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

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

→ connected lamindb: testuser1/test-public-ontologies

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()
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
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
89 7Ent3V2y bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2024-06-17 None 2025-03-10 13:25:14.952000+00:00 1 None 1
90 3RSXOivB bionty.Pathway all go False False Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2023-05-10 None 2025-03-10 13:25:14.952000+00:00 1 None 1
91 40JkiRMw bionty.Pathway all pw False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... None https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.84 None 2025-03-10 13:25:14.952000+00:00 1 None 1
92 3xjF8mmv bionty.Pathway all pw False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... None https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.82 None 2025-03-10 13:25:14.952000+00:00 1 None 1
93 5cYEChgN bionty.Pathway all pw False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... None https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.79 None 2025-03-10 13:25:14.952000+00:00 1 None 1 
# only lists the sources that are currently used
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_code
id
89 7Ent3V2y bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2024-06-17 None 2025-03-10 13:25:14.952000+00:00 1 None 1

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

source = bt.Source.filter(
    name="go", version="2023-05-10", organism="all"
).one()
pathways= bt.Pathway.public(source=source)
pathways

PublicOntology
Entity: Pathway
Organism: all
Source: go, 2023-05-10
#terms: 47514

The currently used ontologies can be displayed using:

bt.Source.filter(currently_used=True).df()
Hide 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 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 2025-03-10 13:25:14.948000+00:00 1 None 1
6 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 2025-03-10 13:25:14.948000+00:00 1 None 1
7 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
8 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
9 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 2025-03-10 13:25:14.948000+00:00 1 None 1
10 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-03-10 13:25:14.948000+00:00 1 None 1
11 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 2025-03-10 13:25:14.948000+00:00 1 None 1
15 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 2025-03-10 13:25:14.948000+00:00 1 None 1
19 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 2025-03-10 13:25:14.948000+00:00 1 None 1
22 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 2025-03-10 13:25:14.948000+00:00 1 None 1
25 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 2025-03-10 13:25:14.948000+00:00 1 None 1
28 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 2025-03-10 13:25:14.948000+00:00 1 None 1
29 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 2025-03-10 13:25:14.948000+00:00 1 None 1
30 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-03-10 13:25:14.948000+00:00 1 None 1
32 3Uw2Va7a 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 2024-08-16 None 2025-03-10 13:25:14.948000+00:00 1 None 1
41 MUtAGdL4 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 2024-08-07 None 2025-03-10 13:25:14.948000+00:00 1 None 1
50 4a3ejKuf bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2024-08-06 None 2025-03-10 13:25:14.948000+00:00 1 None 1
59 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 2025-03-10 13:25:14.952000+00:00 1 None 1
67 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 2025-03-10 13:25:14.952000+00:00 1 None 1
75 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 2025-03-10 13:25:14.952000+00:00 1 None 1
80 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
83 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
87 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 2025-03-10 13:25:14.952000+00:00 1 None 1
89 7Ent3V2y bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2024-06-17 None 2025-03-10 13:25:14.952000+00:00 1 None 1
94 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 2025-03-10 13:25:14.952000+00:00 1 None 1
95 ugaIoIlj Drug all dron False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-03-10 13:25:14.952000+00:00 1 None 1
99 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 2025-03-10 13:25:14.952000+00:00 1 None 1
101 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 2025-03-10 13:25:14.952000+00:00 1 None 1
103 MJRqduf9 bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... None https://github.com/EBISPOT/hancestro 1 None 3.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
104 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 2025-03-10 13:25:14.952000+00:00 1 None 1