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
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
💡 connected lamindb: testuser1/test-public-ontologies
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.Organism.list_source().df()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | release-112 | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.375733+00:00 |
| 2 | 1SRH | bionty.Organism | vertebrates | ensembl | release-111 | False | False | Ensembl | https://ftp.ensembl.org/pub/release-111/specie... | 2846df83899eaa61f8043db4c036e883 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.375913+00:00 |
| 3 | 6I0P | bionty.Organism | vertebrates | ensembl | release-110 | False | False | Ensembl | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376148+00:00 |
| 4 | 2m0D | bionty.Organism | vertebrates | ensembl | release-109 | False | False | Ensembl | https://ftp.ensembl.org/pub/release-109/specie... | 7595bb989f5fec07eaca5e2138f67bd4 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376347+00:00 |
| 5 | 7MMd | bionty.Organism | vertebrates | ensembl | release-108 | False | False | Ensembl | https://ftp.ensembl.org/pub/release-108/specie... | d97c1ee302e4072f5f5c7850eff0b642 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376556+00:00 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376768+00:00 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376957+00:00 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377100+00:00 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377210+00:00 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | 2023-06-20 | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | None | None | 1 | 2024-08-05 13:21:58.377317+00:00 |
# only lists the sources that are currently used
bt.Organism.list_source(currently_used=True).df()
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | release-112 | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.375733+00:00 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376768+00:00 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376957+00:00 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377100+00:00 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377210+00:00 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | 2023-06-20 | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | None | None | 1 | 2024-08-05 13:21:58.377317+00:00 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="ensembl", version="release-110", organism="vertebrates"
).one()
organisms= bt.Organism.public(source=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.Source.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | name | version | in_db | currently_used | description | url | md5 | source_website | dataframe_artifact_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | release-112 | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.375733+00:00 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376768+00:00 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.376957+00:00 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | release-57 | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377100+00:00 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | release-57 | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377210+00:00 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | 2023-06-20 | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | None | None | 1 | 2024-08-05 13:21:58.377317+00:00 |
| 11 | 4UGN | bionty.Gene | human | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377424+00:00 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.377952+00:00 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | release-112 | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | None | None | 1 | 2024-08-05 13:21:58.378601+00:00 |
| 22 | 3EYy | bionty.Protein | human | uniprot | 2024-03 | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | b5b9e7645065b4b3187114f07e3f402f | https://www.uniprot.org | None | None | 1 | 2024-08-05 13:21:58.378914+00:00 |
| 25 | 01RW | bionty.Protein | mouse | uniprot | 2024-03 | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | b1b6a196eb853088d36198d8e3749ec4 | https://www.uniprot.org | None | None | 1 | 2024-08-05 13:21:58.379352+00:00 |
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | None | 1 | 2024-08-05 13:21:58.379886+00:00 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | 2.0 | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | None | None | 1 | 2024-08-05 13:21:58.380085+00:00 |
| 30 | 6LyR | bionty.CellLine | all | clo | 2022-03-21 | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | None | None | 1 | 2024-08-05 13:21:58.380229+00:00 |
| 31 | FxPV | bionty.CellType | all | cl | 2024-02-13 | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | d6d962b58c48f372c2c98b71e0833242 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-05 13:21:58.380335+00:00 |
| 36 | Cwzj | bionty.Tissue | all | uberon | 2024-02-20 | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | 2048667b5fdf93192384bdf53cafba18 | http://obophenotype.github.io/uberon | None | None | 1 | 2024-08-05 13:21:58.380844+00:00 |
| 41 | 5Xov | bionty.Disease | all | mondo | 2024-02-06 | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 78914fa236773c5ea6605f7570df6245 | https://mondo.monarchinitiative.org | None | None | 1 | 2024-08-05 13:21:58.381353+00:00 |
| 46 | 4Pd5 | bionty.Disease | human | doid | 2024-01-31 | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | b36c15a4610757094f8db64b78ae2693 | https://disease-ontology.org | None | None | 1 | 2024-08-05 13:21:58.381857+00:00 |
| 53 | 5Fi2 | bionty.ExperimentalFactor | all | efo | 3.63.0 | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl | 603e6f6981d53d501c5921aa3940b095 | https://bioportal.bioontology.org/ontologies/EFO | None | None | 1 | 2024-08-05 13:21:58.382569+00:00 |
| 56 | 3405 | bionty.Phenotype | human | hp | 2024-03-06 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | 36b0d00c24a68edb9131707bc146a4c7 | https://hpo.jax.org | None | None | 1 | 2024-08-05 13:21:58.382873+00:00 |
| 60 | 3oMT | bionty.Phenotype | mammalian | mp | 2024-02-07 | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 31c27ed2c7d5774f8b20a77e4e1fd278 | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-05 13:21:58.383288+00:00 |
| 62 | 2K58 | bionty.Phenotype | zebrafish | zp | 2024-01-22 | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 01600a5d392419b27fc567362d4cfff8 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-05 13:21:58.383489+00:00 |
| 65 | 3ox8 | bionty.Phenotype | all | pato | 2023-05-18 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | None | None | 1 | 2024-08-05 13:21:58.386013+00:00 |
| 66 | 3RSX | bionty.Pathway | all | go | 2023-05-10 | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | None | None | 1 | 2024-08-05 13:21:58.386124+00:00 |
| 69 | 3rm9 | BFXPipeline | all | lamin | 1.0.0 | False | True | Bioinformatics Pipeline | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | None | None | 1 | 2024-08-05 13:21:58.386433+00:00 |
| 70 | 5alK | Drug | all | dron | 2024-03-02 | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | 84138459de4f65034e979f4e46783747 | https://bioportal.bioontology.org/ontologies/DRON | None | None | 1 | 2024-08-05 13:21:58.386533+00:00 |
| 72 | 7Zm9 | bionty.DevelopmentalStage | human | hsapdv | 2020-03-10 | False | True | Human Developmental Stages | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-05 13:21:58.386735+00:00 |
| 73 | 6vJm | bionty.DevelopmentalStage | mouse | mmusdv | 2020-03-10 | False | True | Mouse Developmental Stages | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-05 13:21:58.386837+00:00 |
| 74 | MJRq | bionty.Ethnicity | human | hancestro | 3.0 | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | None | None | 1 | 2024-08-05 13:21:58.386946+00:00 |
| 75 | 5JnV | BioSample | all | ncbi | 2023-09 | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | None | None | 1 | 2024-08-05 13:21:58.387049+00:00 |