Add Mammalian Phenotype Ontology

config.json

@@ -12,7 +12,7 @@
   "UMLS_UniProtKB_download_raw_url": "https://raw.githubusercontent.com/cbizon/UMLS_UniProtKB/refs/heads/main/outputs/UMLS_UniProtKB.tsv",
 
   "ncbi_files": ["gene2ensembl.gz", "gene_info.gz", "gene_orthologs.gz", "gene_refseq_uniprotkb_collab.gz", "mim2gene_medgen"],
-  "ubergraph_ontologies": ["UBERON", "CL", "GO", "NCIT", "ECO", "ECTO", "ENVO", "HP", "UPHENO","BFO","BSPO","CARO","CHEBI","CP","GOREL","IAO","MAXO","MONDO","PATO","PR","RO","UBPROP"],
+  "ubergraph_ontologies": ["UBERON", "CL", "GO", "NCIT", "ECO", "ECTO", "ENVO", "HP", "MP", "UPHENO","BFO","BSPO","CARO","CHEBI","CP","GOREL","IAO","MAXO","MONDO","PATO","PR","RO","UBPROP"],
   "mods": ["WormBase","FB","MGI","ZFIN","RGD","SGD"],
 
   "anatomy_prefixes": ["UBERON","GO","CL","UMLS","MESH","NCIT","SNOMEDCT"],
@@ -31,9 +31,9 @@
   "protein_concords": ["UniProtKB","PR","NCIT_UniProtKB","NCIT_UMLS", "UMLS_UniProtKB"],
   "protein_outputs": ["Protein.txt"],
 
-  "disease_labelsandsynonyms": ["MONDO","DOID","Orphanet","HP","MESH","NCIT","UMLS","SNOMEDCT","EFO"],
-  "disease_ids": ["MONDO","DOID","Orphanet","HP","MESH","NCIT","UMLS","OMIM","EFO"],
-  "disease_concords": ["HP","MONDO","UMLS","DOID","EFO", "Manual"],
+  "disease_labelsandsynonyms": ["MONDO","DOID","Orphanet","HP","MP","MESH","NCIT","UMLS","SNOMEDCT","EFO"],
+  "disease_ids": ["MONDO","DOID","Orphanet","HP","MP","MESH","NCIT","UMLS","OMIM","EFO"],
+  "disease_concords": ["HP","MONDO","UMLS","DOID","EFO", "HP_MP","Manual"],
   "disease_outputs": ["Disease.txt", "PhenotypicFeature.txt"],
 
   "process_labels": ["GO","REACT","RHEA","EC","SMPDB","PANTHER.PATHWAY"],

requirements.lock

@@ -1,168 +1,190 @@
-aiohttp==3.8.4
+aiohttp==3.9.1
+aioredis==1.3.1
 aiosignal==1.3.1
-airium==0.2.5
+airium==0.2.6
+annotated-types==0.6.0
 antlr4-python3-runtime==4.9.3
-anyio==3.7.0
+anyio==3.7.1
 appdirs==1.4.4
 apybiomart==0.5.3
-async-timeout==4.0.2
+asgiref==3.7.2
+async-timeout==4.0.3
 asyncio==3.4.3
 attrs==23.1.0
-Babel==2.12.1
+Babel==2.13.1
 bcp47==0.0.4
 beautifulsoup4==4.12.2
 biopython==1.81
-bmt==1.1.1
-cattrs==23.1.2
-certifi==2023.5.7
-cffconvert==2.0.0
+bmt==1.1.3
+cachetools==5.3.2
+cattrs==23.2.2
+certifi==2023.11.17
 chardet==5.2.0
-charset-normalizer==3.1.0
+charset-normalizer==3.3.2
 class-resolver==0.4.2
 click==8.1.7
 colorama==0.4.6
 ConfigArgParse==1.7
 connection-pool==0.0.3
-coverage==7.3.0
-curies==0.6.0
+coverage==7.3.2
+curies==0.6.7
 datrie==0.8.2
+deepdiff==5.8.1
 Deprecated==1.2.14
 deprecation==2.1.0
-docopt==0.6.2
+distlib==0.3.7
+docker==6.1.3
 docutils==0.20.1
 dpath==2.1.6
 EditorConfig==0.12.3
-elasticsearch==7.16.3
 eutils==0.6.0
-fastapi==0.95.0
-fastjsonschema==2.18.0
+fastapi==0.83.0
+fastjsonschema==2.19.0
 fastobo==0.12.2
-frozenlist==1.3.3
+filelock==3.13.1
+frozenlist==1.4.0
 funowl==0.2.3
 ghp-import==2.1.0
-gitdb==4.0.10
-GitPython==3.1.34
-greenlet==2.0.1
+gitdb==4.0.11
+GitPython==3.1.40
+greenlet==3.0.1
 gunicorn==20.1.0
-h11==0.14.0
+h11==0.12.0
 hbreader==0.9.1
+hiredis==2.2.3
+httpcore==0.15.0
+httptools==0.5.0
+httpx==0.23.0
 humanfriendly==10.0
-idna==3.4
+idna==3.6
 ijson==3.2.3
 importlib-metadata==6.8.0
 iniconfig==2.0.0
 isodate==0.6.1
-itsdangerous==2.1.2
 Jinja2==3.1.2
-jsbeautifier==1.14.9
+jsbeautifier==1.14.11
 json-flattener==0.1.9
 jsonasobj==1.3.1
 jsonasobj2==1.0.4
 jsonlines==4.0.0
-jsonschema==3.2.0
-jupyter_core==5.3.1
+jsonschema==4.6.2
+jsonschema-specifications==2023.11.1
+jupyter_core==5.5.0
 kgcl-rdflib==0.5.0
 kgcl-schema==0.6.0
-lark==1.1.7
+lark==1.1.8
 linkml-renderer==0.3.0
-linkml-runtime==1.5.6
+linkml-runtime==1.6.2
 lxml==4.9.3
-Markdown==3.4.4
+Markdown==3.5.1
 MarkupSafe==2.1.3
 mergedeep==1.3.4
-mistune==2.0.3
-mkdocs==1.5.2
-mkdocs-material==9.2.7
-mkdocs-material-extensions==1.1.1
+mkdocs==1.5.3
+mkdocs-material==9.4.14
+mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==0.6.0
 more-click==0.1.2
 more-itertools==10.1.0
 multidict==6.0.4
 nbformat==5.9.2
-ndex2==3.5.1
-networkx==3.1
-numpy==1.25.2
-oaklib==0.5.18
+ndex2==3.6.0
+networkx==3.2.1
+numpy==1.26.2
+oaklib==0.5.22
 ols-client==0.1.4
 ontoportal-client==0.0.4
-packaging==23.1
+ordered-set==4.1.0
+orjson==3.8.10
+packaging==23.2
 paginate==0.5.6
-pandas==2.1.0
+pandas==2.1.3
 pansql==0.0.1
 pathspec==0.11.2
-plac==1.3.5
-platformdirs==3.10.0
-pluggy==1.0.0
+plac==1.4.1
+platformdirs==4.0.0
+pluggy==1.3.0
 prefixcommons==0.1.12
-prefixmaps==0.1.5
+prefixmaps==0.1.7
 pronto==2.5.5
-psutil==5.9.5
-psycopg2-binary==2.9.7
+psutil==5.9.6
+psycopg2-binary==2.9.9
 PuLP==2.7.0
-pydantic==1.10.9
-Pygments==2.16.1
+py==1.11.0
+pydantic==1.10.13
+pydantic_core==2.14.5
+Pygments==2.17.2
 PyJSG==0.11.10
-pykwalify==1.8.0
-pymdown-extensions==10.3
+pymdown-extensions==10.5
 pyoxigraph==0.2.5
 pyparsing==3.1.1
-pyrsistent==0.17.3
+pyproject-api==1.6.1
+pyrsistent==0.20.0
 pysolr==3.9.0
-pystow==0.5.0
-pytest==7.3.2
-pytest-cov==4.1.0
+pystow==0.5.2
+pytest==6.2.5
+pytest-asyncio==0.18.3
+pytest-cov==3.0.0
 pytest-logging==2015.11.4
 python-dateutil==2.8.2
 python-Levenshtein-wheels==0.13.2
 PyTrie==0.4.0
-pytz==2021.1
+pytz==2023.3.post1
 PyYAML==6.0.1
 pyyaml_env_tag==0.1
 ratelimit==2.2.1
 rdflib==7.0.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
-redis==4.4.2
-regex==2022.10.31
-requests==2.28.2
-requests-cache==1.1.0
+reasoner-pydantic==4.1.5
+redis==3.5.3
+redis-py-cluster==2.1.3
+referencing==0.31.0
+regex==2023.10.3
+requests==2.31.0
+requests-cache==1.1.1
 requests-toolbelt==1.0.0
 reretry==0.11.8
+rfc3986==1.5.0
 rfc3987==1.3.8
-ruamel.yaml==0.17.26
-ruamel.yaml.clib==0.2.7
-scipy==1.11.2
+rpds-py==0.13.1
+scipy==1.11.4
 semsimian==0.2.1
 semsql==0.3.2
 six==1.16.0
-smart-open==6.3.0
-smmap==5.0.0
-snakemake==7.32.3
+smart-open==6.4.0
+smmap==5.0.1
+snakemake==7.32.4
 sniffio==1.3.0
 sortedcontainers==2.4.0
 soupsieve==2.5
 SPARQLWrapper==2.0.0
-SQLAlchemy==2.0.20
+SQLAlchemy==2.0.23
 SQLAlchemy-Utils==0.38.3
-sssom==0.3.40
+sssom==0.3.41
 sssom-schema==0.15.0
-starlette==0.26.1
+starlette==0.19.1
 stopit==1.1.2
 stringcase==1.2.0
 tabulate==0.9.0
+testcontainers==3.6.1
 throttler==1.2.2
+toml==0.10.2
 toposort==1.10
+tox==4.11.3
 tqdm==4.66.1
-traitlets==5.9.0
-typing_extensions==4.6.3
+traitlets==5.13.0
+typing_extensions==4.8.0
 tzdata==2023.3
 url-normalize==1.4.3
-urllib3==1.26.16
-uvicorn==0.22.0
+urllib3==2.1.0
+uvicorn==0.17.6
+uvloop==0.17.0
 validators==0.22.0
+virtualenv==20.24.7
 watchdog==3.0.0
-wrapt==1.15.0
+websocket-client==1.6.4
+wrapt==1.16.0
 xmltodict==0.13.0
-yarl==1.9.2
+yarl==1.9.3
 yte==1.5.1
-zipp==3.16.2
+zipp==3.17.0

requirements.txt

@@ -25,3 +25,5 @@ beautifulsoup4
 curies
 # Added by Gaurav, May 2024
 duckdb
+# Added by Gaurav, Jul 2024
+sssom