Pathway

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

  1. Gene Ontology

  2. Pathway Ontology

Here we show how to access and search Pathway 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:

pathways = bt.Pathway.public(organism="all")
pathways

PublicOntology
Entity: Pathway
Organism: all
Source: go, 2024-06-17
#terms: 47856

As for registries, you can export the ontology as a DataFrame:

df = pathways.df()
df.head()

/tmp/ipykernel_3605/2827291915.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  df = pathways.df()
name definition synonyms parents
ontology_id
GO:0000001 mitochondrion inheritance The Distribution Of Mitochondria, Including Th... mitochondrial inheritance [GO:0048311, GO:0048308]
GO:0002230 positive regulation of defense response to vir... Any Host Process That Results In The Promotion... upregulation of antiviral response by host|pos... [GO:0050691]
GO:0002231 detection of oomycetes The Series Of Events In Which A Stimulus From ... None [GO:0098543, GO:0002239]
GO:0002232 leukocyte chemotaxis involved in inflammatory ... The Movement Of An Immune Cell In Response To ... None [GO:0030595, GO:0002523]
GO:0002233 leukocyte chemotaxis involved in immune response The Movement Of An Immune Cell In Response To ... immune cell chemotaxis during immune response|... [GO:0030595, GO:0002522]

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 = pathways.lookup()

The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):

lookup.acetyl_coa_assimilation_pathway

Pathway(ontology_id='GO:0019681', name='acetyl-CoA assimilation pathway', definition='The Pathways By Which Acetyl-Coa Is Processed And Converted Into Alpha-Ketoglutarate (2-Oxoglutarate); Methanogenic Archaea Use These Pathways To Assimilate Acetyl-Coa Into The Cell.', synonyms='acetyl-CoA catabolic process to alpha-ketoglutarate|acetyl-CoA catabolic process to 2-ketoglutarate|acetyl-CoA catabolism to 2-ketoglutarate|acetyl-CoA catabolic process to 2-oxoglutarate|acetyl-CoA catabolism to alpha-oxoglutarate|acetyl-CoA catabolic process to alpha-oxoglutarate|acetyl-CoA catabolism to alpha-ketoglutarate|acetyl-CoA catabolism to 2-oxoglutarate', parents=array(['GO:0046356', 'GO:0006103'], dtype=object))

To look up the exact original strings, convert the lookup object to dict and use the [] accessor:

lookup_dict = lookup.dict()
lookup_dict["acetyl-CoA assimilation pathway"]

Pathway(ontology_id='GO:0019681', name='acetyl-CoA assimilation pathway', definition='The Pathways By Which Acetyl-Coa Is Processed And Converted Into Alpha-Ketoglutarate (2-Oxoglutarate); Methanogenic Archaea Use These Pathways To Assimilate Acetyl-Coa Into The Cell.', synonyms='acetyl-CoA catabolic process to alpha-ketoglutarate|acetyl-CoA catabolic process to 2-ketoglutarate|acetyl-CoA catabolism to 2-ketoglutarate|acetyl-CoA catabolic process to 2-oxoglutarate|acetyl-CoA catabolism to alpha-oxoglutarate|acetyl-CoA catabolic process to alpha-oxoglutarate|acetyl-CoA catabolism to alpha-ketoglutarate|acetyl-CoA catabolism to 2-oxoglutarate', parents=array(['GO:0046356', 'GO:0006103'], dtype=object))

By default, the name field is used to generate lookup keys. You can specify another field to look up:

lookup = pathways.lookup(pathways.ontology_id)

lookup.go_0019681

Pathway(ontology_id='GO:0019681', name='acetyl-CoA assimilation pathway', definition='The Pathways By Which Acetyl-Coa Is Processed And Converted Into Alpha-Ketoglutarate (2-Oxoglutarate); Methanogenic Archaea Use These Pathways To Assimilate Acetyl-Coa Into The Cell.', synonyms='acetyl-CoA catabolic process to alpha-ketoglutarate|acetyl-CoA catabolic process to 2-ketoglutarate|acetyl-CoA catabolism to 2-ketoglutarate|acetyl-CoA catabolic process to 2-oxoglutarate|acetyl-CoA catabolism to alpha-oxoglutarate|acetyl-CoA catabolic process to alpha-oxoglutarate|acetyl-CoA catabolism to alpha-ketoglutarate|acetyl-CoA catabolism to 2-oxoglutarate', parents=array(['GO:0046356', 'GO:0006103'], dtype=object))

Search terms

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

pathways.search("acetyl-coa assimilation").head(3)
name definition synonyms parents
ontology_id
GO:0019681 acetyl-CoA assimilation pathway The Pathways By Which Acetyl-Coa Is Processed ... acetyl-CoA catabolic process to alpha-ketoglut... [GO:0046356, GO:0006103]

By default, search also covers synonyms and all other fileds containing strings:

pathways.search("acetyl-CoA catabolism").head(3)
name definition synonyms parents
ontology_id
GO:0046356 acetyl-CoA catabolic process The Chemical Reactions And Pathways Resulting ... acetyl-CoA degradation|acetyl-CoA breakdown|ac... [GO:0034034, GO:0034031, GO:0044273, GO:000608...
GO:0019681 acetyl-CoA assimilation pathway The Pathways By Which Acetyl-Coa Is Processed ... acetyl-CoA catabolic process to alpha-ketoglut... [GO:0046356, GO:0006103]

Search specific field (by default, search is done on all fields containing strings):

pathways.search(
    "chemical reactions and pathways resulting in the breakdown of acetyl-CoA",
    field=pathways.definition,
).head()
name definition synonyms parents
ontology_id
GO:0046356 acetyl-CoA catabolic process The Chemical Reactions And Pathways Resulting ... acetyl-CoA degradation|acetyl-CoA breakdown|ac... [GO:0034034, GO:0034031, GO:0044273, GO:000608...

Standardize Pathway identifiers

Let us generate a DataFrame that stores a number of Pathway identifiers, some of which corrupted:

df_orig = pd.DataFrame(
    index=[
        "GO:1905210",
        "GO:1905211",
        "GO:1905212",
        "GO:1905208",
        "This pathway does not exist",
    ]
)
df_orig
GO:1905210
GO:1905211
GO:1905212
GO:1905208
This pathway does not exist

We can check whether any of our values are validated against the ontology reference:

validated = pathways.validate(df_orig.index, pathways.name)
df_orig.index[~validated]

! 5 unique terms (100.00%) are not validated: 'GO:1905210', 'GO:1905211', 'GO:1905212', 'GO:1905208', 'This pathway does not exist'

Index(['GO:1905210', 'GO:1905211', 'GO:1905212', 'GO:1905208',
       'This pathway 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.Pathway").df()
Hide code cell output 
/tmp/ipykernel_3605/590922682.py:1: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(entity="bionty.Pathway").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
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 2025-09-14 14:08:05.857000+00:00 1 None 1
26 40JkiRMw bionty.Pathway all pw False False Pathway Ontology http://purl.obolibrary.org/obo/pw/7.84/pw.owl None https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.84 None 2025-09-14 14:08:05.857000+00:00 1 None 1 
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.Pathway", currently_used=True).df()

/tmp/ipykernel_3605/3742124327.py:2: DeprecationWarning: Use to_dataframe instead of df, df will be removed in the future.
  bt.Source.filter(entity="bionty.Pathway", 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
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 2025-09-14 14:08:05.857000+00:00 1 None 1

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

source = bt.Source.filter(
    name="go", organism="all"
).first()
pathways= bt.Pathway.public(source=source)
pathways

PublicOntology
Entity: Pathway
Organism: all
Source: go, 2024-06-17
#terms: 47856

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).df()
Hide code cell output 
/tmp/ipykernel_3605/2711573161.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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+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 2025-09-14 14:08:05.857000+00:00 1 None 1