of Compositional material of +concentration_strength_denominator_unit_of Concentration strength denominator unit of +concentration_strength_denominator_value_of Concentration strength denominator value of +concentration_strength_numerator_unit_of Concentration strength numerator unit of +concentration_strength_numerator_value_of Concentration strength numerator value of +concept_in_subset concept in subset +conceptual_part_of Conceptual part of +connected_to connected to +connection_type_of connection type of +consider_from Consider from +consider Consider +consists_of Consists of +constitutes Constitutes +constitutional_part_of Constitutional part of +consumer_friendly_form_of Consumer friendly form of +contained_in Contained in +contains Contains +context_binding_of Context binding of +continuation_branch_of Continuation branch of +continuous_distally_with continuous distally with +continuous_proximally_with continuous proximally with +continuous_with Continuous with +contraindicated_class_of Contraindicated class of +contraindicated_mechanism_of_action_of Contraindicated mechanism of action of +contraindicated_physiologic_effect_of Contraindicated physiologic effect of +contraindicated_with_disease Contraindicated with disease +corresponds_to corresponds to +count_of_active_ingredient_of Count of active ingredient of +count_of_base_of_active_ingredient_of Count of base of active ingredient of +count_of count_of +course_of Course of +ctcae_5_parent_of ctcae_5 parent of +cytogenetic_abnormality_involves_chromosome cytogenetic abnormality involves chromosome +data_element_of data element of +ddx dxx +default_inpatient_classification_of Default inpatient classification of +default_mapped_from Default mapped from +default_mapped_to Default mapped to +default_outpatient_classification_of Default outpatient classification of +defining_characteristic_of Defining characteristic of +definitional_manifestation_of Definitional manifestation of +degree_of Degree of +dependent_of Dependent of +derives_from derives from +derives derives +development_type_of development type of +developmental_stage_of developmental stage of +develops_from Develops from +develops_into develops into +device_characteristic_of Device characteristic of +device_intended_site_of Device intended site of +device_used_by Device used by +diagnosed_by Diagnosed by +diagnoses Diagnoses +diagnostic_criteria_of DSM-5 diagnostic criteria for ICD code +direct_cell_shape_of direct cell shape of +direct_device_of Direct device of +direct_left_of direct left of +direct_morphology_of Direct morphology of +direct_procedure_site_of Direct procedure site of +direct_right_of direct right of +direct_site_of Direct site of +direct_substance_of Direct substance of +disease_excludes_abnormal_cell disease excludes abnormal cell +disease_excludes_cytogenetic_abnormality disease excludes cytogenetic abnormality +disease_excludes_finding disease excludes finding +disease_excludes_metastatic_anatomic_site disease excludes metastatic anatomic site +disease_excludes_molecular_abnormality disease excludes molecular abnormality +disease_excludes_normal_cell_origin disease excludes normal cell origin +disease_excludes_normal_tissue_origin disease excludes normal tissue origin +disease_excludes_primary_anatomic_site disease excludes primary anatomic site +disease_has_abnormal_cell disease has abnormal cell +disease_has_accepted_treatment_with_regimen Disease Has Accepted Treatment With Regimen +disease_has_associated_anatomic_site disease has associated anatomic site +disease_has_associated_disease disease has associated disease +disease_has_associated_gene disease has associated gene +disease_has_cytogenetic_abnormality disease has cytogenetic abnormality +disease_has_finding disease has finding +disease_has_metastatic_anatomic_site disease has metastatic anatomic site +disease_has_molecular_abnormality disease has molecular abnormality +disease_has_normal_cell_origin disease has normal cell origin +disease_has_normal_tissue_origin disease has normal tissue origin +disease_has_primary_anatomic_site disease has primary anatomic site +disease_is_grade disease is grade +disease_is_marked_by_gene disease is marked by gene +disease_is_stage disease is stage +disease_mapped_to_chromosome disease mapped to chromosome +disease_mapped_to_gene Disease mapped to gene +disease_may_have_abnormal_cell disease may have abnormal cell +disease_may_have_associated_disease disease may have associated disease +disease_may_have_cytogenetic_abnormality disease may have cytogenetic abnormality +disease_may_have_finding disease may have finding +disease_may_have_molecular_abnormality disease may have molecular abnormality +disease_may_have_normal_cell_origin disease may have normal cell origin +disease_may_have_normal_tissue_origin disease may have normal tissue origin +disposition_of Disposition of +distal_to distal to +divisor_of Divisor of +do_not_code_with Do not code with (excludes) +dose_form_administration_method_of Dose form administration method of +dose_form_intended_site_of Dose form intended site of +dose_form_of Dose form of +dose_form_release_characteristic_of Dose form release characteristic of +dose_form_transformation_of Dose form transformation of +doseformgroup_of Dose form group of +drains_into drains into +due_to Due to +during During +effect_may_be_inhibited_by Effect may be inhibited by +efferent_to Efferent to +endogenous_product_related_to Endogenous Product Related To +ends_during Ends during +energy_used_by Energy used by +entire_anatomy_structure_of Entire anatomy structure of +entry_combination_of Entry Combination of +entry_term_of Entry term of +entry_version_of Entry version of +enzyme_metabolizes_chemical_or_drug enzyme metabolizes chemical or drug +eo_anatomy_is_associated_with_eo_disease eo anatomy is associated with eo disease +eo_disease_has_associated_cell_type eo disease has associated cell type +eo_disease_has_associated_eo_anatomy eo disease has associated eo anatomy +eo_disease_has_property_or_attribute eo disease has property or attribute +eo_disease_maps_to_human_disease eo disease maps to human disease +episodicity_of Episodicity of +evaluation_of Evaluation of +excised_anatomy_has_procedure excised anatomy has procedure +excised_anatomy_may_have_procedure excised anatomy may have procedure +exhibited_by Exhibited by +exhibits Exhibits +expanded_form_of Expanded form of +expected_outcome_of Expected outcome of +extended_to_by_process Extended to by process +extent_of Extent of +external_to external to +filling_of Filling of +finding_context_of Finding context of +finding_informer_of Finding informer of +finding_method_of Finding method of +finding_site_of Finding site of +focus_of Focus of +form_of Form of +formed_by formed by +forms forms +full_grown_phenotype_of full grown phenotype of +fuses_with fuses with +fusion_of fusion of +gene_associated_with_disease gene associated with disease +gene_encodes_gene_product gene encodes gene product +gene_found_in_organism gene found in organism +gene_has_abnormality gene has abnormality +gene_has_physical_location gene has physical location +gene_in_chromosomal_location gene in chromosomal location +gene_involved_in_molecular_abnormality gene involved in molecular abnormality +gene_involved_in_pathogenesis_of_disease gene involved in pathogenesis of disease +gene_is_biomarker_of gene is biomarker of +gene_is_biomarker_type gene is biomarker type +gene_is_element_in_pathway gene is element in pathway +gene_mapped_to_disease gene mapped to disease +gene_mutant_encodes_gene_product_sequence_variation gene mutant encodes gene product sequence variation +gene_plays_role_in_process gene plays role in process +gene_product_affected_by_chemical_or_drug gene product affected by chemical or drug +gene_product_encoded_by_gene gene product encoded by gene +gene_product_expressed_in_tissue gene product expressed in tissue +gene_product_has_abnormality gene product has abnormality +gene_product_has_associated_anatomy gene product has associated anatomy +gene_product_has_biochemical_function gene product has biochemical function +gene_product_has_chemical_classification gene product has chemical classification +gene_product_has_gene_product_variant gene product has gene product variant +gene_product_has_organism_source gene product has organism source +gene_product_has_structural_domain_or_motif gene product has structural domain or motif +gene_product_is_biomarker_of gene product is biomarker of +gene_product_is_biomarker_type gene product is biomarker type +gene_product_is_element_in_pathway gene product is element in pathway +gene_product_is_physical_part_of gene product is physical part of +gene_product_malfunction_associated_with_disease gene product malfunction associated with disease +gene_product_plays_role_in_biological_process gene product plays role in biological process +gene_product_sequence_variation_encoded_by_gene_mutant gene product sequence variation encoded by gene mutant +gene_product_variant_of_gene_product gene product variant of gene product +genetic_biomarker_related_to genetic biomarker related to +germ_origin_of Germ origin of +grade_of grade of +happens_during Happens during +has_absorbability Has absorbability +has_acc-aha_sars2_authorized_value has ACC-AHA SARS2 authorized value +has_access_instrument Has access instrument +has_access Has access +has_action_guidance Has action guidance +has_active_ingredient Has active ingredient +has_active_metabolites Has active metabolites +has_active_moiety Has Active Moiety +has_actual_outcome Has actual outcome +has_add_on_code Has add on code (Report with) +has_adherent Has adherent +has_adjustment Has adjustment +has_aggregation_view Has aggregation view +has_alias Has alias +has_allelic_variant Has allelic variant +has_alternative Has alternative +has_answer has answer +has_approach_guidance Has approach guidance +has_approach Has approach +has_archetype Has archetype +has_arterial_supply Has arterial supply +has_associated_condition has_associated_condition +has_associated_etiologic_finding Has associated etiologic finding +has_associated_finding Has associated finding +has_associated_function Has associated function +has_associated_morphology Has associated morphology +has_associated_observation Has associated observation +has_associated_procedure Has associated procedure +has_at_risk_population Has at risk population +has_basic_dose_form Has basic dose form +has_basis_of_strength_substance Has basis of strength substance +has_boss Has basis of strength substance +has_branch Has branch +has_british_form Has British form +has_causative_agent Has causative agent +has_challenge Has challenge +has_class Has class +has_clinical_course Has clinical course +has_clinician_form Has clinician form +has_coating_material Has coating material +has_common_name Has common name +has_communication_with_wound Has communication with wound +has_component Has component +has_compositional_material Has compositional material +has_concentration_strength_denominator_unit Has concentration strength denominator unit +has_concentration_strength_denominator_value Has concentration strength denominator value +has_concentration_strength_numerator_unit Has concentration strength numerator unit +has_concentration_strength_numerator_value Has concentration strength numerator value +has_conceptual_part Has conceptual part +has_connection_type has connection type +has_constitutional_part Has constitutional part +has_consumer_friendly_form Has consumer friendly form +has_context_binding Has context binding +has_continuation_branch Has continuation branch +has_contraindicated_class Has contraindicated class +has_contraindicated_drug Has contraindicated drug +has_contraindicated_mechanism_of_action Has contraindicated mechanism of action +has_contraindicated_physiologic_effect Has contraindicated physiologic effect +has_count_of_active_ingredient Has count of active ingredient +has_count_of_base_of_active_ingredient Has count of base of active ingredient +has_count Has count +has_course Has course +has_ctcae_5_parent has ctcae_5 parent +has_ctdc_value has ctdc value +has_data_element has data element +has_default_inpatient_classification Has default inpatient classification +has_default_outpatient_classification Has default outpatient classification +has_defining_characteristic Has defining characteristic +has_definitional_manifestation Has definitional manifestation +has_degree Has degree +has_dependent Has dependent +has_development_type has development type +has_developmental_stage has developmental stage +has_device_characteristic Has device characteristic +has_device_intended_site Has device intended site +has_diagnostic_criteria ICD has DSM-5 diagnostic criteria +has_dipg_dmg_authorized_value has DIPG DMG authorized value +has_direct_cell_shape has direct cell shape +has_direct_device Has direct device +has_direct_morphology Has direct morphology +has_direct_procedure_site Has direct procedure site +has_direct_site Has direct site +has_direct_substance Has direct substance +has_disposition Has disposition +has_divisor Has divisor +has_dose_form_administration_method Has dose form administration method +has_dose_form_intended_site Has dose form intended site +has_dose_form_release_characteristic Has dose form release characteristic +has_dose_form_transformation Has dose form transformation +has_dose_form Has dose form +has_doseformgroup Has dose form group +has_entire_anatomy_structure Has entire anatomy structure +has_entry_combination Has Entry Combination +has_entry_term Has entry term +has_entry_version Has entry version +has_episodicity Has episodicity +has_evaluation Has evaluation +has_exam Has exam +has_excluded_approach Has excluded approach +has_excluded_associated_finding Has excluded associated finding +has_excluded_associated_procedure Has excluded associated procedure +has_excluded_component Has excluded component +has_excluded_locale Has excluded locale +has_excluded_method Has excluded method +has_excluded_pathology Has excluded pathology +has_excluded_patient_type Has excluded patient type +has_excluded_procedure_device Has excluded procedure device +has_excluded_procedure_site Has excluded procedure site +has_excluded_route_of_administration Has excluded route of administration +has_excluded_specimen Has excluded specimen +has_excluded_surgical_extent Has excluded surgical extent +has_expanded_form Has expanded form +has_expected_outcome Has expected outcome +has_extent Has extent +has_filling Has filling +has_finding_context Has finding context +has_finding_informer Has finding informer +has_finding_method Has finding method +has_finding_site Has finding site +has_focus Has focus +has_form Has form +has_free_acid_or_base_form has free acid or base form +has_full_grown_phenotype has full grown phenotype +has_fusion has fusion +has_gdc_value has gdc value +has_gene_product_element has gene product element +has_germ_origin Has germ origin +has_given_pharmaceutical_substance Has given pharmaceutical substance +has_grade has grade +has_icdc_value has icdc value +has_imaged_location Has imaged location +has_imaging_focus Has imaging focus +has_inactive_ingredient Has Inactive Ingredient +has_inc_parent has inc parent +has_indirect_device Has indirect device +has_indirect_morphology Has indirect morphology +has_indirect_procedure_site Has indirect procedure site +has_ingredient_characteristic Has ingredient characteristic +has_ingredient_qualitative_strength Has ingredient qualitative strength +has_ingredients Has ingredients +has_ingredient Has ingredient +has_inherent_3d_shape Has inherent 3-D shape +has_inherent_attribute Has inherent attribute +has_inherent_location Has inherent location +has_inheritance_type Has inheritance type +has_insertion has insertion +has_instrumentation Has instrumentation +has_intent Has intent +has_interpretation Has interpretation +has_lab_number Has lab number +has_lateral_anatomic_location Has lateral anatomic location +has_lateral_location_presence Has lateral location presence +has_laterality Has laterality +has_life_circumstance Has life circumstance +has_locale Has locale +has_location Has location +has_loinc_number Has Loinc number +has_lymphatic_drainage Has lymphatic drainage +has_maneuver_type has maneuver type +has_manifestation Has manifestation +has_mapping_qualifier Has mapping qualifier +has_measured_component Has measured component +has_measurement_method Has measurement method +has_mechanism_of_action Has mechanism of action +has_member Has member +has_method Has method +has_modality_subtype Has modality subtype +has_modality_type has modality type +has_modification Has modification +has_multi_level_category Has multi-level category +has_nerve_supply Has nerve supply +has_object_guidance Has object guidance +has_observed_anatomical_entity has observed anatomical entity +has_occurrence Has occurrence +has_onset Has onset +has_ooro_pc_value has OORO PC value +has_origin Has origin +has_owning_affiliate Has owning affiliate +has_owning_section Has owning section +has_owning_subsection Has owning subsection +has_panel_element CPT laboratory panel code has laboratory panel test member +has_parent_group Has parent group +has_parent Has parent +has_part_anatomy_structure Has part anatomy structure +has_part Has part +has_pathological_process Has pathological process +has_pathology Has pathology +has_patient_type Has patient type +has_pcdc_all_authorized_value has PCDC ALL authorized value +has_pcdc_aml_authorized_value has PCDC AML authorized value +has_pcdc_data_type has pcdc data type +has_pcdc_ews_authorized_value has PCDC EWS authorized value +has_pcdc_gct_authorized_value has PCDC GCT authorized value +has_pcdc_hl_authorized_value has PCDC HL authorized value +has_pcdc_os_authorized_value has PCDC OS authorized value +has_permuted_term Has permuted term +has_pharmaceutical_administration_method has pharmaceutical administration method +has_pharmaceutical_basic_dose_form has pharmaceutical basic dose form +has_pharmaceutical_intended_site has pharmaceutical intended site +has_pharmaceutical_release_characteristics has pharmaceutical release characteristics +has_pharmaceutical_route Has_pharmaceutical_route +has_pharmaceutical_state_of_matter has pharmaceutical state of matter +has_pharmaceutical_transformation has pharmaceutical transformation +has_pharmacokinetics Has pharmacokinetics +has_phenotype Has phenotype +has_physical_part_of_anatomic_structure has physical part of anatomic structure +has_physiologic_effect Has physiologic effect +has_physiologic_state Has physiologic state +has_possibly_included_approach Has possibly included approach +has_possibly_included_associated_finding Has possibly included associated finding +has_possibly_included_associated_procedure Has possibly included associated procedure +has_possibly_included_component Has possibly included component +has_possibly_included_method Has possibly included method +has_possibly_included_panel_element CPT laboratory panel code has possibly included laboratory panel test member +has_possibly_included_pathology Has possibly included pathology +has_possibly_included_patient_type Has possibly included patient type +has_possibly_included_procedure_device Has possibly included procedure device +has_possibly_included_procedure_site Has possibly included procedure site +has_possibly_included_route_of_administration Has possibly included route of administration +has_possibly_included_surgical_extent Has possibly included surgical extent +has_precise_active_ingredient Has precise active ingredient +has_precise_ingredient Has precise ingredient +has_precondition Has precondition +has_presence_guidance Has presence guidance +has_presentation_strength_denominator_unit Has presentation strength denominator unit +has_presentation_strength_denominator_value Has presentation strength denominator value +has_presentation_strength_numerator_unit Has presentation strength numerator unit +has_presentation_strength_numerator_value Has presentation strength numerator value +has_prev_name Has previous name +has_prev_symbol Has previous symbol +has_primary_segmental_supply Has primary segmental supply +has_print_name Has print name +has_priority Has priority +has_procedure_context Has procedure context +has_procedure_device Has procedure device +has_procedure_morphology Has procedure morphology +has_procedure_site Has procedure site +has_process_duration Has process duration +has_process_output Has process output +has_product_characteristic Has product characteristic +has_product_monograph_title has product monograph title +has_projection has projection +has_property_type Has property type +has_property Has property +has_quantified_form Has quantified form +has_realization Has realization +has_recipient_category Has recipient category +has_regional_part Has regional part +has_related_developmental_entity has related developmental entity +has_related_factor Has related factor +has_result Has result +has_revision_status Has revision status +has_risk_factor Has risk factor +has_route_of_administration Has route of administration +has_salt_form has salt form +has_scale_type Has scale type +has_scale Has scale +has_secondary_segmental_supply Has secondary segmental supply +has_segmental_composition Has segmental composition +has_segmental_supply Has segmental supply +has_seronet_authorized_value has seronet authorized value +has_severity Has severity +has_sign_or_symptom Has sign or symptom +has_single_level_category Has single level category +has_sort_version Has sort version +has_specialty Has specialty +has_specimen_procedure Has specimen procedure +has_specimen_source_identity Has specimen source identity +has_specimen_source_morphology Has specimen source morphology +has_specimen_source_topography Has specimen source topography +has_specimen_substance Has specimen substance +has_specimen Has specimen +has_stage Has stage +has_state_of_matter Has state of matter +has_structural_class Structural class of +has_subject_of_information Has subject of information +has_subject_relationship_context Has subject relationship context +has_subject Has subject +has_suffix Has suffix +has_supersystem Has supersystem +has_supported_concept_property Has supported concept property +has_supported_concept_relationship Has supported concept relationship +has_surface_characteristic Has surface characteristic +has_surface_texture Has surface texture +has_surgical_approach has surgical approach +has_surgical_extent Has surgical extent +has_system Has system +has_target_population Has target population +has_target has target +has_technique Has technique +has_temporal_context Has temporal context +has_therapeutic_class Has therapeutic class +has_time_aspect Has time aspect +has_time_modifier Has time modifier +has_timing_of Has timing of +has_tradename Has tradename +has_translation Has translation +has_transliterated_form Has transliterated form +has_tributary Has tributary +has_unit_of_presentation Has unit of presentation +has_units Has units +has_venous_drainage Has venous drainage +has_version Has version +has_view_type Has view type +homonym_for Homonym for +homonym_of Homonym of +human_disease_maps_to_eo_disease human disease maps to eo disease +icd_asterisk ICD asterisk +icd_dagger ICD dagger +icdc_value_of icdc value of +imaged_anatomy_has_procedure imaged anatomy has procedure +inactive_ingredient_of Inactive Ingredient Of +inc_parent_of inc parent of +included_in included_in +includes_sub_specimen Includes sub specimen +includes includes +indirect_device_of Indirect device of +indirect_morphology_of Indirect morphology of +indirect_procedure_site_of Indirect procedure site of +induced_by Induced by +induces Induces +inferior_to inferior to +inferolateral_to inferolateral to +inferomedial_to inferomedial to +ingredient_characteristic_of Ingredient characteristic of +ingredient_of Ingredient of +ingredient_qualitative_strength_of Ingredient qualitative strength of +ingredients_of Ingredients of +inherent_3d_shape_of Inherent 3-D shape of +inherent_location_of Inherent location of +inheres_in Inheres in +inheritance_type_of Inheritance type of +insertion_of insertion of +instrumentation_of Instrumentation of +intent_of Intent of +internal_to internal to +interpretation_of Interpretation of +interprets Interprets +inverse_during Inverse during +inverse_ends_during Inverse ends during +inverse_happens_during Inverse happens during +inverse_isa Inverse is a +inverse_relative_to Inverse relative to +inverse_was_a Inverse was a +is_abnormal_cell_of_disease is abnormal cell of disease +is_abnormality_of_gene_product is abnormality of gene product +is_abnormality_of_gene is abnormality of gene +is_acc-aha_sars2_authorized_value_for_variable is ACC-AHA SARS2 authorized value for variable +is_action_guidance_for Is action guidance for +is_aggregation_view_of Is aggregation view of +is_approach_guidance_for Is approach guidance for +is_associated_anatomic_site_of is associated anatomic site of +is_associated_anatomy_of_gene_product is associated anatomy of gene product +is_associated_disease_of is associated disease of +is_biochemical_function_of_gene_product is biochemical function of gene product +is_chemical_classification_of_gene_product is chemical classification of gene product +is_chromosomal_location_of_gene is chromosomal location of gene +is_component_of_chemotherapy_regimen is component of chemotherapy regimen +is_ctdc_value_of is ctdc value of +is_cytogenetic_abnormality_of_disease is cytogenetic abnormality of disease +is_dipg_dmg_authorized_value_for_variable is DIPG DMG authorized value for variable +is_exam_for Is exam for +is_finding_of_disease is finding of disease +is_given_pharmaceutical_substance_for Is given pharmaceutical substance for +is_grade_of_disease is grade of disease +is_imaged_location_for Is imaged location for +is_imaging_focus_of Is imaging focus of +is_interpreted_by Is interpreted by +is_lateral_anatomic_location_of Is lateral anatomic location of +is_location_of_anatomic_structure is location of anatomic structure +is_location_of_biological_process is location of biological process +is_maneuver_type_for Is maneuver type for +is_marked_by_gene_product is marked by gene product +is_mechanism_of_action_of_chemical_or_drug is mechanism of action of chemical or drug +is_metastatic_anatomic_site_of_disease is metastatic anatomic site of disease +is_modality_subtype_for Is modality subtype for +is_modality_type_for Is modality type for +is_modification_of Is modification of +is_molecular_abnormality_of_disease is molecular abnormality of disease +is_normal_cell_origin_of_disease is normal cell origin of disease +is_normal_tissue_origin_of_disease is normal tissue origin of disease +is_not_abnormal_cell_of_disease is not abnormal cell of disease +is_not_cytogenetic_abnormality_of_disease is not cytogenetic abnormality of disease +is_not_finding_of_disease is not finding of disease +is_not_metastatic_anatomic_site_of_disease is not metastatic anatomic site of disease +is_not_molecular_abnormality_of_disease is not molecular abnormality of disease +is_not_normal_cell_origin_of_disease is not normal cell origin of disease +is_not_normal_tissue_origin_of_disease is not normal tissue origin of disease +is_not_primary_anatomic_site_of_disease is not primary anatomic site of disease +is_object_guidance_for Is object guidance for +is_ooro_pc_value_of is OORO PC value of +is_organism_source_of_gene_product is organism source of gene product +is_paired_with_value_set is paired with value set +is_pcdc_all_authorized_value_for_variable is PCDC ALL authorized value for variable +is_pcdc_aml_authorized_value_for_variable is PCDC AML authorized value for variable +is_pcdc_ews_authorized_value_for_variable is PCDC EWS authorized value for variable +is_pcdc_gct_authorized_value_for_variable is PCDC GCT authorized value for variable +is_pcdc_hl_authorized_value_for_variable is PCDC HL authorized value for variable +is_pcdc_os_authorized_value_for_variable is PCDC OS authorized value for variable +is_pharmaceutical_route_for Is pharmaceutical route for +is_physical_location_of_gene is physical location of gene +is_physiologic_effect_of_chemical_or_drug is physiologic effect of chemical or drug +is_presence_guidance_for Is presence guidance for +is_presence_of_lateral_location Is presence of lateral location +is_primary_anatomic_site_of_disease is primary anatomic site of disease +is_property_or_attribute_of_eo_disease is property or attribute of eo disease +is_qualified_by is qualified by +is_related_to_endogenous_product Is Related To Endogenous Product +is_seronet_authorized_value_for_variable is seronet authorized value for variable +is_stage_of_disease is stage of disease +is_sterile Is sterile +is_structural_domain_or_motif_of_gene_product is structural domain or motif of gene product +is_subject_of Is subject of +is_target is target +is_timing_for Is timing for +is_value_for_gdc_property is value for gdc property +is_view_type_for Is view type for +isa Is a +kind_is_domain_of kind is domain of +kind_is_range_of kind is range of +lab_number_of Lab number +larger_than Larger Than +lateral_to lateral to +laterality_of Laterality of +left_lateral_to left lateral to +left_medial_to left medial to +life_circumstance_of Life circumstance of +locale_of_excluded Locale of excluded +locale_of Locale of +location_of Location of +loinc_number_of Loinc number of +lymphatic_drainage_of Lymphatic drainage of +manifestation_of Manifestation of +manufactured_by manufactured by +manufactures manufactures +mapped_from Mapped from +mapped_to Mapped to +mapping_qualifier_of Mapping qualifier of +matures_from matures from +matures_into matures into +may_be_abnormal_cell_of_disease may be abnormal cell of disease +may_be_associated_disease_of_disease may be associated disease of disease +may_be_cytogenetic_abnormality_of_disease may be cytogenetic abnormality of disease +may_be_diagnosed_by May be diagnosed by +may_be_finding_of_disease may be finding of disease +may_be_molecular_abnormality_of_disease may be molecular abnormality of disease +may_be_normal_cell_origin_of_disease may be normal cell origin of disease +may_be_normal_tissue_origin_of_disease may be normal tissue origin of disease +may_be_prevented_by May be prevented by +may_be_qualified_by May be qualified by +may_be_treated_by May be treated by +may_diagnose May diagnose +may_inhibit_effect_of May inhibit effect of +may_prevent May prevent +may_qualify May qualify +may_treat May treat +measured_by Measured by +measured_component_of Measured component of +measurement_method_of Measurement method of +measures Measures +mechanism_of_action_of Mechanism of action of +medial_to medial to +member_of Member of +merges_with merges with +metabolic_site_of Metabolic site of +method_of_excluded Method of excluded +method_of_possibly_included Method of possibly included +method_of Method of +modified_by Modified by +modifies Modifies +molecular_abnormality_involves_gene molecular abnormality involves gene +moved_from Moved from +moved_to Moved to +mth_british_form_of MTH British form of +mth_expanded_form_of MTH expanded form of +mth_has_british_form MTH has British form +mth_has_expanded_form MTH has expanded form +mth_has_plain_text_form Has plain text form, Metathesaurus-asserted +mth_has_xml_form Has XML form, Metathesaurus-asserted +mth_plain_text_form_of Plain text form of, Metathesaurus-asserted +mth_xml_form_of XML form of, Metathesaurus-asserted +multiply_mapped_from Multiply mapped from +multiply_mapped_to Multiply mapped to +negatively_regulated_by Negatively regulated by +negatively_regulates Negatively regulates +neoplasm_has_special_category neoplasm has special category +nerve_supply_of Nerve supply of +noun_form_of Noun form of +occurs_after Occurs after +occurs_before Occurs before +occurs_in Occurs in +onset_of Onset of +organism_has_gene organism has gene +origin_of Origin of +other_mapped_from Other mapped from +other_mapped_to Other mapped to +owning_affiliate_of Owning affiliate of +owning_section_of Owning section of +owning_subsection_of Owning subsection of +panel_element_of_possibly_included CPT laboratory panel test member is possibly included element of laboratory code +panel_element_of CPT laboratory panel test member is element of laboratory code +parent_group_of Parent group of +parent_of Parent of +part_anatomy_structure_of Part anatomy structure of +part_of Part of +part_referred_to_by Part referred to by +partially_equivalent_to Partially equivalent to +partially_excised_anatomy_has_procedure partially excised anatomy has procedure +partially_excised_anatomy_may_have_procedure partially excised anatomy may have procedure +pathogenesis_of_disease_involves_gene pathogenesis of disease involves gene +pathological_process_of Pathological process of +pathology_of_excluded Pathology of excluded +pathology_of_possibly_included Pathology of possibly included +pathology_of Pathology of +pathway_has_gene_element pathway has gene element +patient_type_of_excluded Patient type of excluded +patient_type_of_possibly_included Patient type of possibly included +patient_type_of Patient type of +pcdc_data_type_of pcdc data type of +permuted_term_of Permuted term of +pharmaceutical_administration_method_of pharmaceutical administration method of +pharmaceutical_basic_dose_form_of pharmaceutical basic dose form of +pharmaceutical_intended_site_of pharmaceutical intended site of +pharmaceutical_release_characteristics_of pharmaceutical release characteristics of +pharmaceutical_state_of_matter_of pharmaceutical state of matter of +pharmaceutical_transformation_of pharmaceutical transformation_of +pharmacokinetics_of Pharmacokinetics of +phenotype_of Phenotype of +physiologic_effect_of Physiologic effect of +physiologic_state_of Physiologic state of +place_traveled_from Place traveled from +place_traveled_to Place traveled to or resided in +plays_role Plays role +population_at_risk_for Population at risk for +positively_regulated_by Positively regulated by +positively_regulates Positively regulates +possibly_equivalent_to Possibly equivalent to +possibly_replaced_by Possibly replaced by +possibly_replaces Possibly replaces +posterior_to posterior to +posteroinferior_to posteroinferior to +posterolateral_to posterolateral to +posteromedial_to posteromedial to +posterosuperior_to posterosuperior to +precise_active_ingredient_of Precise active ingredient of +precise_ingredient_of Precise ingredient of +precondition_of Precondition of +presentation_strength_denominator_unit_of Presentation strength denominator unit of +presentation_strength_denominator_value_of Presentation strength denominator value of +presentation_strength_numerator_unit_of Presentation strength numerator unit of +presentation_strength_numerator_value_of Presentation strength numerator value of +prev_name_of Previous name of +prev_symbol_of Previous symbol of +primary_mapped_from Primary mapped from +primary_mapped_to Primary mapped to +primary_segmental_supply_of Primary segmental supply of +print_name_of Print name of +priority_of Priority of +procedure_context_of Procedure context of +procedure_device_of_excluded Procedure device of excluded +procedure_device_of_possibly_included Procedure device of possibly included +procedure_device_of Procedure device of +procedure_has_completely_excised_anatomy procedure has completely excised anatomy +procedure_has_excised_anatomy procedure has excised anatomy +procedure_has_imaged_anatomy procedure has imaged anatomy +procedure_has_partially_excised_anatomy procedure has partially excised anatomy +procedure_has_target_anatomy procedure has target anatomy +procedure_may_have_completely_excised_anatomy procedure may have completely excised anatomy +procedure_may_have_excised_anatomy procedure may have excised anatomy +procedure_may_have_partially_excised_anatomy procedure may have partially excised anatomy +procedure_morphology_of Procedure morphology of +procedure_site_of_excluded Procedure site of excluded +procedure_site_of_possibly_included Procedure site of possibly included +procedure_site_of Procedure site of +process_acts_on Process acts on +process_altered_by_allele process altered by allele +process_duration_of Process duration of +process_extends_to Process extends to +process_includes_biological_process process includes biological process +process_initiates_biological_process process initiates biological process +process_involves_gene process involves gene +process_output_of Process output of +product_characteristic_of Product characteristic of +product_monograph_title_of product monograph title of +projects_from projects from +projects_to projects to +property_of Property of +property_type_of Property type of +proximal_to proximal to +qualifier_applies_to qualifier applies to +quantified_form_of Quantified form of +realization_of Realization of +receives_attachment_from receives attachment from +receives_drainage_from receives drainage from +receives_input_from Receives input from +receives_projection receives projection +recipient_category_of Recipient category of +referred_to_by referred to by +refers_to refers to +reformulated_to Reformulated to +reformulation_of Reformulation of +regimen_has_accepted_use_for_disease Regimen Has Accepted Use For Disease +regional_part_of Regional part of +regulated_by Regulated by +regulates Regulates +related_developmental_entity_of related developmental entity of +related_factor_of Related factor of +related_object related object +related_part related part +related_to_genetic_biomarker related to genetic biomarker +related_to Is Related to +relative_to_part_of Relative to part of +relative_to Relative to +replaced_by Replaced by +replaces Replaces +result_of Result of +revision_status_of Revision status of +right_lateral_to right lateral to +right_medial_to right medial to +risk_factor_of Risk factor of +role_has_domain role has domain +role_has_parent role has parent +role_has_range role has range +role_is_parent_of role is parent of +role_played_by Role played by +route_of_administration_of_excluded Route of administration of excluded +route_of_administration_of_possibly_included Route of administration of possibly included +route_of_administration_of Route of administration of +same_as Same as +scale_of Scale of +scale_type_of Scale type of +secondary_segmental_supply_of Secondary segmental supply of +see_from See from +see See +segmental_composition_of Segmental composition of +segmental_supply_of Segmental supply of +sends_output_to Sends output to +severity_of Severity of +sign_or_symptom_of Sign or symptom of +site_of_metabolism Site of metabolism +smaller_than Smaller Than +sort_version_of Sort version of +special_category_includes_neoplasm special category includes neoplasm +specialty_of Specialty of +specimen_of_excluded Specimen of excluded +specimen_of Specimen of +specimen_procedure_of Specimen procedure of +specimen_source_identity_of Specimen source identity of +specimen_source_morphology_of Specimen source morphology of +specimen_source_topography_of specimen source topography of +specimen_substance_of Specimen substance of +ssc scc +stage_of Stage of +state_of_matter_of State of matter of +structural_class_of Has structural class +sub_specimen_included_by Sub specimen included by +subject_of_information_of Subject of information of +subject_relationship_context_of Subject relationship context of +subset_includes_concept subset includes concept +substance_used_by_excluded Substance used by excluded +substance_used_by_possibly_included Substance used by possibly included +substance_used_by Substance used by +suffix_of Suffix of +superior_to superior to +superolateral_to superolateral to +superomedial_to superomedial to +supersystem_of Supersystem of +supported_concept_property_in Supported concept property in +supported_concept_relationship_in Supported concept relationship in +surface_characteristic_of Surface characteristic of +surface_texture_of Surface texture of +surgical_approach_of surgical approach of +surgical_extent_of_excluded Surgical extent of excluded +surgical_extent_of_possibly_included Surgical extent of possibly included +surgical_extent_of Surgical extent of +surrounded_by Surrounded by +surrounds Surrounds +system_of System of +target_anatomy_has_procedure target anatomy has procedure +target_population_of Target population of +technique_of Technique of +temporal_context_of Temporal context of +temporally_followed_by Temporally followed by +temporally_follows Temporally follows +temporally_related_to Temporally related to +therapeutic_class_of Therapeutic class of +time_aspect_of Time aspect of +time_modifier_of Time modifier of +tissue_is_expression_site_of_gene_product tissue is expression site of gene product +towards Towards +tradename_of Tradename of +transforms_from transforms from +transforms_into transforms into +translation_of Translation of +transliterated_form_of transliterated_form_of +treated_by Treated by +treats Treats +tributary_of Tributary of +uniquely_mapped_from Uniquely mapped from +uniquely_mapped_to Uniquely mapped to +unit_of_presentation_of Unit of presentation of +units_of Units of +used_by Used by +used_for Used for +uses_access_device Uses access device +uses_device Uses device +uses_energy Uses energy +uses_excluded_substance Uses excluded substance +uses_possibly_included_substance Uses possibly included substance +uses_substance Uses substance +uses Uses +use Use +value_set_is_paired_with value set is paired with +venous_drainage_of Venous drainage of +version_of Version of +was_a Was a +wound_has_communication_with Wound has communication with diff --git a/cumulus_library_umls/static_files/umls_tty.tsv b/cumulus_library_umls/static_files/umls_tty.tsv new file mode 100644 index 0000000..596b676 --- /dev/null +++ b/cumulus_library_umls/static_files/umls_tty.tsv @@ -0,0 +1,243 @@ +TTY TTY_STR +AA Attribute type abbreviation +AB Abbreviation in any source vocabulary +ACR Acronym +AC Activities +AD Adjective +AM Short form of modifier +AS Attribute type synonym +AT Attribute type +BD Fully-specified drug brand name that can be prescribed +BN Fully-specified drug brand name that can not be prescribed +BPCK Branded Drug Delivery Device +BR Binding realm +CA2 ISO 3166-1 standard country code in alpha-2 (two-letter) format +CA3 ISO 3166-1 standard country code in alpha-3 (three-letter) format +CCN Chemical code name +CCS FIPS 10-4 country code +CC Trimmed ICPC component process +CDA Clinical drug name in abbreviated format +CDC Clinical drug name in concatenated format (NDDF) +CDD Clinical drug name in delimited format +CDO Concept domain +CD Clinical Drug +CE Entry term for a Supplementary Concept +CHN Chemical structure name +CL Class +CMN Common name +CN LOINC official component name +CO Component name (hierarchical terms, not LOINC analytes) +CPR Concept property +CP ICPC component process (in original form) +CR Concept relationship +CSN Chemical Structure Name +CSY Code system +CS Short component process in ICPC, i.e. include some abbreviations +CU Common usage +CV Content view +CX Component, with abbreviations expanded. +DC10 Diagnostic criteria for ICD10 code +DC9 Diagnostic criteria for ICD9 code +DEV Descriptor entry version +DE Descriptor +DFG Dose Form Group +DF Dose Form +DI Disease name +DN Display Name +DO Domain +DP Drug Product +DSV Descriptor sort version +DS Short form of descriptor +DT Definitional term +EP Print entry term +EQ Equivalent name +ES Short form of entry term +ETAL Entry Term Alias +ETCF Entry term, consumer friendly description +ETCLIN Entry term, clinician description +ET Entry term +EX Expanded form of entry term +FBD Foreign brand name +FI Finding name +FN Full form of descriptor +FSY Foreign Synonym +GLP Global period +GN Generic drug name +GO Goal +GPCK Generic Drug Delivery Device +GT Glossary term +HC Hierarchical class +HD Hierarchical descriptor +HGJKN1 Japanese High Level Group Term (kana1) +HGJKN Japanese High Level Group Term (kana) +HG High Level Group Term +HS Short or alternate version of hierarchical term +HTJKN1 Japanese Hierarchical term (kana1) +HTJKN Japanese Hierarchical term (kana) +HTN HL7 Table Name +HT Hierarchical term +HX Expanded version of short hierarchical term +ID Nursing indicator +IN Name for an ingredient +IS Obsolete Synonym +IT Index term +IVC Intervention categories +IV Intervention +LA LOINC answer +LC Long common name +LG LOINC group +LLTJKN1 Japanese Lower Level Term (kana1) +LLTJKN Japanese Lower Level Term (kana) +LLT Lower Level Term +LN LOINC official fully specified name +LO Obsolete official fully specified name +LPDN LOINC parts display name +LPN LOINC parts name +LS Expanded system/sample type +LVDN Linguistic variant display name +LV Lexical variant +MD CCS multi-level diagnosis categories +MH Main heading +MIN name for a multi-ingredient +MP Preferred names of modifiers +MS Multum names of branded and generic supplies or supplements +MTH_ACR MTH acronym +MTH_CN MTH Component, with abbreviations expanded. +MTH_ET Metathesaurus entry term +MTH_FN MTH Full form of descriptor +MTH_HG MTH High Level Group Term +MTH_HT MTH Hierarchical term +MTH_HX MTH Hierarchical term expanded +MTH_IS Metathesaurus-supplied form of obsolete synonym +MTH_LLT MTH Lower Level Term +MTH_LN MTH Official fully specified name with expanded abbreviations +MTH_LO MTH Expanded LOINC obsolete fully specified name +MTH_OAF Metathesaurus-supplied form of obsolete active fully specified name +MTH_OAP Metathesaurus-supplied form of obsolete active preferred term +MTH_OAS Metathesaurus-supplied form of obsolete active synonym +MTH_OET Metathesaurus obsolete entry term +MTH_OF Metathesaurus-supplied form of obsolete fully specified name +MTH_OL MTH Non-current Lower Level Term +MTH_OPN Metathesaurus obsolete preferred term, natural language form +MTH_OP Metathesaurus obsolete preferred term +MTH_OS MTH System-organ class +MTH_PTGB Metathesaurus-supplied form of British preferred term +MTH_PTN Metathesaurus preferred term, natural language form +MTH_PT Metathesaurus preferred term +MTH_RXN_BD RxNorm Created BD +MTH_RXN_CDC RxNorm Created CDC +MTH_RXN_CD RxNorm Created CD +MTH_RXN_DP RxNorm Created DP +MTH_SI MTH Sign or symptom of +MTH_SMQ Metathesaurus version of Standardised MedDRA Query +MTH_SYGB Metathesaurus-supplied form of British synonym +MTH_SY MTH Designated synonym +MV Multi-level procedure category +N1 Chemical Abstracts Service Type 1 name of a chemical +NA Name aliases +NM Name of Supplementary Concept +NPT HL7 non-preferred for language term +NP Non-preferred term +NS Short form of non-preferred term +NX Expanded form of non-preferred term +OAF Obsolete active fully specified name +OAM Obsolete Modifier Abbreviation +OAP Obsolete active preferred term +OAS Obsolete active synonym +OA Obsolete abbreviation +OC Nursing outcomes +OET Obsolete entry term +OF Obsolete fully specified name +OLC Obsolete Long common name +OLG Obsolete LOINC group name +OLJKN1 Japanese Non-current Lower Level Term (kana1) +OLJKN Japanese Non-current Lower Level Term (kana) +OL Non-current Lower Level Term +OM Obsolete modifiers in HCPCS +ONP Obsolete non-preferred for language term +OOSN Obsolete official short name +OPN Obsolete preferred term, natural language form +OP Obsolete preferred name +OR Orders +OSJKN1 Japanese System-organ class WHO Adverse Reaction Terminology (kana1) +OSJKN Japanese System-organ class WHO Adverse Reaction Terminology (kana) +OSN Official short name +OS System-organ class +PCE Preferred entry term for Supplementary Concept +PC Preferred "trimmed term" in ICPC +PEP Preferred entry term +PHENO_ET Phenotype entry term +PHENO Phenotype +PIN Name from a precise ingredient +PM Machine permutation +PN Metathesaurus preferred name +POS Place of service +PQ Qualifier for a problem +PR Name of a problem +PSC Protocol selection criteria +PSN Prescribable Names +PS Short forms that needed full specification +PTAV Preferred Allelic Variant +PTCS Preferred Clinical Synopsis +PTGB British preferred term +PTJKN1 Japanese Designated preferred name (kana1) +PTJKN Japanese Designated preferred name (kana) +PTN Preferred term, natural language form +PT Designated preferred name +PXQ Preferred qualifier term +PX Expanded preferred terms (pair with PS) +QAB Qualifier abbreviation +QEV Qualifier entry version +QSV Qualifier sort version +RAB Root abbreviation +RHT Root hierarchical term +RPT Root preferred term +RSY Root synonym +RS Extracted related names in SNOMED2 +RT Term is related to, but often non-synonymous with, the preferred term +RXN_IN Rxnorm Preferred Ingredient +RXN_PT Rxnorm Preferred +SBDC Semantic Branded Drug Component +SBDFP Semantic branded drug and form w/ precise ingredient as basis strength +SBDF Semantic branded drug and form +SBDG Semantic branded drug group +SBD Semantic branded drug +SB Named subset of a source +SCALE Scale +SCDC Semantic Drug Component +SCDFP Semantic clinical drug and form w/ precise ingredient as basis strength +SCDF Semantic clinical drug and form +SCDGP Semantic clinical drug group w/ precise ingredient as basis strength +SCDG Semantic clinical drug group +SCD Semantic Clinical Drug +SCN Scientific name +SC Special Category term +SD CCS diagnosis categories +SI Name of a sign or symptom of a problem +SMQ Standardised MedDRA Query +SP CCS procedure categories +SSN Source short name, used in the UMLS Knowledge Source Server +SS Synonymous "short" forms +ST Step +SU Active Substance +SX Mixed-case component synonym with expanded abbreviations +SYGB British synonym +SYN Designated alias +SY Designated synonym +TA Task +TC Term class +TG Name of the target of an intervention +TMSY Tall Man synonym +TQ Topical qualifier +TX CCPSS synthesized problems for TC termgroup +UCN Unique common name +UE Unique equivalent name +USN Unique scientific name +USY Unique synonym +VAB Versioned abbreviation +VPT Versioned preferred term +VSY Versioned synonym +VS Value Set +XD Expanded descriptor in AOD +XM Cross mapping set +XQ Alternate name for a qualifier \ No newline at end of file diff --git a/cumulus_library_umls/static_files/umls_tui.tsv b/cumulus_library_umls/static_files/umls_tui.tsv new file mode 100644 index 0000000..d2f6f8c --- /dev/null +++ b/cumulus_library_umls/static_files/umls_tui.tsv @@ -0,0 +1,128 @@ +aabr TUI STY +aapp T116 Amino Acid, Peptide, or Protein +acab T020 Acquired Abnormality +acty T052 Activity +aggp T100 Age Group +amas T087 Amino Acid Sequence +amph T011 Amphibian +anab T190 Anatomical Abnormality +anim T008 Animal +anst T017 Anatomical Structure +antb T195 Antibiotic +arch T194 Archaeon +bacs T123 Biologically Active Substance +bact T007 Bacterium +bdsu T031 Body Substance +bdsy T022 Body System +bhvr T053 Behavior +biof T038 Biologic Function +bird T012 Bird +blor T029 Body Location or Region +bmod T091 Biomedical Occupation or Discipline +bodm T122 Biomedical or Dental Material +bpoc T023 Body Part, Organ, or Organ Component +bsoj T030 Body Space or Junction +celc T026 Cell Component +celf T043 Cell Function +cell T025 Cell +cgab T019 Congenital Abnormality +chem T103 Chemical +chvf T120 Chemical Viewed Functionally +chvs T104 Chemical Viewed Structurally +clas T185 Classification +clna T201 Clinical Attribute +clnd T200 Clinical Drug +cnce T077 Conceptual Entity +comd T049 Cell or Molecular Dysfunction +crbs T088 Carbohydrate Sequence +diap T060 Diagnostic Procedure +dora T056 Daily or Recreational Activity +drdd T203 Drug Delivery Device +dsyn T047 Disease or Syndrome +edac T065 Educational Activity +eehu T069 Environmental Effect of Humans +elii T196 Element, Ion, or Isotope +emod T050 Experimental Model of Disease +emst T018 Embryonic Structure +enty T071 Entity +enzy T126 Enzyme +euka T204 Eukaryote +evnt T051 Event +famg T099 Family Group +ffas T021 Fully Formed Anatomical Structure +fish T013 Fish +fndg T033 Finding +fngs T004 Fungus +food T168 Food +ftcn T169 Functional Concept +genf T045 Genetic Function +geoa T083 Geographic Area +gngm T028 Gene or Genome +gora T064 Governmental or Regulatory Activity +grpa T102 Group Attribute +grup T096 Group +hcpp T068 Human-caused Phenomenon or Process +hcro T093 Health Care Related Organization +hlca T058 Health Care Activity +hops T131 Hazardous or Poisonous Substance +horm T125 Hormone +humn T016 Human +idcn T078 Idea or Concept +imft T129 Immunologic Factor +inbe T055 Individual Behavior +inch T197 Inorganic Chemical +inpo T037 Injury or Poisoning +inpr T170 Intellectual Product +irda T130 Indicator, Reagent, or Diagnostic Aid +lang T171 Language +lbpr T059 Laboratory Procedure +lbtr T034 Laboratory or Test Result +mamm T015 Mammal +mbrt T063 Molecular Biology Research Technique +mcha T066 Machine Activity +medd T074 Medical Device +menp T041 Mental Process +mnob T073 Manufactured Object +mobd T048 Mental or Behavioral Dysfunction +moft T044 Molecular Function +mosq T085 Molecular Sequence +neop T191 Neoplastic Process +nnon T114 Nucleic Acid, Nucleoside, or Nucleotide +npop T070 Natural Phenomenon or Process +nusq T086 Nucleotide Sequence +ocac T057 Occupational Activity +ocdi T090 Occupation or Discipline +orch T109 Organic Chemical +orga T032 Organism Attribute +orgf T040 Organism Function +orgm T001 Organism +orgt T092 Organization +ortf T042 Organ or Tissue Function +patf T046 Pathologic Function +phob T072 Physical Object +phpr T067 Phenomenon or Process +phsf T039 Physiologic Function +phsu T121 Pharmacologic Substance +plnt T002 Plant +podg T101 Patient or Disabled Group +popg T098 Population Group +prog T097 Professional or Occupational Group +pros T094 Professional Society +qlco T080 Qualitative Concept +qnco T081 Quantitative Concept +rcpt T192 Receptor +rept T014 Reptile +resa T062 Research Activity +resd T075 Research Device +rnlw T089 Regulation or Law +sbst T167 Substance +shro T095 Self-help or Relief Organization +socb T054 Social Behavior +sosy T184 Sign or Symptom +spco T082 Spatial Concept +tisu T024 Tissue +tmco T079 Temporal Concept +topp T061 Therapeutic or Preventive Procedure +virs T005 Virus +vita T127 Vitamin +vtbt T010 Vertebrate diff --git a/cumulus_library_umls/umls/umls_builder.py b/cumulus_library_umls/umls_builder.py similarity index 100% rename from cumulus_library_umls/umls/umls_builder.py rename to cumulus_library_umls/umls_builder.py diff --git a/tests/test_static_builder.py b/tests/test_static_builder.py new file mode 100644 index 0000000..7829022 --- /dev/null +++ b/tests/test_static_builder.py @@ -0,0 +1,73 @@ +from cumulus_library import base_utils, databases, db_config, study_manifest + +from cumulus_library_umls import static_builder + + +def test_static_tables(tmp_path): + db_config.db_type = "duckdb" + config = base_utils.StudyConfig( + db=databases.DuckDatabaseBackend(f"{tmp_path}/duckdb"), + umls_key="123", + schema="main", + ) + cursor = config.db.cursor() + cursor.execute("CREATE SCHEMA umls") + manifest = study_manifest.StudyManifest() + manifest._study_config = { + "study_prefix": "umls", + "advanced_options": {"dedicated_schema": "umls"}, + } + manifest._advanced_config = {} + builder = static_builder.StaticBuilder() + builder.execute_queries(config=config, manifest=manifest) + + for table_conf in [ + { + "name": "semantic_types", + "size": 127, + "first": ("aapp", "T116", "Amino Acid, Peptide, or Protein"), + "last": ("vtbt", "T010", "Vertebrate"), + }, + { + "name": "semantic_groups", + "size": 127, + "first": ("ACTI", "Activities & Behaviors", "T052", "Activity"), + "last": ( + "PROC", + "Procedures", + "T061", + "Therapeutic or Preventive Procedure", + ), + }, + { + "name": "rel_description", + "size": 13, + "first": ("AQ", "Allowed qualifier"), + "last": ("XR", "Not related, no mapping"), + }, + { + "name": "rela_description", + "size": 1023, + "first": ( + "abnormal_cell_affected_by_chemical_or_drug", + "abnormal cell affected by chemical or drug", + ), + "last": ("wound_has_communication_with", "Wound has communication with"), + }, + { + "name": "tty_description", + "size": 242, + "first": ("AA", "Attribute type abbreviation"), + "last": ("XQ", "Alternate name for a qualifier"), + }, + { + "name": "tui_description", + "size": 127, + "first": ("aapp", "T116", "Amino Acid, Peptide, or Protein"), + "last": ("vtbt", "T010", "Vertebrate"), + }, + ]: + res = cursor.execute(f"SELECT * from umls.{table_conf['name']}").fetchall() + assert len(res) == table_conf["size"] + assert res[0] == table_conf["first"] + assert res[-1] == table_conf["last"]