Pathway

lamindb provides access to the following public protein 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 PublicSource. 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, 2023-05-10
#terms: 47514

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:0048308, GO:0048311]
GO:0000002 mitochondrial genome maintenance The Maintenance Of The Structure And Integrity... None [GO:0007005]
GO:0000003 reproduction The Production Of New Individuals That Contain... reproductive physiological process [GO:0008150]
GO:0000005 obsolete ribosomal chaperone activity Obsolete. Assists In The Correct Assembly Of R... ribosomal chaperone activity []
GO:0000006 high-affinity zinc transmembrane transporter a... Enables The Transfer Of Zinc Ions (Zn2+) From ... high affinity zinc uptake transmembrane transp... [GO:0005385]

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 catabolism to 2-ketoglutarate|acetyl-CoA catabolism to 2-oxoglutarate|acetyl-CoA catabolic process to 2-oxoglutarate|acetyl-CoA catabolism to alpha-ketoglutarate|acetyl-CoA catabolic process to 2-ketoglutarate|acetyl-CoA catabolic process to alpha-oxoglutarate|acetyl-CoA catabolism to alpha-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 catabolism to 2-ketoglutarate|acetyl-CoA catabolism to 2-oxoglutarate|acetyl-CoA catabolic process to 2-oxoglutarate|acetyl-CoA catabolism to alpha-ketoglutarate|acetyl-CoA catabolic process to 2-ketoglutarate|acetyl-CoA catabolic process to alpha-oxoglutarate|acetyl-CoA catabolism to alpha-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 catabolism to 2-ketoglutarate|acetyl-CoA catabolism to 2-oxoglutarate|acetyl-CoA catabolic process to 2-oxoglutarate|acetyl-CoA catabolism to alpha-ketoglutarate|acetyl-CoA catabolic process to 2-ketoglutarate|acetyl-CoA catabolic process to alpha-oxoglutarate|acetyl-CoA catabolism to alpha-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)
ontology_id definition synonyms parents __ratio__
name
acetyl-CoA assimilation pathway GO:0019681 The Pathways By Which Acetyl-Coa Is Processed ... acetyl-CoA catabolic process to alpha-ketoglut... [GO:0046356, GO:0006103] 85.185185
acetyl-CoA biosynthetic process GO:0006085 The Chemical Reactions And Pathways Resulting ... acetyl-CoA anabolism|acetyl-CoA synthesis|acet... [GO:0071616, GO:0006084] 79.069767
acetyl-CoA catabolic process GO:0046356 The Chemical Reactions And Pathways Resulting ... acetyl-CoA catabolism|acetyl-CoA breakdown|ace... [GO:0044273, GO:0006084, GO:0009154, GO:003403... 75.555556

By default, search also covers synonyms:

pathways.search("acetyl-CoA catabolism").head(3)
ontology_id definition synonyms parents __ratio__
name
acetyl-CoA catabolic process GO:0046356 The Chemical Reactions And Pathways Resulting ... acetyl-CoA catabolism|acetyl-CoA breakdown|ace... [GO:0044273, GO:0006084, GO:0009154, GO:003403... 100.000000
acetyl-CoA biosynthetic process GO:0006085 The Chemical Reactions And Pathways Resulting ... acetyl-CoA anabolism|acetyl-CoA synthesis|acet... [GO:0071616, GO:0006084] 92.682927
acetyl-CoA metabolic process GO:0006084 The Chemical Reactions And Pathways Involving ... acetyl-CoA metabolism|acetyl coenzyme A metabo... [GO:0006637] 90.476190

You can turn this off synonym by passing synonyms_field=None:

pathways.search("acetyl-CoA catabolism", synonyms_field=None).head(3)
ontology_id definition synonyms parents __ratio__
name
acetyl-CoA catabolic process GO:0046356 The Chemical Reactions And Pathways Resulting ... acetyl-CoA catabolism|acetyl-CoA breakdown|ace... [GO:0044273, GO:0006084, GO:0009154, GO:003403... 81.632653
acetyl-CoA metabolic process GO:0006084 The Chemical Reactions And Pathways Involving ... acetyl-CoA metabolism|acetyl coenzyme A metabo... [GO:0006637] 73.469388
acetyl-CoA carboxylase complex GO:0009317 A Protein Complex That Catalyzes The First Ste... ACCase complex [GO:1902494] 70.588235

Search another field (default is .name):

pathways.search(
    "Chemical reactions and pathways resulting in the breakdown of Cinnamic Acid,3-Phenyl-2-Propenoic Acid.",
    field=pathways.definition,
).head()
ontology_id name synonyms parents __ratio__
definition
The Chemical Reactions And Pathways Resulting In The Breakdown Of Cinnamic Acid, 3-Phenyl-2-Propenoic Acid. GO:0046281 cinnamic acid catabolic process cinnamic acid catabolism|phenylacrylic acid ca... [GO:0120256, GO:0046271, GO:0009803, GO:0072329] 97.584541
The Chemical Reactions And Pathways Resulting In The Formation Of Cinnamic Acid, 3-Phenyl-2-Propenoic Acid. GO:0009800 cinnamic acid biosynthetic process cinnamylic acid biosynthesis|cinnamic acid ana... [GO:0009699, GO:0009803, GO:0120255, GO:0072330] 92.753623
The Chemical Reactions And Pathways Resulting In The Breakdown Of Ester Derivatives Of Cinnamic Acid, Phenylpropenoic Acid. GO:0046282 cinnamic acid ester catabolic process cinnamic acid ester breakdown|cinnamic acid es... [GO:0120256, GO:0046271, GO:0009801] 86.995516
The Chemical Reactions And Pathways Resulting In The Breakdown Of Phenylalanine, 2-Amino-3-Phenylpropanoic Acid. GO:0006559 L-phenylalanine catabolic process L-phenylalanine degradation|L-phenylalanine ca... [GO:0006558, GO:1902222, GO:0009074] 84.905660
The Chemical Reactions And Pathways Resulting In The Breakdown Of Alanine, 2-Aminopropanoic Acid. GO:0006524 alanine catabolic process alanine breakdown|alanine catabolism|alanine d... [GO:0009080, GO:0006522] 83.248731

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 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.PublicSource.filter(entity="Pathway").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-06-19 23:14:43.640094+00:00
65 4FmN Pathway all False pw Pathway Ontology 7.82 https://data.bioontology.org/ontologies/PW/sub... 392eb131d0513f9a186128ea4935edc9 https://www.ebi.ac.uk/ols/ontologies/pw None 1 2024-06-19 23:14:43.640191+00:00
66 QfYh Pathway all False pw Pathway Ontology 7.79 https://data.bioontology.org/ontologies/PW/sub... 02e2337bb1ab7cc4332ef6acc4cbdfa6 https://www.ebi.ac.uk/ols/ontologies/pw None 1 2024-06-19 23:14:43.640288+00:00

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

public_source = bt.PublicSource.filter(
    source="go", version="2023-05-10", organism="all"
).one()
pathways= bt.Pathway.public(public_source=public_source)
pathways
PublicOntology
Entity: Pathway
Organism: all
Source: go, 2023-05-10
#terms: 47514

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide code cell output
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-06-19 23:14:43.633921+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-06-19 23:14:43.634460+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-06-19 23:14:43.634557+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-06-19 23:14:43.634654+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-06-19 23:14:43.634750+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-06-19 23:14:43.634846+00:00
11 1hx4 Gene human True ensembl Ensembl release-112 s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None 1 2024-06-19 23:14:43.634944+00:00
15 76FX Gene mouse True ensembl Ensembl release-112 s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None 1 2024-06-19 23:14:43.635343+00:00
19 7LW6 Gene saccharomyces cerevisiae True ensembl Ensembl release-112 s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None 1 2024-06-19 23:14:43.635731+00:00
22 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org None 1 2024-06-19 23:14:43.636031+00:00
24 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org None 1 2024-06-19 23:14:43.636233+00:00
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-06-19 23:14:43.636426+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-06-19 23:14:43.636524+00:00
28 6cbC CellLine all True clo Cell Line Ontology 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None 1 2024-06-19 23:14:43.636619+00:00
29 3DeN CellType all True cl Cell Ontology 2024-02-13 http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 1 2024-06-19 23:14:43.636715+00:00
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-06-19 23:14:43.637192+00:00
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-06-19 23:14:43.637670+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-06-19 23:14:43.638168+00:00
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-06-19 23:14:43.638843+00:00
54 2WLc Phenotype human True hp Human Phenotype Ontology 2024-03-06 https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None 1 2024-06-19 23:14:43.639132+00:00
58 6zE1 Phenotype mammalian True mp Mammalian Phenotype Ontology 2024-02-07 https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None 1 2024-06-19 23:14:43.639514+00:00
60 7EnA Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2024-01-22 https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None 1 2024-06-19 23:14:43.639706+00:00
63 55lY Phenotype all True pato Phenotype And Trait Ontology 2023-05-18 http://purl.obolibrary.org/obo/pato/releases/2... bd472f4971492109493d4ad8a779a8dd https://github.com/pato-ontology/pato None 1 2024-06-19 23:14:43.639997+00:00
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-06-19 23:14:43.640094+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-06-19 23:14:43.640389+00:00
68 5alK Drug all True dron Drug Ontology 2024-03-02 https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None 1 2024-06-19 23:14:43.640486+00:00
70 7CRn DevelopmentalStage human True hsapdv Human Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 https://github.com/obophenotype/developmental-... None 1 2024-06-19 23:14:43.640679+00:00
71 16tR DevelopmentalStage mouse True mmusdv Mouse Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 https://github.com/obophenotype/developmental-... None 1 2024-06-19 23:14:43.640781+00:00
72 3Tlc Ethnicity human True hancestro Human Ancestry Ontology 3.0 https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None 1 2024-06-19 23:14:43.642901+00:00
73 5JnV BioSample all True ncbi NCBI BioSample attributes 2023-09 s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None 1 2024-06-19 23:14:43.643010+00:00