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- Delete: Unnecessary files and goals: temp analysis, getting of ordo.owl and querying it via SPARQL. - Add: SSSOM validation - Update: Replaced ad hoc SSSOM utilities with the ones from sssom-py - Add: mondo-icd11 mappings
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,15 @@ | ||
| creator_id: 0000-0002-2906-7319 | ||
| creator_id: orcid:0000-0002-2906-7319 | ||
| curie_map: | ||
| Orphanet: http://www.orpha.net/ORDO/Orphanet_ | ||
| icd11.foundation: http://id.who.int/icd/entity/ | ||
| MONDO: http://purl.obolibrary.org/obo/MONDO_ | ||
| oboInOwl: http://www.geneontology.org/formats/oboInOwl# | ||
| orcid: https://orcid.org/ | ||
| owl: http://www.w3.org/2002/07/owl# | ||
| Orphanet: http://www.orpha.net/ORDO/Orphanet_ | ||
| rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# | ||
| rdfs: http://www.w3.org/2000/01/rdf-schema# | ||
| semapv: https://w3id.org/semapv/ | ||
| skos: http://www.w3.org/2004/02/skos/core# | ||
| sssom: https://w3id.org/sssom/ | ||
| license: http://w3id.org/sssom/license/unspecified | ||
| mapping_provider: https://www.orpha.net/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,3 @@ | ||
| pandas | ||
| pyyaml | ||
| sssom |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,60 @@ | ||
| distlib==0.3.6 | ||
| filelock==3.9.0 | ||
| numpy==1.25.1 | ||
| pandas==2.0.3 | ||
| pbr==5.11.1 | ||
| platformdirs==3.1.0 | ||
| python-dateutil==2.8.2 | ||
| pytz==2023.3 | ||
| 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==0.3.8 | ||
| exceptiongroup==1.2.0 | ||
| filelock==3.13.1 | ||
| 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==1.26.4 | ||
| packaging==24.0 | ||
| pandas==2.2.1 | ||
| pansql==0.0.1 | ||
| pbr==6.0.0 | ||
| platformdirs==4.2.0 | ||
| 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==2.9.0.post0 | ||
| PyTrie==0.4.0 | ||
| pytz==2024.1 | ||
| 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 | ||
| stevedore==5.0.0 | ||
| tzdata==2023.3 | ||
| virtualenv==20.20.0 | ||
| sortedcontainers==2.4.0 | ||
| SPARQLWrapper==2.0.0 | ||
| SQLAlchemy==2.0.29 | ||
| sssom==0.4.6 | ||
| sssom-schema==0.15.2 | ||
| stevedore==5.1.0 | ||
| tomli==2.0.1 | ||
| typing_extensions==4.11.0 | ||
| tzdata==2024.1 | ||
| urllib3==2.2.1 | ||
| validators==0.28.0 | ||
| virtualenv==20.25.0 | ||
| virtualenv-clone==0.5.7 | ||
| wrapt==1.16.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,56 +1,20 @@ | ||
| """Utilities""" | ||
| import os | ||
| from pathlib import Path | ||
| from typing import Set, Union | ||
| from typing import Dict, Union | ||
|
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| import curies | ||
| import pandas as pd | ||
| import yaml | ||
| from sssom import MappingSetDataFrame | ||
| from sssom.writers import write_table | ||
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| 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 | ||
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| # todo: Add to sssom-py. Shared between, at the least, ICD11 and MedGen repos | ||
| 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) | ||
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| 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) |