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laminlabs / bionty-base

Access public biological ontologies.
https://bionty-base.lamin.ai
Apache License 2.0
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✅ New records found in the public sources.yaml, updated /home/zeth/.lamin/bionty/versions/sources.local.yaml! #432

Closed Zethson closed 1 year ago

Zethson commented 1 year ago

Every time I import Bionty. Might be confusing for new users.

sunnyosun commented 1 year ago

Hmm, it doesn't log that for me, and based on the code, it should only logs when there's an update in the public source.yaml:https://github.com/laminlabs/bionty/blob/main/bionty/dev/_handle_sources.py#L162-L169

Could you try to print additional_records from the above function, and see why it's doing it every time?

Zethson commented 1 year ago

[{'entity': 'Species', 'source': 'ensembl', 'species': 'all', 'version': 'release-108', 'url': 'https://ftp.ensembl.org/pub/release-108/species_EnsemblVertebrates.txt', 'md5': '', 'source_name': 'Ensembl', 'source_website': 'https://www.ensembl.org/index.html'}, {'entity': 'Gene', 'source': 'ensembl', 'species': 'human', 'version': 'release-108', 'url': 'https://ftp.ensembl.org/pub/release-108/mysql/homo_sapiens_core_108_38/', 'md5': '', 'source_name': 'Ensembl', 'source_website': 'https://www.ensembl.org/index.html'}, {'entity': 'Gene', 'source': 'ensembl', 'species': 'human', 'version': 'release-107', 'url': 'https://ftp.ensembl.org/pub/release-107/mysql/homo_sapiens_core_107_38/', 'md5': '', 'source_name': 'Ensembl', 'source_website': 'https://www.ensembl.org/index.html'}, {'entity': 'Gene', 'source': 'ensembl', 'species': 'mouse', 'version': 'release-108', 'url': 'https://ftp.ensembl.org/pub/release-108/mysql/mus_musculus_core_108_39/', 'md5': '', 'source_name': 'Ensembl', 'source_website': 'https://www.ensembl.org/index.html'}, {'entity': 'Protein', 'source': 'uniprot', 'species': 'human', 'version': '2022-04', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_04/', 'md5': '', 'source_name': 'Uniprot', 'source_website': 'https://www.uniprot.org/'}, {'entity': 'Protein', 'source': 'uniprot', 'species': 'human', 'version': '2022-03', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_03/', 'md5': '', 'source_name': 'Uniprot', 'source_website': 'https://www.uniprot.org/'}, {'entity': 'Protein', 'source': 'uniprot', 'species': 'mouse', 'version': '2022-04', 'url': 'https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_04/', 'md5': '', 'source_name': 'Uniprot', 'source_website': 'https://www.uniprot.org/'}, {'entity': 'CellMarker', 'source': 'cellmarker', 'species': 'human', 'version': '2.0', 'url': 'http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx', 'md5': '', 'source_name': 'CellMarker', 'source_website': 'http://bio-bigdata.hrbmu.edu.cn/CellMarker/'}, {'entity': 'CellMarker', 'source': 'cellmarker', 'species': 'mouse', 'version': '2.0', 'url': 'http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx', 'md5': '', 'source_name': 'CellMarker', 'source_website': 'http://bio-bigdata.hrbmu.edu.cn/CellMarker/'}, {'entity': 'CellLine', 'source': 'clo', 'species': 'all', 'version': '2022-03-21', 'url': 'https://data.bioontology.org/ontologies/CLO/submissions/65/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb', 'md5': 'ea58a1010b7e745702a8397a526b3a33', 'source_name': 'Cell Line Ontology', 'source_website': 'https://bioportal.bioontology.org/ontologies/CLO'}, {'entity': 'CellType', 'source': 'cl', 'species': 'all', 'version': '2023-02-15', 'url': 'http://purl.obolibrary.org/obo/cl/releases/2023-02-15/cl-base.owl', 'md5': '9331a6a029cb1863bd0584ab41508df7', 'source_name': 'Cell Ontology', 'source_website': 'https://obophenotype.github.io/cell-ontology/'}, {'entity': 'CellType', 'source': 'cl', 'species': 'all', 'version': '2022-08-16', 'url': 'http://purl.obolibrary.org/obo/cl/releases/2022-08-16/cl.owl', 'md5': 'd0655766574e63f3fe5ed56d3c030880', 'source_name': 'Cell Ontology', 'source_website': 'https://obophenotype.github.io/cell-ontology/'}, {'entity': 'Tissue', 'source': 'uberon', 'species': 'all', 'version': '2023-02-14', 'url': 'http://purl.obolibrary.org/obo/uberon/releases/2023-02-14/uberon.owl', 'md5': '3f94e22fae4cdde88a555c5cd59c47da', 'source_name': 'Uberon multi-species anatomy ontology', 'source_website': 'http://obophenotype.github.io/uberon/'}, {'entity': 'Tissue', 'source': 'uberon', 'species': 'all', 'version': '2022-08-19', 'url': 'http://purl.obolibrary.org/obo/uberon/releases/2022-08-19/uberon.owl', 'md5': 'c7c958a1ee48fdce146f2c1763eed27e', 'source_name': 'Uberon multi-species anatomy ontology', 'source_website': 'http://obophenotype.github.io/uberon/'}, {'entity': 'Disease', 'source': 'mondo', 'species': 'all', 'version': '2023-02-06', 'url': 'http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl', 'md5': '2b7d479d4bd02a94eab47d1c9e64c5db', 'source_name': 'Mondo Disease Ontology', 'source_website': 'https://mondo.monarchinitiative.org/'}, {'entity': 'Disease', 'source': 'mondo', 'species': 'all', 'version': '2022-10-11', 'url': 'http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl', 'md5': '04b808d05c2c2e81430b20a0e87552bb', 'source_name': 'Mondo Disease Ontology', 'source_website': 'https://mondo.monarchinitiative.org/'}, {'entity': 'Disease', 'source': 'doid', 'species': 'human', 'version': '2023-01-30', 'url': 'http://purl.obolibrary.org/obo/doid/releases/2023-01-30/doid.obo', 'md5': '9f0c92ad2896dda82195e9226a06dc36', 'source_name': 'Human Disease Ontology', 'source_website': 'https://disease-ontology.org/'}, {'entity': 'Readout', 'source': 'efo', 'species': 'all', 'version': '3.48.0', 'url': 'http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl', 'md5': '3367e9a9ae3dee9113024e5108c49091', 'source_name': 'The Experimental Factor Ontology', 'source_website': 'https://bioportal.bioontology.org/ontologies/EFO'}, {'entity': 'Phenotype', 'source': 'hp', 'species': 'human', 'version': '2023-01-27', 'url': 'https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-01-27/hp.owl', 'md5': 'ceeb3ada771908deef620d74cd8e6b0f', 'source_name': 'Human Phenotype Ontology', 'source_website': 'https://hpo.jax.org/'}, {'entity': 'Pathway', 'source': 'go', 'species': 'all', 'version': '2023-05-10', 'url': 'https://data.bioontology.org/ontologies/GO/submissions/1814/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb', 'md5': '', 'source_name': 'Gene Ontology', 'source_website': 'http://geneontology.org/docs/download-ontology/'}, {'entity': 'Pathway', 'source': 'pw', 'species': 'all', 'version': '7.79', 'url': 'https://data.bioontology.org/ontologies/PW/submissions/109/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb', 'md5': '02e2337bb1ab7cc4332ef6acc4cbdfa6', 'source_name': 'Pathway Ontology', 'source_website': 'https://www.ebi.ac.uk/ols/ontologies/pw'}, {'entity': 'BFXPipeline', 'source': 'lamin', 'species': 'all', 'version': '1.0.0', 'url': 's3://bionty-assets/bfxpipelines.json', 'md5': '', 'source_name': 'Bioinformatics Pipeline', 'source_website': 'https://lamin.ai'}, {'entity': 'Drug', 'source': 'dron', 'species': 'all', 'version': '2023-03-10', 'url': 'https://data.bioontology.org/ontologies/DRON/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb', 'md5': '', 'source_name': 'Drug Ontology', 'source_website': 'https://bioportal.bioontology.org/ontologies/DRON/?p=summary'}]

is the output

Zethson commented 1 year ago

source.local.yaml

version: 0.2.0 Species: ensembl: all: release-108: source: https://ftp.ensembl.org/pub/release-108/species_EnsemblVertebrates.txt md5: '' name: Ensembl website: https://www.ensembl.org/index.html Gene: ensembl: human: release-108: source: https://ftp.ensembl.org/pub/release-108/mysql/homo_sapiens_core_108_38/ md5: '' release-107: source: https://ftp.ensembl.org/pub/release-107/mysql/homo_sapiens_core_107_38/ md5: '' name: Ensembl website: https://www.ensembl.org/index.html mouse: release-108: source: https://ftp.ensembl.org/pub/release-108/mysql/mus_musculus_core_108_39/ md5: '' Protein: uniprot: human: 2022-04: source: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_04/ md5: '' 2022-03: source: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_03/ md5: '' name: Uniprot website: https://www.uniprot.org/ mouse: 2022-04: source: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_04/ md5: '' CellMarker: cellmarker: human: '2.0': source: http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx md5: '' name: CellMarker website: http://bio-bigdata.hrbmu.edu.cn/CellMarker/ mouse: '2.0': source: http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx md5: '' CellLine: clo: all: '2022-03-21': source: https://data.bioontology.org/ontologies/CLO/submissions/65/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: ea58a1010b7e745702a8397a526b3a33 name: Cell Line Ontology website: https://bioportal.bioontology.org/ontologies/CLO CellType: cl: all: '2023-02-15': source: http://purl.obolibrary.org/obo/cl/releases/2023-02-15/cl-base.owl md5: 9331a6a029cb1863bd0584ab41508df7 '2022-08-16': source: http://purl.obolibrary.org/obo/cl/releases/2022-08-16/cl.owl md5: d0655766574e63f3fe5ed56d3c030880 name: Cell Ontology website: https://obophenotype.github.io/cell-ontology/ Tissue: uberon: all: '2023-02-14': source: http://purl.obolibrary.org/obo/uberon/releases/2023-02-14/uberon.owl md5: 3f94e22fae4cdde88a555c5cd59c47da '2022-08-19': source: http://purl.obolibrary.org/obo/uberon/releases/2022-08-19/uberon.owl md5: c7c958a1ee48fdce146f2c1763eed27e name: Uberon multi-species anatomy ontology website: http://obophenotype.github.io/uberon/ Disease: mondo: all: '2023-02-06': source: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl md5: 2b7d479d4bd02a94eab47d1c9e64c5db '2022-10-11': source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl md5: 04b808d05c2c2e81430b20a0e87552bb name: Mondo Disease Ontology website: https://mondo.monarchinitiative.org/ doid: human: '2023-01-30': source: http://purl.obolibrary.org/obo/doid/releases/2023-01-30/doid.obo md5: 9f0c92ad2896dda82195e9226a06dc36 name: Human Disease Ontology website: https://disease-ontology.org/ Readout: efo: all: 3.48.0: source: http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl md5: 3367e9a9ae3dee9113024e5108c49091 name: The Experimental Factor Ontology website: https://bioportal.bioontology.org/ontologies/EFO Phenotype: hp: human: '2023-01-27': source: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-01-27/hp.owl md5: ceeb3ada771908deef620d74cd8e6b0f name: Human Phenotype Ontology website: https://hpo.jax.org/ Pathway: go: all: '2023-05-10': source: https://data.bioontology.org/ontologies/GO/submissions/1814/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: '' name: Gene Ontology website: http://geneontology.org/docs/download-ontology/ pw: all: '7.79': source: https://data.bioontology.org/ontologies/PW/submissions/109/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: 02e2337bb1ab7cc4332ef6acc4cbdfa6 name: Pathway Ontology website: https://www.ebi.ac.uk/ols/ontologies/pw BFXPipeline: lamin: all: 1.0.0: source: s3://bionty-assets/bfxpipelines.json md5: '' name: Bioinformatics Pipeline website: https://lamin.ai Drug: dron: all: '2023-03-10': source: https://data.bioontology.org/ontologies/DRON/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: '' name: Drug Ontology website: https://bioportal.bioontology.org/ontologies/DRON/?p=summary

Zethson commented 1 year ago

source.yaml

version: "0.2.0" Species: ensembl: all: release-108: url: https://ftp.ensembl.org/pub/release-108/species_EnsemblVertebrates.txt name: Ensembl website: https://www.ensembl.org/index.html Gene: ensembl: human: release-108: url: https://ftp.ensembl.org/pub/release-108/mysql/homo_sapiens_core_108_38/ release-107: url: https://ftp.ensembl.org/pub/release-107/mysql/homo_sapiens_core_107_38/ mouse: release-108: url: https://ftp.ensembl.org/pub/release-108/mysql/mus_musculus_core_108_39/ name: Ensembl website: https://www.ensembl.org/index.html Protein: uniprot: human: 2022-04: url: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_04/ 2022-03: url: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_03/ mouse: 2022-04: url: https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2022_04/ name: Uniprot website: https://www.uniprot.org/ CellMarker: cellmarker: human: 2.0: url: http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx mouse: 2.0: url: http://bio-bigdata.hrbmu.edu.cn/CellMarker/CellMarker_download_files/file/Cell_marker_All.xlsx name: CellMarker website: http://bio-bigdata.hrbmu.edu.cn/CellMarker/ CellLine: clo: all: 2022-03-21: url: https://data.bioontology.org/ontologies/CLO/submissions/65/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: ea58a1010b7e745702a8397a526b3a33 name: Cell Line Ontology website: https://bioportal.bioontology.org/ontologies/CLO CellType: cl: all: 2023-02-15: url: http://purl.obolibrary.org/obo/cl/releases/2023-02-15/cl-base.owl md5: 9331a6a029cb1863bd0584ab41508df7 2022-08-16: url: http://purl.obolibrary.org/obo/cl/releases/2022-08-16/cl.owl md5: d0655766574e63f3fe5ed56d3c030880 name: Cell Ontology website: https://obophenotype.github.io/cell-ontology/ Tissue: uberon: all: 2023-02-14: url: http://purl.obolibrary.org/obo/uberon/releases/2023-02-14/uberon.owl md5: 3f94e22fae4cdde88a555c5cd59c47da 2022-08-19: url: http://purl.obolibrary.org/obo/uberon/releases/2022-08-19/uberon.owl md5: c7c958a1ee48fdce146f2c1763eed27e name: Uberon multi-species anatomy ontology website: http://obophenotype.github.io/uberon/ Disease: mondo: all: 2023-02-06: url: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl md5: 2b7d479d4bd02a94eab47d1c9e64c5db 2022-10-11: url: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl md5: 04b808d05c2c2e81430b20a0e87552bb name: Mondo Disease Ontology website: https://mondo.monarchinitiative.org/ doid: human: 2023-01-30: url: http://purl.obolibrary.org/obo/doid/releases/2023-01-30/doid.obo md5: 9f0c92ad2896dda82195e9226a06dc36 name: Human Disease Ontology website: https://disease-ontology.org/ Readout: efo: all: 3.48.0: url: http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl md5: 3367e9a9ae3dee9113024e5108c49091 name: The Experimental Factor Ontology website: https://bioportal.bioontology.org/ontologies/EFO Phenotype: hp: human: 2023-01-27: url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-01-27/hp.owl md5: ceeb3ada771908deef620d74cd8e6b0f name: Human Phenotype Ontology website: https://hpo.jax.org/ Pathway: go: all: 2023-05-10: url: https://data.bioontology.org/ontologies/GO/submissions/1814/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: "" name: Gene Ontology website: http://geneontology.org/docs/download-ontology/ pw: all: 7.79: url: https://data.bioontology.org/ontologies/PW/submissions/109/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: 02e2337bb1ab7cc4332ef6acc4cbdfa6 name: Pathway Ontology website: https://www.ebi.ac.uk/ols/ontologies/pw BFXPipeline: lamin: all: 1.0.0: url: s3://bionty-assets/bfxpipelines.json md5: "" name: Bioinformatics Pipeline website: https://lamin.ai Drug: dron: all: 2023-03-10: url: https://data.bioontology.org/ontologies/DRON/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb md5: "" name: Drug Ontology website: https://bioportal.bioontology.org/ontologies/DRON/?p=summary

Zethson commented 1 year ago

Github ate the formatting eww

Zethson commented 1 year ago

The burden of being a dev. I had some slightly older format or something.