Organism¶
lamindb provides access to the following public Organism ontologies through bionty:
Here we show how to access and search Organism ontologies to standardize new data.
import bionty as bt
import pandas as pd
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology objects¶
Let us create a public ontology accessor with .public method, which chooses a default public ontology source from Source.
It’s a PublicOntology object, which you can think about as a public registry:
organisms = bt.Organism.public(organism="vertebrates")
organisms
PublicOntology
Entity: Organism
Organism: vertebrates
Source: ensembl, release-112
#terms: 324
As for registries, you can export the ontology as a DataFrame:
df = organisms.df()
df.head()
/tmp/ipykernel_3585/50703996.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
df = organisms.df()
| scientific_name | division | ontology_id | assembly | assembly_accession | genebuild | variation | microarray | pan_compara | peptide_compara | genome_alignments | other_alignments | core_db | species_id | synonyms | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| name | |||||||||||||||
| spiny chromis | Acanthochromis polyacanthus | EnsemblVertebrates | NCBITaxon:80966 | ASM210954v1 | GCA_002109545.1 | 2018-05-Ensembl/2020-03 | N | N | N | Y | Y | Y | acanthochromis_polyacanthus_core_112_1 | 1 | None |
| eurasian sparrowhawk | Accipiter nisus | EnsemblVertebrates | NCBITaxon:211598 | Accipiter_nisus_ver1.0 | GCA_004320145.1 | 2019-07-Ensembl/2019-09 | N | N | N | N | N | Y | accipiter_nisus_core_112_1 | 1 | None |
| giant panda | Ailuropoda melanoleuca | EnsemblVertebrates | NCBITaxon:9646 | ASM200744v2 | GCA_002007445.2 | 2020-05-Ensembl/2020-06 | N | N | N | Y | Y | Y | ailuropoda_melanoleuca_core_112_2 | 1 | None |
| yellow-billed parrot | Amazona collaria | EnsemblVertebrates | NCBITaxon:241587 | ASM394721v1 | GCA_003947215.1 | 2019-07-Ensembl/2019-09 | N | N | N | N | N | Y | amazona_collaria_core_112_1 | 1 | None |
| midas cichlid | Amphilophus citrinellus | EnsemblVertebrates | NCBITaxon:61819 | Midas_v5 | GCA_000751415.1 | 2018-05-Ensembl/2018-07 | N | N | N | Y | Y | Y | amphilophus_citrinellus_core_112_5 | 1 | None |
Unlike registries, you can also export it as a Pronto object via public.ontology.
Look up terms¶
As for registries, terms can be looked up with auto-complete:
lookup = organisms.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.giant_panda
Organism(name='giant panda', scientific_name='Ailuropoda melanoleuca', division='EnsemblVertebrates', ontology_id='NCBITaxon:9646', assembly='ASM200744v2', assembly_accession='GCA_002007445.2', genebuild='2020-05-Ensembl/2020-06', variation='N', microarray='N', pan_compara='N', peptide_compara='Y', genome_alignments='Y', other_alignments='Y', core_db='ailuropoda_melanoleuca_core_112_2', species_id=1, synonyms=None)
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["giant panda"]
Organism(name='giant panda', scientific_name='Ailuropoda melanoleuca', division='EnsemblVertebrates', ontology_id='NCBITaxon:9646', assembly='ASM200744v2', assembly_accession='GCA_002007445.2', genebuild='2020-05-Ensembl/2020-06', variation='N', microarray='N', pan_compara='N', peptide_compara='Y', genome_alignments='Y', other_alignments='Y', core_db='ailuropoda_melanoleuca_core_112_2', species_id=1, synonyms=None)
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = organisms.lookup(organisms.scientific_name)
lookup.ailuropoda_melanoleuca
Organism(name='giant panda', scientific_name='Ailuropoda melanoleuca', division='EnsemblVertebrates', ontology_id='NCBITaxon:9646', assembly='ASM200744v2', assembly_accession='GCA_002007445.2', genebuild='2020-05-Ensembl/2020-06', variation='N', microarray='N', pan_compara='N', peptide_compara='Y', genome_alignments='Y', other_alignments='Y', core_db='ailuropoda_melanoleuca_core_112_2', species_id=1, synonyms=None)
Search terms¶
Search behaves in the same way as it does for registries:
organisms.search("rabbit").head(3)
| name | scientific_name | division | assembly | assembly_accession | genebuild | variation | microarray | pan_compara | peptide_compara | genome_alignments | other_alignments | core_db | species_id | synonyms | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ontology_id | |||||||||||||||
| NCBITaxon:9986 | rabbit | Oryctolagus cuniculus | EnsemblVertebrates | OryCun2.0 | GCA_000003625.1 | 2009-11-Ensembl/2019-05 | N | Y | N | Y | Y | Y | oryctolagus_cuniculus_core_112_2 | 1 | None |
By default, search also covers synonyms and all other fileds containing strings:
organisms.search("sapiens").head(3)
| name | scientific_name | division | assembly | assembly_accession | genebuild | variation | microarray | pan_compara | peptide_compara | genome_alignments | other_alignments | core_db | species_id | synonyms | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ontology_id | |||||||||||||||
| NCBITaxon:9606 | human | Homo sapiens | EnsemblVertebrates | GRCh38.p14 | GCA_000001405.29 | 2014-01-Ensembl/2023-12 | Y | Y | Y | Y | Y | Y | homo_sapiens_core_112_38 | 1 | None |
Search specific field (by default, search is done on all fields containing strings):
organisms.search(
"oryctolagus_cuniculus",
field=organisms.scientific_name,
).head()
| name | scientific_name | division | assembly | assembly_accession | genebuild | variation | microarray | pan_compara | peptide_compara | genome_alignments | other_alignments | core_db | species_id | synonyms | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ontology_id |
Standardize Organism identifiers¶
Let us generate a DataFrame that stores a number of Organism identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"spiny chromis",
"silver-eye",
"platyfish",
"california sea lion",
"This organism does not exist",
]
)
df_orig
| spiny chromis |
|---|
| silver-eye |
| platyfish |
| california sea lion |
| This organism does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = organisms.validate(df_orig.index, organisms.name)
df_orig.index[~validated]
! 1 unique term (20.00%) is not validated: 'This organism does not exist'
Index(['This organism does not exist'], dtype='object')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.Organism").df()
Show code cell output
/tmp/ipykernel_3585/2798978696.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
bt.Source.filter(entity="bionty.Organism").df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TUF039 | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 2 | 6bbVUTCS | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 3 | 6s9nV6xh | bionty.Organism | fungi | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 4 | 2PmTrc8x | bionty.Organism | metazoa | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 5 | 7GPHh16S | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 6 | 4tsksCMX | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | http://purl.obolibrary.org/obo/ncbitaxon/2023-... | None | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Organism", currently_used=True).df()
/tmp/ipykernel_3585/2728461179.py:2: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
bt.Source.filter(entity="bionty.Organism", currently_used=True).df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TUF039 | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 2 | 6bbVUTCS | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 3 | 6s9nV6xh | bionty.Organism | fungi | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 4 | 2PmTrc8x | bionty.Organism | metazoa | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 5 | 7GPHh16S | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 6 | 4tsksCMX | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | http://purl.obolibrary.org/obo/ncbitaxon/2023-... | None | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="ensembl", organism="vertebrates"
).first()
organisms= bt.Organism.public(source=source)
organisms
PublicOntology
Entity: Organism
Organism: vertebrates
Source: ensembl, release-112
#terms: 324
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()
Show code cell output
/tmp/ipykernel_3585/2711573161.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
bt.Source.filter(currently_used=True).df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | branch_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TUF039 | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 2 | 6bbVUTCS | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 3 | 6s9nV6xh | bionty.Organism | fungi | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/fungi... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 4 | 2PmTrc8x | bionty.Organism | metazoa | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/metaz... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 5 | 7GPHh16S | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | None | https://www.ensembl.org | 1 | None | release-57 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 6 | 4tsksCMX | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | http://purl.obolibrary.org/obo/ncbitaxon/2023-... | None | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 7 | 4UGNz3fr | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 8 | 4r4fvV0S | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 9 | 4RPA3Re0 | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | None | https://www.ensembl.org | 1 | None | release-112 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 10 | 3EYyGRYN | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 11 | 01RWXN2V | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | None | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 12 | 3kDh8qAX | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 13 | 7bV5uJo3 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | None | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 14 | 6LyRtvz8 | bionty.CellLine | all | clo | False | True | Cell Line Ontology | s3://bionty-assets/df_all__clo__2022-03-21__Ce... | None | https://bioportal.bioontology.org/ontologies/CLO | 1 | None | 2022-03-21 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 16 | 3T9KZcjQ | bionty.CellType | all | cl | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | None | https://obophenotype.github.io/cell-ontology | 1 | None | 2025-04-10 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 17 | 4U5uYTlc | bionty.Tissue | all | uberon | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | None | http://obophenotype.github.io/uberon | 1 | None | 2025-05-28 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 18 | IGIkseWQ | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | None | https://mondo.monarchinitiative.org | 1 | None | 2025-06-03 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 19 | 4kswnHVF | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | None | https://disease-ontology.org | 1 | None | 2024-05-29 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 21 | 2a1HvjdB | bionty.ExperimentalFactor | all | efo | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl | None | https://bioportal.bioontology.org/ontologies/EFO | 1 | None | 3.70.0 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 22 | 6S4qkDx1 | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | None | https://github.com/pato-ontology/pato | 1 | None | 2024-03-28 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 23 | 48fBFLmn | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | None | https://hpo.jax.org | 1 | None | 2024-04-26 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 25 | 7Ent3V2y | bionty.Pathway | all | go | False | True | Gene Ontology | http://purl.obolibrary.org/obo/go/releases/202... | None | http://geneontology.org | 1 | None | 2024-06-17 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 27 | 3rm9aOzL | BFXPipeline | all | lamin | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | None | https://lamin.ai | 1 | None | 1.0.0 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 28 | ugaIoIlj | Drug | all | dron | False | True | Drug Ontology | http://purl.obolibrary.org/obo/dron/releases/2... | None | https://bioportal.bioontology.org/ontologies/DRON | 1 | None | 2024-08-05 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 30 | 1GbFkOdz | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 31 | 10va5JSt | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | None | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 32 | MJRqduf9 | bionty.Ethnicity | human | hancestro | False | True | Human Ancestry Ontology | http://purl.obolibrary.org/obo/hancestro/relea... | None | https://github.com/EBISPOT/hancestro | 1 | None | 3.0 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |
| 33 | 5JnVODh4 | BioSample | all | ncbi | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | None | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 1 | None | 2023-09 | None | 2025-09-18 06:40:29.074000+00:00 | 1 | None | 1 |