From 97b84923f3f5841e5fd78ea0ca88443c51f97d74 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 29 Apr 2024 12:54:33 -0700 Subject: [PATCH] Added SDGIO --- ontologies.Makefile | 15 +- poetry.lock | 1174 ++++++++--------- pyproject.toml | 2 + src/semsql/builder/prefixes/prefixes.csv | 2 +- .../builder/prefixes/prefixes_local.csv | 1 + src/semsql/builder/registry/ontologies.yaml | 4 + 6 files changed, 599 insertions(+), 599 deletions(-) diff --git a/ontologies.Makefile b/ontologies.Makefile index bcec603..eb569ad 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -219,7 +219,7 @@ db/mondo-ingest.owl: download/mondo-ingest.owl download/oeo.owl: STAMP - curl -L -s http://openenergy-platform.org/ontology/oeo/ > $@.tmp + curl -L -s https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 mv $@.tmp $@ @@ -229,6 +229,17 @@ db/oeo.owl: download/oeo.owl cp $< $@ +download/sdgio.owl: STAMP + curl -L -s https://raw.githubusercontent.com/SDG-InterfaceOntology/sdgio/master/sdgio.owl > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/sdgio.owl + +db/sdgio.owl: download/sdgio.owl + cp $< $@ + + download/biovoices.owl: STAMP curl -L -s https://zenodo.org/record/5589773/files/ontology.owl?download=1 > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -921,4 +932,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo biovoices omop cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time +EXTRA_ONTOLOGIES = upheno chiro ncit fma maxo foodon chebiplus msio modl phenio phenio_test comploinc bero aio reacto bcio icd10who ordo gard mondo-ingest oeo sdgio biovoices omop cco occo iof upa go go-lego go-amigo neo bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo hcao hpinternational edam sweetAll lov schema-dot-org prov cellosaurus cosmo fhkb dbpendiaont uberoncm icd10cm co_324 ppeo interpro hgnc.genegroup hgnc sgd dictybase eccode uniprot rhea swisslipid drugbank drugcentral complexportal wikipathways drugmechdb rxnorm vccf ontobiotope nando ontie ecosim nmdc_schema mixs fibo bfo2020 bfo2020_core bfo2020_notime bfo2020_time diff --git a/poetry.lock b/poetry.lock index a4eb44e..12ad757 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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{file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"}, - {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"}, + {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"}, + {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, ] [[package]] name = "importlib-metadata" version = "7.1.0" description = "Read metadata from Python packages" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -906,7 +948,6 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", name = "importlib-resources" version = "6.4.0" description = "Read resources from Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -925,7 +966,6 @@ testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "p name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -937,7 +977,6 @@ files = [ name = "ipykernel" version = "6.29.4" description = "IPython Kernel for Jupyter" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -951,7 +990,7 @@ comm = ">=0.1.1" debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" @@ -971,7 +1010,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio name = "ipython" version = "8.12.3" description = "IPython: Productive Interactive Computing" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1011,7 +1049,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pa name = "ipython-genutils" version = "0.2.0" description = "Vestigial utilities from IPython" -category = "dev" optional = false python-versions = "*" files = [ @@ -1023,7 +1060,6 @@ files = [ name = "ipython-sql" version = "0.4.1" description = "RDBMS access via IPython" -category = "dev" optional = false python-versions = "*" files = [ @@ -1043,7 +1079,6 @@ sqlparse = "*" name = "ipywidgets" version = "8.1.2" description = "Jupyter interactive widgets" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1065,7 +1100,6 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"] name = "isodate" version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" -category = "main" optional = false python-versions = "*" files = [ @@ -1080,7 +1114,6 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1095,7 +1128,6 @@ arrow = ">=0.15.0" name = "jedi" version = "0.19.1" description = "An autocompletion tool for Python that can be used for text editors." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1115,7 +1147,6 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] name = "jinja2" version = "3.1.3" description = "A very fast and expressive template engine." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1133,7 +1164,6 @@ i18n = ["Babel (>=2.7)"] name = "jsbeautifier" version = "1.15.1" description = "JavaScript unobfuscator and beautifier." -category = "dev" optional = false python-versions = "*" files = [ @@ -1148,7 +1178,6 @@ six = ">=1.13.0" name = "json-flattener" version = "0.1.9" description = "Python library for denormalizing nested dicts or json objects to tables and back" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -1162,21 +1191,19 @@ pyyaml = "*" [[package]] name = "json5" -version = "0.9.24" +version = "0.9.25" description = "A Python implementation of the JSON5 data format." -category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "json5-0.9.24-py3-none-any.whl", hash = "sha256:4ca101fd5c7cb47960c055ef8f4d0e31e15a7c6c48c3b6f1473fc83b6c462a13"}, - {file = "json5-0.9.24.tar.gz", hash = "sha256:0c638399421da959a20952782800e5c1a78c14e08e1dc9738fa10d8ec14d58c8"}, + {file = "json5-0.9.25-py3-none-any.whl", hash = "sha256:34ed7d834b1341a86987ed52f3f76cd8ee184394906b6e22a1e0deb9ab294e8f"}, + {file = "json5-0.9.25.tar.gz", hash = "sha256:548e41b9be043f9426776f05df8635a00fe06104ea51ed24b67f908856e151ae"}, ] [[package]] name = "jsonasobj" version = "1.3.1" description = "JSON as python objects" -category = "dev" optional = false python-versions = "*" files = [ @@ -1188,7 +1215,6 @@ files = [ name = "jsonasobj2" version = "1.0.4" description = "JSON as python objects - version 2" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1203,7 +1229,6 @@ hbreader = "*" name = "jsonpatch" version = "1.33" description = "Apply JSON-Patches (RFC 6902)" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1218,7 +1243,6 @@ jsonpointer = ">=1.9" name = "jsonpath-ng" version = "1.6.1" description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming." -category = "dev" optional = false python-versions = "*" files = [ @@ -1233,7 +1257,6 @@ ply = "*" name = "jsonpointer" version = "2.4" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1245,7 +1268,6 @@ files = [ name = "jsonschema" version = "4.21.1" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1278,7 +1300,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.12.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1294,7 +1315,6 @@ referencing = ">=0.31.0" name = "jupyter" version = "1.0.0" description = "Jupyter metapackage. Install all the Jupyter components in one go." -category = "dev" optional = false python-versions = "*" files = [ @@ -1315,7 +1335,6 @@ qtconsole = "*" name = "jupyter-client" version = "8.6.1" description = "Jupyter protocol implementation and client libraries" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1325,7 +1344,7 @@ files = [ [package.dependencies] importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" @@ -1339,7 +1358,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt name = "jupyter-console" version = "6.6.3" description = "Jupyter terminal console" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1351,7 +1369,7 @@ files = [ ipykernel = ">=6.14" ipython = "*" jupyter-client = ">=7.0.0" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" prompt-toolkit = ">=3.0.30" pygments = "*" pyzmq = ">=17" @@ -1364,7 +1382,6 @@ test = ["flaky", "pexpect", "pytest"] name = "jupyter-core" version = "5.7.2" description = "Jupyter core package. A base package on which Jupyter projects rely." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1385,7 +1402,6 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout" name = "jupyter-events" version = "0.10.0" description = "Jupyter Event System library" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1409,14 +1425,13 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p [[package]] name = "jupyter-lsp" -version = "2.2.4" +version = "2.2.5" description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server" -category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "jupyter-lsp-2.2.4.tar.gz", hash = "sha256:5e50033149344065348e688608f3c6d654ef06d9856b67655bd7b6bac9ee2d59"}, - {file = "jupyter_lsp-2.2.4-py3-none-any.whl", hash = "sha256:da61cb63a16b6dff5eac55c2699cc36eac975645adee02c41bdfc03bf4802e77"}, + {file = "jupyter-lsp-2.2.5.tar.gz", hash = "sha256:793147a05ad446f809fd53ef1cd19a9f5256fd0a2d6b7ce943a982cb4f545001"}, + {file = "jupyter_lsp-2.2.5-py3-none-any.whl", hash = "sha256:45fbddbd505f3fbfb0b6cb2f1bc5e15e83ab7c79cd6e89416b248cb3c00c11da"}, ] [package.dependencies] @@ -1425,46 +1440,44 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.13.0" +version = "2.14.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." -category = "dev" optional = false python-versions = ">=3.8" files = [ - 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"typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"}, + {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, + {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, ] [[package]] name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3768,7 +3739,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "2.2.1" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3782,11 +3752,30 @@ h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] +[[package]] +name = "virtualenv" +version = "20.26.1" +description = "Virtual Python Environment builder" +optional = false +python-versions = ">=3.7" +files = [ + {file = "virtualenv-20.26.1-py3-none-any.whl", hash = "sha256:7aa9982a728ae5892558bff6a2839c00b9ed145523ece2274fad6f414690ae75"}, + {file = "virtualenv-20.26.1.tar.gz", hash = "sha256:604bfdceaeece392802e6ae48e69cec49168b9c5f4a44e483963f9242eb0e78b"}, +] + +[package.dependencies] +distlib = ">=0.3.7,<1" +filelock = ">=3.12.2,<4" +platformdirs = ">=3.9.1,<5" + +[package.extras] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] + [[package]] name = "watchdog" version = "4.0.0" description = "Filesystem events monitoring" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3828,7 +3817,6 @@ watchmedo = ["PyYAML (>=3.10)"] name = "wcwidth" version = "0.2.13" description = "Measures the displayed width of unicode strings in a terminal" -category = "dev" optional = false python-versions = "*" files = [ @@ -3840,7 +3828,6 @@ files = [ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3856,7 +3843,6 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "dev" optional = false python-versions = "*" files = [ @@ -3866,18 +3852,17 @@ files = [ [[package]] name = "websocket-client" -version = "1.7.0" +version = "1.8.0" description = "WebSocket client for Python with low level API options" -category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"}, - {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"}, + {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, + {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, ] [package.extras] -docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] @@ -3885,7 +3870,6 @@ test = ["websockets"] name = "widgetsnbextension" version = "4.0.10" description = "Jupyter interactive widgets for Jupyter Notebook" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3897,7 +3881,6 @@ files = [ name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3977,7 +3960,6 @@ files = [ name = "zipp" version = "3.18.1" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3992,4 +3974,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8.1" -content-hash = "78411e9dade75915a8a6b9f71a8537a9199b643cd248d769457be7cc1a0d3dc0" +content-hash = "0844636a8a5c5cc804871b7e7e3c8c99f53ac4c7f66a8f75de429a6cb7289e02" diff --git a/pyproject.toml b/pyproject.toml index 8eed1e4..845e939 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,6 +17,8 @@ linkml = ">=1.7.4" mkdocs-mermaid2-plugin = "^0.6.0" jupyter = "^1.0.0" ipython-sql = "^0.4.1" +tox = "*" +black = "*" [tool.poetry.scripts] semsql = "semsql.builder.cli:main" diff --git a/src/semsql/builder/prefixes/prefixes.csv b/src/semsql/builder/prefixes/prefixes.csv index afa6299..093b53c 100644 --- a/src/semsql/builder/prefixes/prefixes.csv +++ b/src/semsql/builder/prefixes/prefixes.csv @@ -72,12 +72,12 @@ loinc,https://loinc.org/ BCIO,http://humanbehaviourchange.org/ontology/BCIO_ BCIOR,http://humanbehaviourchange.org/ontology/BCIOR_ icd10who,https://icd.who.int/browse10/2019/en#/ -icd11f,http://id.who.int/icd/entity/ GARD,http://purl.obolibrary.org/obo/GARD_ OMIM,https://omim.org/entry/ OMIMPS,https://www.omim.org/phenotypicSeries/PS CHR,http://purl.obolibrary.org/obo/CHR_ OEO,http://openenergy-platform.org/ontology/oeo/OEO_ +SDGIO,http://purl.unep.org/sdg/SDGIO_ ontorion,http://ontorion.com/namespace# omop,https://athena.ohdsi.org/search-terms/terms/ CCO,http://www.ontologyrepository.com/CommonCoreOntologies/ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index bebb757..cf5ec45 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -14,6 +14,7 @@ OMIM,https://omim.org/entry/ OMIMPS,https://www.omim.org/phenotypicSeries/PS CHR,http://purl.obolibrary.org/obo/CHR_ OEO,http://openenergy-platform.org/ontology/oeo/OEO_ +SDGIO,http://purl.unep.org/sdg/SDGIO_ ontorion,http://ontorion.com/namespace# omop,https://athena.ohdsi.org/search-terms/terms/ CCO,http://www.ontologyrepository.com/CommonCoreOntologies/ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 59e95cc..272ddc6 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -98,6 +98,10 @@ ontologies: url: https://openenergyplatform.org/ontology/oeo/releases/oeo-full.owl prefixmap: OEO: http://openenergy-platform.org/ontology/oeo/OEO_ + sdgio: + url: https://raw.githubusercontent.com/SDG-InterfaceOntology/sdgio/master/sdgio.owl + prefixmap: + SDGIO: http://purl.unep.org/sdg/SDGIO_ biovoices: url: https://zenodo.org/record/5589773/files/ontology.owl?download=1 build_command: "robot relax -i $< merge -o $@"