SSSOM outputs

- Update: Utilizing standard sssom-py functionality
- Add: sssom validate
- Add: mapping_justification
- Update: Subject/object order & filename
- Add: Mandatory filtering of UMLS matches only in HPO-UMLS SSSOM.

.github/workflows/buid_and_release.yml

@@ -39,5 +39,5 @@ jobs:
           output/release/medgen.obo
           output/release/medgen-disease-extract.obo
           output/release/medgen-xrefs.robot.template.tsv
-          output/release/hpo-umls.sssom.tsv
+          output/release/umls-hpo.sssom.tsv
           output/release/hpo-mesh.sssom.tsv

config/medgen.sssom-metadata.yml

@@ -1,4 +1,4 @@
-creator_id: 0000-0002-2906-7319
+creator_id: orcid:0000-0002-2906-7319
 curie_map:
   GTR: http://purl.obolibrary.org/obo/mondo/mappings/unknown_prefix/GTR/
   HP: http://purl.obolibrary.org/obo/HP_
@@ -9,6 +9,7 @@ curie_map:
   NCIT: http://purl.obolibrary.org/obo/NCIT_
   OMIM: https://omim.org/entry/
   Orphanet: http://www.orpha.net/ORDO/Orphanet_
+  orcid: https://orcid.org/
   SCTID: http://identifiers.org/snomedct/
   UMLS: http://purl.obolibrary.org/obo/UMLS_
   oboInOwl: http://www.geneontology.org/formats/oboInOwl#

makefile

@@ -85,9 +85,11 @@ medgen-disease-extract.owl: medgen-disease-extract.obo
 #
 #medgen.sssom.tsv: medgen.obographs.json
 #	sssom parse medgen.obographs.json -I obographs-json -m config/medgen.sssom-metadata.yml -o $@
-sssom: hpo-umls.sssom.tsv
+sssom: umls-hpo.sssom.tsv
+	sssom validate umls-hpo.sssom.tsv
+	sssom validate hpo-mesh.sssom.tsv
 
-hpo-umls.sssom.tsv hpo-mesh.sssom.tsv: ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt
+umls-hpo.sssom.tsv hpo-mesh.sssom.tsv: ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt
 	python src/create_sssom.py --input-mappings $< --input-sssom-config config/medgen.sssom-metadata.yml
 
 # ----------------------------------------

requirements-unlocked.txt

@@ -1,2 +1,3 @@
 pandas
 pyyaml
+sssom

requirements.txt

@@ -1,14 +1,61 @@
+annotated-types==0.6.0
+attrs==23.2.0
+certifi==2024.2.2
+charset-normalizer==3.3.2
+click==8.1.7
+curies==0.7.9
+Deprecated==1.2.14
+deprecation==2.1.0
 distlib==0.3.6
+exceptiongroup==1.2.0
 filelock==3.9.0
+hbreader==0.9.1
+idna==3.6
+importlib_resources==6.4.0
+iniconfig==2.0.0
+isodate==0.6.1
+json-flattener==0.1.9
+jsonasobj2==1.0.4
+jsonschema==4.21.1
+jsonschema-specifications==2023.12.1
+linkml-runtime==1.7.5
+networkx==3.3
 numpy==1.25.1
+packaging==24.0
 pandas==2.0.3
+pansql==0.0.1
 pbr==5.11.1
 platformdirs==3.1.0
+pluggy==1.4.0
+prefixcommons==0.1.12
+prefixmaps==0.2.3
+pydantic==2.6.4
+pydantic_core==2.16.3
+pyparsing==3.1.2
+pytest==8.1.1
+pytest-logging==2015.11.4
 python-dateutil==2.8.2
+PyTrie==0.4.0
 pytz==2023.3
 PyYAML==6.0.1
+rdflib==7.0.0
+referencing==0.34.0
+requests==2.31.0
+rpds-py==0.18.0
+scipy==1.13.0
 six==1.16.0
+sortedcontainers==2.4.0
+SPARQLWrapper==2.0.0
+SQLAlchemy==2.0.29
+sssom==0.4.6
+sssom-schema==0.15.2
 stevedore==5.0.0
+tomli==2.0.1
+typing_extensions==4.11.0
 tzdata==2023.3
+urllib3==2.2.1
+validators==0.28.0
 virtualenv==20.20.0
 virtualenv-clone==0.5.7
+virtualenvwrapper==4.8.4
+wrapt==1.16.0

src/create_sssom.py

@@ -12,7 +12,7 @@
 CONFIG_DIR = PROJECT_DIR / "config"
 INPUT_MAPPINGS = str(FTP_DIR / "MedGenIDMappings.txt")
 INPUT_CONFIG = str(CONFIG_DIR / "medgen.sssom-metadata.yml")
-OUTPUT_FILE_HPO_UMLS = str(PROJECT_DIR / "hpo-umls.sssom.tsv")
+OUTPUT_FILE_HPO_UMLS = str(PROJECT_DIR / "umls-hpo.sssom.tsv")
 OUTPUT_FILE_HPO_MESH = str(PROJECT_DIR / "hpo-mesh.sssom.tsv")
 
 
@@ -21,10 +21,17 @@ def _filter_and_format_cols(df: pd.DataFrame, source: str) -> pd.DataFrame:
     return df[df['source'] == source][['subject_id', 'subject_label', 'predicate_id', 'object_id']]
 
 
-def run(input_mappings: str = INPUT_MAPPINGS, input_sssom_config: str = INPUT_CONFIG):
-    """Create SSSOM outputs"""
+def run(input_mappings: str = INPUT_MAPPINGS, input_sssom_config: str = INPUT_CONFIG, hpo_match_only_with_umls=True):
+    """Create SSSOM outputs
+
+    :param hpo_match_only_with_umls: If True, only create SSSOM outputs for HPO mappings that have UMLS mappings, and
+    will filter out other matches. This is purely edge case handling. As of 2024/04/06, 100% of the mappings were UMLS
+    anyway."""
     # SSSOM 1: HPO<->UMLS
     df_hpo_umls = get_mapping_set(input_mappings, ['HPO'], add_prefixes=True)
+    if hpo_match_only_with_umls:
+        df_hpo_umls = df_hpo_umls[df_hpo_umls['subject_id'].str.startswith('UMLS:')]
+    df_hpo_umls['mapping_justification'] = 'semapv:ManualMappingCuration'
     write_sssom(df_hpo_umls, input_sssom_config, OUTPUT_FILE_HPO_UMLS)
 
     # SSSOM 2: HPO<->MeSH
@@ -45,7 +52,10 @@ def run(input_mappings: str = INPUT_MAPPINGS, input_sssom_config: str = INPUT_CO
     df_hpo_mesh['object_id'] = df_hpo_mesh['object_id'].apply(lambda x: 'MESH:' + x)
     # todo: temp; (1) remove later: saving dataset with no matches, for review (2) after remove, will need to
     #  move the col removals below (umls) to above
-    write_sssom(df_hpo_mesh, input_sssom_config, OUTPUT_FILE_HPO_MESH.replace('.sssom.tsv', '-no-matches.sssom.tsv'))
+    # - add mapping_justification
+    df_hpo_mesh['mapping_justification'] = 'semapv:ManualMappingCuration'
+    write_sssom(df_hpo_mesh, input_sssom_config,
+                OUTPUT_FILE_HPO_MESH.replace('.sssom.tsv', '-non-matches-included.sssom.tsv'))
     # -- filter non-matches & drop unneeded cols
     df_hpo_mesh = df_hpo_mesh[df_hpo_mesh['subject_id'].notna()][[
         x for x in df_hpo_mesh.columns if not x.startswith('umls')]]

src/utils.py

@@ -1,10 +1,12 @@
 """Utils"""
-import os
 from pathlib import Path
-from typing import List, Set, Union
+from typing import Dict, List, Union
 
+import curies
 import pandas as pd
 import yaml
+from sssom import MappingSetDataFrame
+from sssom.writers import write_table
 
 
 def add_prefixes_to_plain_id(x: str) -> str:
@@ -21,53 +23,14 @@ def add_prefixes_to_plain_id(x: str) -> str:
         else f'MEDGEN:{x}'
 
 
-def find_prefixes_in_mapping_set(source_df: pd.DataFrame) -> Set[str]:
-    """Find prefixes in mapping set"""
-    df = source_df.copy()
-    cols_with_prefixes = ['subject_id', 'object_id', 'predicate_id']
-    prefixes = set()
-    for col in cols_with_prefixes:
-        col2 = col.replace('id', 'prefix')
-        df[col2] = df[col].apply(lambda x: x.split(':')[0]
-            if isinstance(x, str) else x)  # handles nan
-        prefixes.update(set(df[col2].to_list()))
-    return prefixes
-
-
 def write_sssom(df: pd.DataFrame, config_path: Union[Path, str], outpath: Union[Path, str]):
-    """Writes a SSSOM file with commented metadata at the top of the file.
-
-    Filters only prefxes in curie_map that exist in the mapping set."""
-    temp_filtered_config_path = str(config_path) + '.tmp'
-    # Load config
-    config = yaml.safe_load(open(config_path, 'r'))
-    # Filter curie_map
-    prefixes: Set[str] = find_prefixes_in_mapping_set(df)
-    config['curie_map'] = {k: v for k, v in config['curie_map'].items() if k in prefixes}
-    # Write
-    with open(temp_filtered_config_path, 'w') as f:
-        yaml.dump(config, f)
-    write_tsv_with_comments(df, temp_filtered_config_path, outpath)
-    os.remove(temp_filtered_config_path)
-
-
-def write_tsv_with_comments(df: pd.DataFrame, comments_file: Union[Path, str], outpath: Union[Path, str]):
-    """Write a TSV with comments at the top"""
-    # write metadata
-    f = open(comments_file, "r")
-    lines = f.readlines()
-    f.close()
-    output_lines = []
-    for line in lines:
-        output_lines.append("# " + line)
-    metadata_str = ''.join(output_lines)
-    if os.path.exists(outpath):
-        os.remove(outpath)
-    f = open(outpath, 'a')
-    f.write(metadata_str)
-    f.close()
-    # write data
-    df.to_csv(outpath, index=False, sep='\t', mode='a')
+    """Writes a SSSOM file"""
+    with open(config_path, 'r') as yaml_file:
+        metadata: Dict = yaml.load(yaml_file, Loader=yaml.FullLoader)
+    converter = curies.Converter.from_prefix_map(metadata['curie_map'])
+    msdf: MappingSetDataFrame = MappingSetDataFrame(converter=converter, df=df, metadata=metadata)
+    with open(outpath, 'w') as f:
+        write_table(msdf, f)
 
 
 # todo: for the SSSOM use case, it is weird to rename #CUI as xref_id. so maybe _get_mapping_set() should either not