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 | 2023-04-20 |
| 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 |
| DevelopmentalStage | human | hsapdv | 2020-03-10 |
| DevelopmentalStage | mouse | mmusdv | 2020-03-10 |
| Ethnicity | human | hancestro | 2023-07-313.0 |
| 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 | 2023-04-20 | 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 |
| DevelopmentalStage | hsapdv | human | 2020-03-10 | http://purl.obolibrary.org/obo/hsapdv.owl | 0423f338c50161880df4d5d1523d24ed | Human Developmental Stages | https://github.com/obophenotype/developmental-... |
| DevelopmentalStage | mmusdv | mouse | 2020-03-10 | http://purl.obolibrary.org/obo/mmusdv.owl | 6342b59cf3082b10c54f90a8c3336b72 | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... |
| Ethnicity | hancestro | human | 2023-07-313.0 | http://purl.obolibrary.org/obo/hancestro.owl | af731447e95b4ca341a91b018edd4885 | 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, 2023-04-20
#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
Organism: 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 organism for multi-organism models:
gene_bt = bt.Gene()
gene_bt
Gene
Organism: 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(organism="mouse")
gene_bt
Gene
Organism: 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
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 “doid” used when “organism” 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 “organism” 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/