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	all	ensembl	release-109
Gene	human	ensembl	release-109
Gene	mouse	ensembl	release-109
Protein	human	uniprot	2023-02
Protein	mouse	uniprot	2023-02
CellMarker	human	cellmarker	2.0
CellMarker	mouse	cellmarker	2.0
CellLine	all	clo	2022-03-21
CellType	all	cl	2023-02-15
Tissue	all	uberon	2023-02-14
Disease	all	mondo	2023-02-06
Disease	human	doid	2023-01-30
Readout	all	efo	3.48.0
Phenotype	human	hp	2023-01-27
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	all	release-109	https://ftp.ensembl.org/pub/release-109/specie...		Ensembl	https://www.ensembl.org
Species	ensembl	all	release-108	https://ftp.ensembl.org/pub/release-108/specie...		Ensembl	https://www.ensembl.org
Gene	ensembl	human	release-109	s3://bionty-assets/human_ensembl_release-109_G...		Ensembl	https://www.ensembl.org
Gene	ensembl	mouse	release-109	s3://bionty-assets/mouse_ensembl_release-109_G...		Ensembl	https://www.ensembl.org
Protein	uniprot	human	2023-02	s3://bionty-assets/human_uniprot_2023-02_Prote...		Uniprot	https://www.uniprot.org
Protein	uniprot	mouse	2023-02	s3://bionty-assets/mouse_uniprot_2023-02_Prote...		Uniprot	https://www.uniprot.org
CellMarker	cellmarker	human	2.0	s3://bionty-assets/human_cellmarker_2.0_CellMa...		CellMarker	http://bio-bigdata.hrbmu.edu.cn/CellMarker
CellMarker	cellmarker	mouse	2.0	s3://bionty-assets/mouse_cellmarker_2.0_CellMa...		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	2023-02-15	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	2023-02-14	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	2023-02-06	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	2023-01-30	http://purl.obolibrary.org/obo/doid/releases/2...	9f0c92ad2896dda82195e9226a06dc36	Human Disease Ontology	https://disease-ontology.org
Readout	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	2023-01-27	https://github.com/obophenotype/human-phenotyp...	ceeb3ada771908deef620d74cd8e6b0f	Human Phenotype Ontology	https://hpo.jax.org
Pathway	go	all	2023-05-10	https://data.bioontology.org/ontologies/GO/sub...		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		Bioinformatics Pipeline	https://lamin.ai
Drug	dron	all	2023-03-10	https://data.bioontology.org/ontologies/DRON/s...		Drug Ontology	https://bioportal.bioontology.org/ontologies/DRON

Initialize a Bionty model#

When initializing a Bionty class, default source is used:

celltype_bionty = bt.CellType()

celltype_bionty

CellType
Species: all
Source: cl, 2023-02-15

📖 CellType.df(): ontology reference table
🔎 CellType.lookup(): autocompletion of terms
🎯 CellType.search(): free text search of terms
🧐 CellType.inspect(): check if identifiers are mappable
👽 CellType.map_synonyms(): map synonyms to standardized names
🔗 CellType.ontology: Pronto.Ontology object

You may specify a different source or version:

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

celltype_bionty

CellType
Species: all
Source: cl, 2022-08-16

📖 CellType.df(): ontology reference table
🔎 CellType.lookup(): autocompletion of terms
🎯 CellType.search(): free text search of terms
🧐 CellType.inspect(): check if identifiers are mappable
👽 CellType.map_synonyms(): map synonyms to standardized names
🔗 CellType.ontology: Pronto.Ontology object

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

gene_bionty = bt.Gene()

gene_bionty

Gene
Species: human
Source: ensembl, release-109

📖 Gene.df(): ontology reference table
🔎 Gene.lookup(): autocompletion of terms
🎯 Gene.search(): free text search of terms
🧐 Gene.inspect(): check if identifiers are mappable
👽 Gene.map_synonyms(): map synonyms to standardized names
🔗 Gene.ontology: Pronto.Ontology object

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

gene_bionty

Gene
Species: mouse
Source: ensembl, release-109

📖 Gene.df(): ontology reference table
🔎 Gene.lookup(): autocompletion of terms
🎯 Gene.search(): free text search of terms
🧐 Gene.inspect(): check if identifiers are mappable
👽 Gene.map_synonyms(): map synonyms to standardized names
🔗 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/