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laminlabs / cellxgene-lamin

Access the cellxgene data using LaminDB.
https://docs.lamin.ai/cellxgene
Apache License 2.0
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Not all by cellxgene used sources for schema 5.0.0 can be found #79

Closed Zethson closed 1 month ago

Zethson commented 1 month ago

When fetching the bionty versions for all by cxg schema 5.0.0 versions, not all Bionty sources can be found.

We should ensure that these versions are available in Bionty and check that the cellxgene records were registered with the right versions.

Field Source
var_index Source(uid='5dmX', entity='bionty.Gene', organism='human', name='ensembl', version='release-110', in_db=False, currently_used=True, description='Ensembl', url='s3://bionty-assets/df_humanensemblrelease-110__Gene.parquet', md5='832f3947e83664588d419608a469b528', source_website='https://www.ensembl.org/', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
gene Source(uid='5dmX', entity='bionty.Gene', organism='human', name='ensembl', version='release-110', in_db=False, currently_used=True, description='Ensembl', url='s3://bionty-assets/df_humanensemblrelease-110__Gene.parquet', md5='832f3947e83664588d419608a469b528', source_website='https://www.ensembl.org/', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
gene_ontology_id Source(uid='5dmX', entity='bionty.Gene', organism='human', name='ensembl', version='release-110', in_db=False, currently_used=True, description='Ensembl', url='s3://bionty-assets/df_humanensemblrelease-110__Gene.parquet', md5='832f3947e83664588d419608a469b528', source_website='https://www.ensembl.org/', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
cell_type None
cell_type_ontology_id None
assay None
assay_ontology_id None
self_reported_ethnicity Source(uid='MJRq', entity='bionty.Ethnicity', organism='human', name='hancestro', version='3.0', in_db=False, currently_used=True, description='Human Ancestry Ontology', url='https://github.com/EBISPOT/hancestro/raw/3.0/hancestro-base.owl', md5='76dd9efda9c2abd4bc32fc57c0b755dd', source_website='https://github.com/EBISPOT/hancestro', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
self_reported_ethnicity_ontology_id Source(uid='MJRq', entity='bionty.Ethnicity', organism='human', name='hancestro', version='3.0', in_db=False, currently_used=True, description='Human Ancestry Ontology', url='https://github.com/EBISPOT/hancestro/raw/3.0/hancestro-base.owl', md5='76dd9efda9c2abd4bc32fc57c0b755dd', source_website='https://github.com/EBISPOT/hancestro', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
development_stage Source(uid='7Zm9', entity='bionty.DevelopmentalStage', organism='human', name='hsapdv', version='2020-03-10', in_db=False, currently_used=True, description='Human Developmental Stages', url='http://aber-owl.net/media/ontologies/HSAPDV/11/hsapdv.owl', md5='52181d59df84578ed69214a5cb614036', source_website='https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
development_stage_ontology_id Source(uid='7Zm9', entity='bionty.DevelopmentalStage', organism='human', name='hsapdv', version='2020-03-10', in_db=False, currently_used=True, description='Human Developmental Stages', url='http://aber-owl.net/media/ontologies/HSAPDV/11/hsapdv.owl', md5='52181d59df84578ed69214a5cb614036', source_website='https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
disease None
disease_ontology_id None
organism Source(uid='4tsk', entity='bionty.Organism', organism='all', name='ncbitaxon', version='2023-06-20', in_db=False, currently_used=False, description='NCBItaxon Ontology', url='s3://bionty-assets/df_allncbitaxon2023-06-20__Organism.parquet', md5='00d97ba65627f1cd65636d2df22ea76c', source_website='https://github.com/obophenotype/ncbitaxon', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
organism_ontology_id Source(uid='4tsk', entity='bionty.Organism', organism='all', name='ncbitaxon', version='2023-06-20', in_db=False, currently_used=False, description='NCBItaxon Ontology', url='s3://bionty-assets/df_allncbitaxon2023-06-20__Organism.parquet', md5='00d97ba65627f1cd65636d2df22ea76c', source_website='https://github.com/obophenotype/ncbitaxon', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
sex Source(uid='3ox8', entity='bionty.Phenotype', organism='all', name='pato', version='2023-05-18', in_db=False, currently_used=True, description='Phenotype And Trait Ontology', url='http://purl.obolibrary.org/obo/pato/releases/2023-05-18/pato.owl', md5='bd472f4971492109493d4ad8a779a8dd', source_website='https://github.com/pato-ontology/pato', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
sex_ontology_id Source(uid='3ox8', entity='bionty.Phenotype', organism='all', name='pato', version='2023-05-18', in_db=False, currently_used=True, description='Phenotype And Trait Ontology', url='http://purl.obolibrary.org/obo/pato/releases/2023-05-18/pato.owl', md5='bd472f4971492109493d4ad8a779a8dd', source_website='https://github.com/pato-ontology/pato', created_by_id=1, updated_at='2024-08-02 15:15:21 UTC')
tissue None
tissue_ontology_id None