Organism

lamindb provides access to the following public Organism ontologies through bionty:

  1. Ensembl Species

  2. NCBI Taxonomy

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 PublicSource. 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()
scientific_name division ontology_id assembly assembly_accession genebuild variation microarray pan_compara peptide_compara genome_alignments other_alignments core_db species_id
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
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
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
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
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

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)

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)

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)

Search terms

Search behaves in the same way as it does for registries:

organisms.search("rabbit").head(3)
scientific_name division ontology_id assembly assembly_accession genebuild variation microarray pan_compara peptide_compara genome_alignments other_alignments core_db species_id __ratio__
name
rabbit oryctolagus_cuniculus EnsemblVertebrates NCBITaxon:9986 OryCun2.0 GCA_000003625.1 2009-11-Ensembl/2019-05 N Y N Y Y Y oryctolagus_cuniculus_core_112_2 1 100.0
blue-ringed sea krait laticauda_laticaudata EnsemblVertebrates NCBITaxon:8630 latLat_1.0 GCA_004320025.1 2019-11-Ensembl/2019-12 N N N Y Y Y laticauda_laticaudata_core_112_1 1 72.0
rat rattus_norvegicus EnsemblVertebrates NCBITaxon:10116 mRatBN7.2 GCA_015227675.2 2020-11-Ensembl/2022-03 Y Y N Y Y Y rattus_norvegicus_core_112_72 1 72.0

By default, search also covers synonyms:

organisms.search("sapiens").head(3)
scientific_name division ontology_id assembly assembly_accession genebuild variation microarray pan_compara peptide_compara genome_alignments other_alignments core_db species_id __ratio__
name
swainson's thrush catharus_ustulatus EnsemblVertebrates NCBITaxon:91951 bCatUst1.pri GCA_009819885.1 2020-01-Ensembl/2020-03 N N N N N Y catharus_ustulatus_core_112_1 1 69.230769
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 65.454545
common snapping turtle chelydra_serpentina EnsemblVertebrates NCBITaxon:8475 Chelydra_serpentina-1.0 GCA_007922165.1 2019-11-Ensembl/2019-12 N N N N N Y chelydra_serpentina_core_112_1 1 64.285714

You can turn this off synonym by passing synonyms_field=None:

organisms.search("sapiens", synonyms_field=None).head(3)
scientific_name division ontology_id assembly assembly_accession genebuild variation microarray pan_compara peptide_compara genome_alignments other_alignments core_db species_id __ratio__
name
swainson's thrush catharus_ustulatus EnsemblVertebrates NCBITaxon:91951 bCatUst1.pri GCA_009819885.1 2020-01-Ensembl/2020-03 N N N N N Y catharus_ustulatus_core_112_1 1 69.230769
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 65.454545
common snapping turtle chelydra_serpentina EnsemblVertebrates NCBITaxon:8475 Chelydra_serpentina-1.0 GCA_007922165.1 2019-11-Ensembl/2019-12 N N N N N Y chelydra_serpentina_core_112_1 1 64.285714

Search another field (default is .name):

organisms.search(
    "oryctolagus_cuniculus",
    field=organisms.scientific_name,
).head()
name division ontology_id assembly assembly_accession genebuild variation microarray pan_compara peptide_compara genome_alignments other_alignments core_db species_id __ratio__
scientific_name
oryctolagus_cuniculus rabbit EnsemblVertebrates NCBITaxon:9986 OryCun2.0 GCA_000003625.1 2009-11-Ensembl/2019-05 N Y N Y Y Y oryctolagus_cuniculus_core_112_2 1 100.000000
mus_musculus mouse EnsemblVertebrates NCBITaxon:10090 GRCm39 GCA_000001635.9 2020-08-Ensembl/2023-12 Y Y Y Y Y Y mus_musculus_core_112_39 1 67.500000
mola_mola ocean sunfish EnsemblVertebrates NCBITaxon:94237 ASM169857v1 GCA_001698575.1 2018-05-Ensembl/2018-07 N N N N N Y mola_mola_core_112_1 1 64.125000
oryzias_javanicus javanese ricefish EnsemblVertebrates NCBITaxon:123683 OJAV_1.1 GCA_003999625.1 2019-09-Ensembl/2019-11 N N N Y Y Y oryzias_javanicus_core_112_11 1 57.894737
meriones_unguiculatus mongolian gerbil EnsemblVertebrates NCBITaxon:10047 MunDraft-v1.0 GCA_002204375.1 2018-12-Ensembl/2020-03 N N N N N Y meriones_unguiculatus_core_112_1 1 57.142857

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 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.PublicSource.filter(entity="Organism").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-07-26 12:19:48.322631+00:00
2 6ZRH Organism vertebrates False ensembl Ensembl release-111 https://ftp.ensembl.org/pub/release-111/specie... 2846df83899eaa61f8043db4c036e883 https://www.ensembl.org None 1 2024-07-26 12:19:48.322744+00:00
3 6IUo Organism vertebrates False ensembl Ensembl release-110 https://ftp.ensembl.org/pub/release-110/specie... f3faf95648d3a2b50fd3625456739706 https://www.ensembl.org None 1 2024-07-26 12:19:48.322842+00:00
4 JTGk Organism vertebrates False ensembl Ensembl release-109 https://ftp.ensembl.org/pub/release-109/specie... 7595bb989f5fec07eaca5e2138f67bd4 https://www.ensembl.org None 1 2024-07-26 12:19:48.322938+00:00
5 3LoR Organism vertebrates False ensembl Ensembl release-108 https://ftp.ensembl.org/pub/release-108/specie... d97c1ee302e4072f5f5c7850eff0b642 https://www.ensembl.org None 1 2024-07-26 12:19:48.323033+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-07-26 12:19:48.323129+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-07-26 12:19:48.323223+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-07-26 12:19:48.323318+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-07-26 12:19:48.323411+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-07-26 12:19:48.323506+00:00

When instantiating a Bionty object, we can choose a source or version:

public_source = bt.PublicSource.filter(
    source="ensembl", version="release-110", organism="vertebrates"
).one()
organisms= bt.Organism.public(public_source=public_source)
organisms

❗ loading non-default source inside a LaminDB instance

PublicOntology
Entity: Organism
Organism: vertebrates
Source: ensembl, release-110
#terms: 317

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide code cell output
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-07-26 12:19:48.322631+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-07-26 12:19:48.323129+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-07-26 12:19:48.323223+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-07-26 12:19:48.323318+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-07-26 12:19:48.323411+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-07-26 12:19:48.323506+00:00
11 1hx4 Gene human True ensembl Ensembl release-112 s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None 1 2024-07-26 12:19:48.323601+00:00
15 76FX Gene mouse True ensembl Ensembl release-112 s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None 1 2024-07-26 12:19:48.323976+00:00
19 7LW6 Gene saccharomyces cerevisiae True ensembl Ensembl release-112 s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None 1 2024-07-26 12:19:48.324354+00:00
22 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org None 1 2024-07-26 12:19:48.324642+00:00
24 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org None 1 2024-07-26 12:19:48.324829+00:00
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-07-26 12:19:48.325016+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-07-26 12:19:48.325111+00:00
28 6cbC CellLine all True clo Cell Line Ontology 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None 1 2024-07-26 12:19:48.325204+00:00
29 3DeN CellType all True cl Cell Ontology 2024-02-13 http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 1 2024-07-26 12:19:48.325298+00:00
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-07-26 12:19:48.325766+00:00
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-07-26 12:19:48.326243+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-07-26 12:19:48.326743+00:00
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-07-26 12:19:48.327398+00:00
54 2WLc Phenotype human True hp Human Phenotype Ontology 2024-03-06 https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None 1 2024-07-26 12:19:48.327687+00:00
58 6zE1 Phenotype mammalian True mp Mammalian Phenotype Ontology 2024-02-07 https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None 1 2024-07-26 12:19:48.328058+00:00
60 7EnA Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2024-01-22 https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None 1 2024-07-26 12:19:48.328243+00:00
63 55lY Phenotype all True pato Phenotype And Trait Ontology 2023-05-18 http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd https://github.com/pato-ontology/pato None 1 2024-07-26 12:19:48.328519+00:00
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-07-26 12:19:48.328612+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-07-26 12:19:48.328895+00:00
68 5alK Drug all True dron Drug Ontology 2024-03-02 https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None 1 2024-07-26 12:19:48.328989+00:00
70 7CRn DevelopmentalStage human True hsapdv Human Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 https://github.com/obophenotype/developmental-... None 1 2024-07-26 12:19:48.329178+00:00
71 16tR DevelopmentalStage mouse True mmusdv Mouse Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 https://github.com/obophenotype/developmental-... None 1 2024-07-26 12:19:48.329271+00:00
72 3Tlc Ethnicity human True hancestro Human Ancestry Ontology 3.0 https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 1 2024-07-26 12:19:48.331560+00:00
73 5JnV BioSample all True ncbi NCBI BioSample attributes 2023-09 s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None 1 2024-07-26 12:19:48.331669+00:00