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
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 2025-01-20 07:34:38.670000+00:00 1 None 1
89 3RSX bionty.Pathway all go False False Gene Ontology https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org 1 None 2023-05-10 None 2025-01-20 07:34:38.670000+00:00 1 None 1
90 40Jk bionty.Pathway all pw False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... d7d7fc41833dff97910863ca429eb769 https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.84 None 2025-01-20 07:34:38.670000+00:00 1 None 1
91 3xjF bionty.Pathway all pw False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... 392eb131d0513f9a186128ea4935edc9 https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.82 None 2025-01-20 07:34:38.670000+00:00 1 None 1
92 5cYE bionty.Pathway all pw False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... 02e2337bb1ab7cc4332ef6acc4cbdfa6 https://www.ebi.ac.uk/ols/ontologies/pw 1 None 7.79 None 2025-01-20 07:34:38.670000+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
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 2025-01-20 07:34:38.670000+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 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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.666000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+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 2025-01-20 07:34:38.670000+00:00 1 None 1