Gene¶
lamindb provides access to the following public gene ontologies through bionty:
Here we show how to access and search gene ontologies to standardize new data.
# pip install 'lamindb[bionty]'
!lamin init --storage ./test-public-ontologies --schema bionty
→ initialized lamindb: testuser1/test-public-ontologies
import bionty as bt
import pandas as pd
PublicOntology objects¶
Let us create a public ontology accessor with public(), which chooses a default public ontology source from Source. It’s a PublicOntology object, which you can think about as a public registry:
public = bt.Gene.public(organism="human")
public
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: Gene
Organism: human
Source: ensembl, release-112
#terms: 75829
As for registries, you can export the ontology as a DataFrame:
df = public.df()
df.head()
| ensembl_gene_id | symbol | ncbi_gene_id | biotype | description | synonyms | |
|---|---|---|---|---|---|---|
| 0 | ENSG00000000003 | TSPAN6 | 7105 | protein_coding | tetraspanin 6 | TSPAN-6|T245|TM4SF6 |
| 1 | ENSG00000000005 | TNMD | 64102 | protein_coding | tenomodulin | TEM|MYODULIN|CHM1L|TENDIN|BRICD4 |
| 2 | ENSG00000000419 | DPM1 | 8813 | protein_coding | dolichyl-phosphate mannosyltransferase subunit... | CDGIE|MPDS |
| 3 | ENSG00000000457 | SCYL3 | 57147 | protein_coding | SCY1 like pseudokinase 3 | PACE1|PACE-1 |
| 4 | ENSG00000000460 | FIRRM | 55732 | protein_coding | FIGNL1 interacting regulator of recombination ... | C1ORF112|FLJ10706|APOLO1|FLIP|MEICA1 |
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 = public.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.tcf7
Gene(ensembl_gene_id='ENSG00000081059', symbol='TCF7', ncbi_gene_id='6932', biotype='protein_coding', description='transcription factor 7 ', synonyms='TCF-1')
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["TCF7"]
Gene(ensembl_gene_id='ENSG00000081059', symbol='TCF7', ncbi_gene_id='6932', biotype='protein_coding', description='transcription factor 7 ', synonyms='TCF-1')
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = public.lookup(public.ncbi_gene_id)
If multiple entries are matched, they are returned as a list:
lookup.bt_100126572
Gene(ensembl_gene_id='ENSG00000203733', symbol='GJE1', ncbi_gene_id='100126572', biotype='protein_coding', description='gap junction protein epsilon 1 ', synonyms='CX23')
Search terms¶
Search behaves in the same way as it does for registries:
public.search("TP53").head(3)
| ensembl_gene_id | symbol | ncbi_gene_id | biotype | description | synonyms | |
|---|---|---|---|---|---|---|
| 8175 | ENSG00000141510 | TP53 | 7157 | protein_coding | tumor protein p53 | LFS1|P53 |
| 15311 | ENSG00000182165 | TP53TG1 | None | lncRNA | TP53 target 1 | TP53AP1|H_RG012D21.9|LINC00096|TP53LC12 |
| 15671 | ENSG00000183632 | TP53TG3 | 24150 | protein_coding | TP53 target 3 | P53TG3|TP53TG3A |
By default, search also covers synonyms and all other fields containing strings:
public.search("PDL1").head(3)
| ensembl_gene_id | symbol | ncbi_gene_id | biotype | description | synonyms | |
|---|---|---|---|---|---|---|
| 5053 | ENSG00000120217 | CD274 | 29126 | protein_coding | CD274 molecule | PD-L1|PDCD1LG1|B7H1|PDL1|B7-H1|B7-H |
| 567 | ENSG00000040275 | SPDL1 | 54908 | protein_coding | spindle apparatus coiled-coil protein 1 | CCDC99|HSPINDLY|FLJ20364 |
| 31380 | ENSG00000229570 | GAPDHP58 | None | processed_pseudogene | glyceraldehyde 3 phosphate dehydrogenase pseud... | GAPDHL1|GAPDL1 |
You can turn search only in symbols by passing field="symbol":
public.search("PDL1", field="symbol").head(3)
| ensembl_gene_id | symbol | ncbi_gene_id | biotype | description | synonyms | |
|---|---|---|---|---|---|---|
| 567 | ENSG00000040275 | SPDL1 | 54908 | protein_coding | spindle apparatus coiled-coil protein 1 | CCDC99|HSPINDLY|FLJ20364 |
Search specific field (by default, search is done on all fields containing strings):
public.search("tumor protein p53", field=public.description).head()
| ensembl_gene_id | symbol | ncbi_gene_id | biotype | description | synonyms | |
|---|---|---|---|---|---|---|
| 1014 | ENSG00000067369 | TP53BP1 | 7158 | protein_coding | tumor protein p53 binding protein 1 | 53BP1|TDRD30|P202 |
| 1445 | ENSG00000078804 | TP53INP2 | 58476 | protein_coding | tumor protein p53 inducible nuclear protein 2 | PINH|FLJ21759|DJ1181N3.1|DKFZP434O0827|FLJ2350... |
| 4396 | ENSG00000115129 | TP53I3 | 9540 | protein_coding | tumor protein p53 inducible protein 3 | PIG3 |
| 5088 | ENSG00000120471 | TP53AIP1 | 63970 | protein_coding | tumor protein p53 regulated apoptosis inducing... | P53AIP1 |
| 8175 | ENSG00000141510 | TP53 | 7157 | protein_coding | tumor protein p53 | LFS1|P53 |
Standardize gene identifiers¶
Let us generate a DataFrame that stores a number of gene identifiers, some of which corrupted:
data = {
"gene symbol": ["A1CF", "A1BG", "FANCD1", "corrupted"],
"ncbi id": ["29974", "1", "5133", "corrupted"],
"ensembl_gene_id": [
"ENSG00000148584",
"ENSG00000121410",
"ENSG00000188389",
"ENSGcorrupted",
],
}
df_orig = pd.DataFrame(data).set_index("ensembl_gene_id")
df_orig
| gene symbol | ncbi id | |
|---|---|---|
| ensembl_gene_id | ||
| ENSG00000148584 | A1CF | 29974 |
| ENSG00000121410 | A1BG | 1 |
| ENSG00000188389 | FANCD1 | 5133 |
| ENSGcorrupted | corrupted | corrupted |
First we can check whether any of our values are validated against the ontology reference:
validated = public.validate(df_orig.index, public.ensembl_gene_id)
df_orig.index[~validated]
! 1 unique term (25.00%) is not validated: 'ENSGcorrupted'
Index(['ENSGcorrupted'], dtype='object', name='ensembl_gene_id')
Next, we validate which symbols are mappable against the ontology:
# based on NCBI gene ID
public.validate(df_orig["ncbi id"], public.ncbi_gene_id)
! 1 unique term (25.00%) is not validated: 'corrupted'
array([ True, True, True, False])
# based on Gene symbols
validated_symbols = public.validate(df_orig["gene symbol"], public.symbol)
df_orig["gene symbol"][~validated_symbols]
! 2 unique terms (50.00%) are not validated: 'FANCD1', 'corrupted'
ensembl_gene_id
ENSG00000188389 FANCD1
ENSGcorrupted corrupted
Name: gene symbol, dtype: object
Here, 2 of the gene symbols are not validated. Inspect why:
public.inspect(df_orig["gene symbol"], public.symbol);
! 2 unique terms (50.00%) are not validated for symbol: 'FANCD1', 'corrupted'
detected 1 unique terms with synonym: FANCD1
→ standardize terms via .standardize()
Logging suggests to use .standardize():
mapped_symbol_synonyms = public.standardize(df_orig["gene symbol"])
mapped_symbol_synonyms
['A1CF', 'A1BG', 'BRCA2', 'corrupted']
Optionally, you can return a mapper in the form of {synonym1: standardized_name1, ...}:
public.standardize(df_orig["gene symbol"], return_mapper=True)
{'FANCD1': 'BRCA2'}
We can use the standardized symbols as the new standardized index:
df_curated = df_orig.reset_index()
df_curated.index = mapped_symbol_synonyms
df_curated
| ensembl_gene_id | gene symbol | ncbi id | |
|---|---|---|---|
| A1CF | ENSG00000148584 | A1CF | 29974 |
| A1BG | ENSG00000121410 | A1BG | 1 |
| BRCA2 | ENSG00000188389 | FANCD1 | 5133 |
| corrupted | ENSGcorrupted | corrupted | corrupted |
You can convert identifiers by passing return_field to standardize():
public.standardize(
df_curated.index,
field=public.symbol,
return_field=public.ensembl_gene_id,
)
['ENSG00000148584', 'ENSG00000121410', 'ENSG00000139618', 'corrupted']
And return mappable identifiers as a dict:
public.standardize(
df_curated.index,
field=public.symbol,
return_field=public.ensembl_gene_id,
return_mapper=True,
)
{'A1BG': 'ENSG00000121410',
'BRCA2': 'ENSG00000139618',
'A1CF': 'ENSG00000148584'}
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.Gene").df()
Show code cell output
| 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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 11 | 4UGN | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 12 | 1HoN | bionty.Gene | human | ensembl | False | False | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | f9183bc44abb34459984e137b5de8af1 | https://www.ensembl.org | 1 | None | release-111 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 13 | 5dmX | bionty.Gene | human | ensembl | False | False | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 1 | None | release-110 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 14 | 404r | bionty.Gene | human | ensembl | False | False | Ensembl | s3://bionty-assets/human_ensembl_release-109_G... | 72da9968c74e96d136a489a6102a4546 | https://www.ensembl.org | 1 | None | release-109 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 16 | 5yZh | bionty.Gene | mouse | ensembl | False | False | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 5c071655347458307ac92b208f3c903a | https://www.ensembl.org | 1 | None | release-111 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 17 | 34Tj | bionty.Gene | mouse | ensembl | False | False | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 1 | None | release-110 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 18 | PGj9 | bionty.Gene | mouse | ensembl | False | False | Ensembl | s3://bionty-assets/mouse_ensembl_release-109_G... | 08a1165061151b270b985317322bd2ed | https://www.ensembl.org | 1 | None | release-109 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 20 | 4Yyq | bionty.Gene | saccharomyces cerevisiae | ensembl | False | False | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | a15fab1d9d15a56d32fd2fd8a8fa250a | https://www.ensembl.org | 1 | None | release-111 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 21 | 772a | bionty.Gene | saccharomyces cerevisiae | ensembl | False | False | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 1 | None | release-110 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Gene", 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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 11 | 4UGN | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.get(name="ensembl", version="release-112", organism="human")
public = bt.Gene.public(source=source)
public
PublicOntology
Entity: Gene
Organism: human
Source: ensembl, release-112
#terms: 75829
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()
Show code cell output
| 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_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 11 | 4UGN | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 22 | 3EYy | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | b5b9e7645065b4b3187114f07e3f402f | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 25 | 01RW | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | b1b6a196eb853088d36198d8e3749ec4 | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 30 | 6LyR | bionty.CellLine | all | clo | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 1 | None | 2022-03-21 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 |
| 32 | 3Uw2 | bionty.CellType | all | cl | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | https://obophenotype.github.io/cell-ontology | 1 | None | 2024-08-16 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 | |
| 41 | MUtA | bionty.Tissue | all | uberon | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | http://obophenotype.github.io/uberon | 1 | None | 2024-08-07 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 | |
| 50 | 4a3e | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | https://mondo.monarchinitiative.org | 1 | None | 2024-08-06 | None | 2025-01-24 13:56:36.815000+00:00 | 1 | None | 1 | |
| 59 | 4ksw | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | bbefd72247d638edfcd31ec699947407 | https://disease-ontology.org | 1 | None | 2024-05-29 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 67 | 2a1H | bionty.ExperimentalFactor | all | efo | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl | https://bioportal.bioontology.org/ontologies/EFO | 1 | None | 3.70.0 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 | |
| 74 | 48fB | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | e0f2e534eb2ad44a4d45573ef27b508f | https://hpo.jax.org | 1 | None | 2024-04-26 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 79 | 4t7Q | bionty.Phenotype | mammalian | mp | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 795d8378fe48ec13b41d01a86dd1c86c | https://github.com/mgijax/mammalian-phenotype-... | 1 | None | 2024-06-18 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 82 | sqPX | bionty.Phenotype | zebrafish | zp | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 2231ebaa95becf8ff34a33c95a8d4350 | https://github.com/obophenotype/zebrafish-phen... | 1 | None | 2024-04-18 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 86 | 6S4q | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | 6b1eaacd3d453b34375ce2e31c16328a | https://github.com/pato-ontology/pato | 1 | None | 2024-03-28 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 88 | 7Ent | bionty.Pathway | all | go | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | 7fa7ade5e3e26eab3959a7e4bc89ad4f | http://geneontology.org | 1 | None | 2024-06-17 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 93 | 3rm9 | BFXPipeline | all | lamin | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | https://lamin.ai | 1 | None | 1.0.0 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 | |
| 94 | ugaI | Drug | all | dron | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | https://bioportal.bioontology.org/ontologies/DRON | 1 | None | 2024-08-05 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 | |
| 98 | 1GbF | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 | |
| 100 | 10va | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 | |
| 102 | MJRq | bionty.Ethnicity | human | hancestro | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 1 | None | 3.0 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |
| 103 | 5JnV | BioSample | all | ncbi | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 1 | None | 2023-09 | None | 2025-01-24 13:56:36.819000+00:00 | 1 | None | 1 |