Ontology sources configuration#

import bionty as bt

Display sources#

The currently active and available ontologies can also be printed with:

bt.display_currently_used_sources()
organism source version
entity
Organism vertebrates ensembl release-110
Organism bacteria ensembl release-57
Organism fungi ensembl release-57
Organism metazoa ensembl release-57
Organism plants ensembl release-57
Organism all ncbitaxon 2023-06-20
Gene human ensembl release-110
Gene mouse ensembl release-110
Gene saccharomyces cerevisiae ensembl release-110
Protein human uniprot 2023-03
Protein mouse uniprot 2023-03
CellMarker human cellmarker 2.0
CellMarker mouse cellmarker 2.0
CellLine all clo 2022-03-21
CellType all cl 2023-08-24
Tissue all uberon 2023-09-05
Disease all mondo 2023-08-02
Disease human doid 2023-03-31
ExperimentalFactor all efo 3.57.0
Phenotype human hp 2023-06-17
Phenotype mammalian mp 2023-05-31
Phenotype zebrafish zp 2022-12-17
Phenotype all pato 2023-05-18
Pathway all go 2023-05-10
BFXPipeline all lamin 1.0.0
Drug all dron 2023-03-10
DevelopmentalStage human hsapdv 2020-03-10
DevelopmentalStage mouse mmusdv 2020-03-10
Ethnicity human hancestro 3.0
BioSample all ncbi 2023-09
bt.display_available_sources()
source organism version url md5 source_name source_website
entity
Organism ensembl vertebrates release-110 https://ftp.ensembl.org/pub/release-110/specie... f3faf95648d3a2b50fd3625456739706 Ensembl https://www.ensembl.org
Organism ensembl vertebrates release-109 https://ftp.ensembl.org/pub/release-109/specie... 7595bb989f5fec07eaca5e2138f67bd4 Ensembl https://www.ensembl.org
Organism ensembl vertebrates release-108 https://ftp.ensembl.org/pub/release-108/specie... d97c1ee302e4072f5f5c7850eff0b642 Ensembl https://www.ensembl.org
Organism ensembl bacteria release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 Ensembl https://www.ensembl.org
Organism ensembl fungi release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a Ensembl https://www.ensembl.org
Organism ensembl metazoa release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 Ensembl https://www.ensembl.org
Organism ensembl plants release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 Ensembl https://www.ensembl.org
Organism ncbitaxon all 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c NCBItaxon Ontology https://github.com/obophenotype/ncbitaxon
Gene ensembl human release-110 s3://bionty-assets/df_human__ensembl__release-... 832f3947e83664588d419608a469b528 Ensembl https://www.ensembl.org
Gene ensembl human release-109 s3://bionty-assets/human_ensembl_release-109_G... 72da9968c74e96d136a489a6102a4546 Ensembl https://www.ensembl.org
Gene ensembl mouse release-110 s3://bionty-assets/df_mouse__ensembl__release-... fa4ce130f2929aefd7ac3bc8eaf0c4de Ensembl https://www.ensembl.org
Gene ensembl mouse release-109 s3://bionty-assets/mouse_ensembl_release-109_G... 08a1165061151b270b985317322bd2ed Ensembl https://www.ensembl.org
Gene ensembl saccharomyces cerevisiae release-110 s3://bionty-assets/df_saccharomyces cerevisiae... 2e59495a3e87ea6575e408697dd73459 Ensembl https://www.ensembl.org
Protein uniprot human 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 Uniprot https://www.uniprot.org
Protein uniprot human 2023-02 s3://bionty-assets/human_uniprot_2023-02_Prote... 0cb7264eb43f91bd04dac792dd879241 Uniprot https://www.uniprot.org
Protein uniprot mouse 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c Uniprot https://www.uniprot.org
Protein uniprot mouse 2023-02 s3://bionty-assets/mouse_uniprot_2023-02_Prote... dcae4f62f5df145a5c15163fce7e9135 Uniprot https://www.uniprot.org
CellMarker cellmarker human 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 CellMarker http://bio-bigdata.hrbmu.edu.cn/CellMarker
CellMarker cellmarker mouse 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 CellMarker http://bio-bigdata.hrbmu.edu.cn/CellMarker
CellLine clo all 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 Cell Line Ontology https://bioportal.bioontology.org/ontologies/CLO
CellType cl all 2023-08-24 http://purl.obolibrary.org/obo/cl/releases/202... 46e7dd89421f1255cf0191eca1548f73 Cell Ontology https://obophenotype.github.io/cell-ontology
CellType cl all 2023-04-20 http://purl.obolibrary.org/obo/cl/releases/202... 58cdc1545f0d35e6fce76a65331b00fb Cell Ontology https://obophenotype.github.io/cell-ontology
CellType cl all 2023-02-15 http://purl.obolibrary.org/obo/cl/releases/202... 9331a6a029cb1863bd0584ab41508df7 Cell Ontology https://obophenotype.github.io/cell-ontology
CellType cl all 2022-08-16 http://purl.obolibrary.org/obo/cl/releases/202... d0655766574e63f3fe5ed56d3c030880 Cell Ontology https://obophenotype.github.io/cell-ontology
Tissue uberon all 2023-09-05 http://purl.obolibrary.org/obo/uberon/releases... abcee3ede566d1311d758b853ccdf5aa Uberon multi-species anatomy ontology http://obophenotype.github.io/uberon
Tissue uberon all 2023-04-19 http://purl.obolibrary.org/obo/uberon/releases... 5611dd1375d5a95ac7d7de8e25e6016f Uberon multi-species anatomy ontology http://obophenotype.github.io/uberon
Tissue uberon all 2023-02-14 http://purl.obolibrary.org/obo/uberon/releases... 3f94e22fae4cdde88a555c5cd59c47da Uberon multi-species anatomy ontology http://obophenotype.github.io/uberon
Tissue uberon all 2022-08-19 http://purl.obolibrary.org/obo/uberon/releases... c7c958a1ee48fdce146f2c1763eed27e Uberon multi-species anatomy ontology http://obophenotype.github.io/uberon
Disease mondo all 2023-08-02 http://purl.obolibrary.org/obo/mondo/releases/... 7f33767422042eec29f08b501fc851db Mondo Disease Ontology https://mondo.monarchinitiative.org
Disease mondo all 2023-04-04 http://purl.obolibrary.org/obo/mondo/releases/... 700c43dd9ba51aecc7a8edfc3bc2dab1 Mondo Disease Ontology https://mondo.monarchinitiative.org
Disease mondo all 2023-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 2b7d479d4bd02a94eab47d1c9e64c5db Mondo Disease Ontology https://mondo.monarchinitiative.org
Disease mondo all 2022-10-11 http://purl.obolibrary.org/obo/mondo/releases/... 04b808d05c2c2e81430b20a0e87552bb Mondo Disease Ontology https://mondo.monarchinitiative.org
Disease doid human 2023-03-31 http://purl.obolibrary.org/obo/doid/releases/2... 64f083a1e47867c307c8eae308afc3bb Human Disease Ontology https://disease-ontology.org
Disease doid human 2023-01-30 http://purl.obolibrary.org/obo/doid/releases/2... 9f0c92ad2896dda82195e9226a06dc36 Human Disease Ontology https://disease-ontology.org
ExperimentalFactor efo all 3.57.0 http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl 2ecafc69b3aba7bdb31ad99438505c05 The Experimental Factor Ontology https://bioportal.bioontology.org/ontologies/EFO
ExperimentalFactor efo all 3.48.0 http://www.ebi.ac.uk/efo/releases/v3.48.0/efo.owl 3367e9a9ae3dee9113024e5108c49091 The Experimental Factor Ontology https://bioportal.bioontology.org/ontologies/EFO
Phenotype hp human 2023-06-17 https://github.com/obophenotype/human-phenotyp... 65e8d96bc81deb893163927063b10c06 Human Phenotype Ontology https://hpo.jax.org
Phenotype hp human 2023-04-05 https://github.com/obophenotype/human-phenotyp... bdf866e11d37cf6fd2aef25c325b2c8a Human Phenotype Ontology https://hpo.jax.org
Phenotype hp human 2023-01-27 https://github.com/obophenotype/human-phenotyp... ceeb3ada771908deef620d74cd8e6b0f Human Phenotype Ontology https://hpo.jax.org
Phenotype mp mammalian 2023-05-31 https://github.com/mgijax/mammalian-phenotype-... be89052cf6d9c0b6197038fe347ef293 Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-...
Phenotype zp zebrafish 2022-12-17 https://github.com/obophenotype/zebrafish-phen... 03430b567bf153216c0fa4c3440b3b24 Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen...
Phenotype phe human 1.2 s3://bionty-assets/df_human__phe__1.2__Phenoty... 741033ee1b13df7c41b4849e8bd02f13 Phecodes ICD10 map https://phewascatalog.org/phecodes_icd10
Phenotype pato all 2023-05-18 http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd Phenotype And Trait Ontology https://github.com/pato-ontology/pato
Pathway go all 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e Gene Ontology http://geneontology.org
Pathway pw all 7.79 https://data.bioontology.org/ontologies/PW/sub... 02e2337bb1ab7cc4332ef6acc4cbdfa6 Pathway Ontology https://www.ebi.ac.uk/ols/ontologies/pw
BFXPipeline lamin all 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 Bioinformatics Pipeline https://lamin.ai
Drug dron all 2023-03-10 https://data.bioontology.org/ontologies/DRON/s... 75e86011158fae76bb46d96662a33ba3 Drug Ontology https://bioportal.bioontology.org/ontologies/DRON
DevelopmentalStage hsapdv human 2020-03-10 http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 Human Developmental Stages https://github.com/obophenotype/developmental-...
DevelopmentalStage mmusdv mouse 2020-03-10 http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 Mouse Developmental Stages https://github.com/obophenotype/developmental-...
Ethnicity hancestro human 3.0 https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd Human Ancestry Ontology https://github.com/EBISPOT/hancestro
BioSample ncbi all 2023-09 s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 NCBI BioSample attributes https://www.ncbi.nlm.nih.gov/biosample/docs/at...

Initialize a Bionty model#

When initializing a Bionty class, default source is used:

celltype_bt = bt.CellType()

celltype_bt
CellType
Organism: all
Source: cl, 2023-08-24
#terms: 2894

๐Ÿ“– CellType.df(): ontology reference table
๐Ÿ”Ž CellType.lookup(): autocompletion of terms
๐ŸŽฏ CellType.search(): free text search of terms
โœ… CellType.validate(): strictly validate values
๐Ÿง CellType.inspect(): full inspection of values
๐Ÿ‘ฝ CellType.standardize(): convert to standardized names
๐Ÿชœ CellType.diff(): difference between two versions
๐Ÿ”— CellType.ontology: Pronto.Ontology object

You may specify a different source or version:

celltype_bt = bt.CellType(source="cl", version="2022-08-16")

celltype_bt
CellType
Organism: all
Source: cl, 2022-08-16
#terms: 2672

๐Ÿ“– CellType.df(): ontology reference table
๐Ÿ”Ž CellType.lookup(): autocompletion of terms
๐ŸŽฏ CellType.search(): free text search of terms
โœ… CellType.validate(): strictly validate values
๐Ÿง CellType.inspect(): full inspection of values
๐Ÿ‘ฝ CellType.standardize(): convert to standardized names
๐Ÿชœ CellType.diff(): difference between two versions
๐Ÿ”— CellType.ontology: Pronto.Ontology object

You may also specify a organism for multi-organism models:

gene_bt = bt.Gene()

gene_bt
Gene
Organism: human
Source: ensembl, release-110
#terms: 75719

๐Ÿ“– Gene.df(): ontology reference table
๐Ÿ”Ž Gene.lookup(): autocompletion of terms
๐ŸŽฏ Gene.search(): free text search of terms
โœ… Gene.validate(): strictly validate values
๐Ÿง Gene.inspect(): full inspection of values
๐Ÿ‘ฝ Gene.standardize(): convert to standardized names
๐Ÿชœ Gene.diff(): difference between two versions
๐Ÿ”— Gene.ontology: Pronto.Ontology object
gene_bt = bt.Gene(organism="mouse")

gene_bt
Gene
Organism: mouse
Source: ensembl, release-110
#terms: 57283

๐Ÿ“– Gene.df(): ontology reference table
๐Ÿ”Ž Gene.lookup(): autocompletion of terms
๐ŸŽฏ Gene.search(): free text search of terms
โœ… Gene.validate(): strictly validate values
๐Ÿง Gene.inspect(): full inspection of values
๐Ÿ‘ฝ Gene.standardize(): convert to standardized names
๐Ÿชœ Gene.diff(): difference between two versions
๐Ÿ”— Gene.ontology: Pronto.Ontology object

Public bionty sources#

Bionty maintains a sources.yaml listing public sources of each entity.

These sources are curated (biony-assets) and stored at s3://bionty-assets to provide fast and reliable access.

Cached sources files are stored at your local bionty/bionty/_dynamic/ directory.

Local bionty sources#

File $home:/.lamin/bionty/sources.local.yaml stores all locally available ontologies.

The content of this file is identical to the public sources.yaml for a freshly-installed Bionty.

Users may edit this file in order to configure customized sources.

Format of the sources yaml file#

entity: # Bionty entity class name, e.g. CellType
  source: # short name of the source, (CURIE prefix for ontologies) e.g. cl
    organism: # organism common name, (if none applied, use 'all') e.g. human
      version: # version of the source
        url: "link to the source file"
        md5: "md5 of the source file"

Configure default ontologies and versions#

For each entity, the first source and its maximum version in sources.local.yaml is used as default.

To set your own default ontology and version, shift the order of entries.

For example, in the following โ€œdoidโ€ used when โ€œorganismโ€ is specified as โ€œhumanโ€:

(highlighted sources are considered the default)

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/
  inhouse_diseases:
    human:
      2000-01-01:
        source: http://download-my-diseases.com/releases/2000-01-01/mydiseases.owl
        md5: md5 if available or leave out this row
    name: My in-house Disease Ontology
    website: http://my-website.com

We may change the default to โ€œinhouse_diseasesโ€ when โ€œorganismโ€ is specified as โ€œhumanโ€, by the following:

Note: changing the order of versions wonโ€™t have an effect, as most recent version is taken as default.

Disease:
  mondo:
    all:
      2022-10-11:
        source: http://purl.obolibrary.org/obo/mondo/releases/2022-10-11/mondo.owl
        md5: 04b808d05c2c2e81430b20a0e87552bb
      2023-02-06:
        source: http://purl.obolibrary.org/obo/mondo/releases/2023-02-06/mondo.owl
        md5: 2b7d479d4bd02a94eab47d1c9e64c5db
    name: Mondo Disease Ontology
    website: https://mondo.monarchinitiative.org/
  inhouse_diseases:
    human:
      2000-01-01:
        source: http://download-my-diseases.com/releases/2000-01-01/mydiseases.owl
        md5: md5 if available or leave out this row
    name: My in-house Disease Ontology
    website: http://my-website.com
  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/