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()

	species	source	version
entity
Species	vertebrates	ensembl	release-110
Species	bacteria	ensembl	release-57
Species	fungi	ensembl	release-57
Species	metazoa	ensembl	release-57
Species	plants	ensembl	release-57
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	2023-04-20
Tissue	all	uberon	2023-04-19
Disease	all	mondo	2023-04-04
Disease	human	doid	2023-03-31
ExperimentalFactor	all	efo	3.48.0
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

bt.display_available_sources()

	source	species	version	url	md5	source_name	source_website
entity
Species	ensembl	vertebrates	release-110	https://ftp.ensembl.org/pub/release-110/specie...	f3faf95648d3a2b50fd3625456739706	Ensembl	https://www.ensembl.org
Species	ensembl	vertebrates	release-109	https://ftp.ensembl.org/pub/release-109/specie...	7595bb989f5fec07eaca5e2138f67bd4	Ensembl	https://www.ensembl.org
Species	ensembl	vertebrates	release-108	https://ftp.ensembl.org/pub/release-108/specie...	d97c1ee302e4072f5f5c7850eff0b642	Ensembl	https://www.ensembl.org
Species	ensembl	bacteria	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte...	ee28510ed5586ea7ab4495717c96efc8	Ensembl	https://www.ensembl.org
Species	ensembl	fungi	release-57	http://ftp.ensemblgenomes.org/pub/fungi/releas...	dbcde58f4396ab8b2480f7fe9f83df8a	Ensembl	https://www.ensembl.org
Species	ensembl	metazoa	release-57	http://ftp.ensemblgenomes.org/pub/metazoa/rele...	424636a574fec078a61cbdddb05f9132	Ensembl	https://www.ensembl.org
Species	ensembl	plants	release-57	https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant...	eadaa1f3e527e4c3940c90c7fa5c8bf4	Ensembl	https://www.ensembl.org
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	2023-04-20	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	2023-04-19	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	2023-04-04	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	3.48.0	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

Initialize a Bionty model#

When initializing a Bionty class, default source is used:

celltype_bt = bt.CellType()

celltype_bt

CellType
Species: all
Source: cl, 2023-04-20
#terms: 2862

📖 CellType.df(): ontology reference table
🔎 CellType.lookup(): autocompletion of terms
🎯 CellType.search(): free text search of terms
✅ CellType.validate(): strictly validate values
🧐 CellType.inspect(): full inspection of values
👽 CellType.standardize(): convert to standardized names
🪜 CellType.diff(): difference between two versions
🔗 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
Species: all
Source: cl, 2022-08-16
#terms: 2672

📖 CellType.df(): ontology reference table
🔎 CellType.lookup(): autocompletion of terms
🎯 CellType.search(): free text search of terms
✅ CellType.validate(): strictly validate values
🧐 CellType.inspect(): full inspection of values
👽 CellType.standardize(): convert to standardized names
🪜 CellType.diff(): difference between two versions
🔗 CellType.ontology: Pronto.Ontology object

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

gene_bt = bt.Gene()

gene_bt

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

📖 Gene.df(): ontology reference table
🔎 Gene.lookup(): autocompletion of terms
🎯 Gene.search(): free text search of terms
✅ Gene.validate(): strictly validate values
🧐 Gene.inspect(): full inspection of values
👽 Gene.standardize(): convert to standardized names
🪜 Gene.diff(): difference between two versions
🔗 Gene.ontology: Pronto.Ontology object

gene_bt = bt.Gene(species="mouse")

gene_bt

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

📖 Gene.df(): ontology reference table
🔎 Gene.lookup(): autocompletion of terms
🎯 Gene.search(): free text search of terms
✅ Gene.validate(): strictly validate values
🧐 Gene.inspect(): full inspection of values
👽 Gene.standardize(): convert to standardized names
🪜 Gene.diff(): difference between two versions
🔗 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
    species: # species 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 “doid” used when “species” is specified as “human”:

(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 “inhouse_diseases” when “species” is specified as “human”, by the following:

Note: changing the order of versions won’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/