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)
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 formation|acetyl-CoA biosynthesis|a... [GO:0006084, GO:0071616] 79.069767
acetyl-CoA catabolic process GO:0046356 The Chemical Reactions And Pathways Resulting ... acetyl-CoA degradation|acetyl-CoA breakdown|ac... [GO:0034034, GO:0034031, GO:0044273, GO:000608... 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 degradation|acetyl-CoA breakdown|ac... [GO:0034034, GO:0034031, GO:0044273, GO:000608... 100.000000
acetyl-CoA biosynthetic process GO:0006085 The Chemical Reactions And Pathways Resulting ... acetyl-CoA formation|acetyl-CoA biosynthesis|a... [GO:0006084, GO:0071616] 92.682927
acetyl-CoA metabolic process GO:0006084 The Chemical Reactions And Pathways Involving ... acetyl coenzyme A metabolic process|acetyl-CoA... [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 degradation|acetyl-CoA breakdown|ac... [GO:0034034, GO:0034031, GO:0044273, GO:000608... 81.632653
acetyl-CoA metabolic process GO:0006084 The Chemical Reactions And Pathways Involving ... acetyl coenzyme A metabolic process|acetyl-CoA... [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 cinnamylic acid catabolic process|phenylacryli... [GO:0046271, GO:0072329, GO:0009803, GO:0120256] 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 cinnamic acid biosynthesis|phenylpropenoic aci... [GO:0072330, GO:0120255, GO:0009803, GO:0009699] 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 catabolism|cinnamic acid e... [GO:0009801, GO:0046271, GO:0120256] 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:0009074, GO:1902222] 84.905660
The Chemical Reactions And Pathways Resulting In The Breakdown Of Alanine, 2-Aminopropanoic Acid. GO:0006524 alanine catabolic process alanine catabolism|alanine breakdown|alanine d... [GO:1901606, 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.Pathway.list_source().df()
Hide code cell output
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_by_id updated_at
id
81 7Ent bionty.Pathway all go 2024-06-17 False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None None 1 2024-09-04 11:37:26.400358+00:00
82 3RSX bionty.Pathway all go 2023-05-10 False False Gene Ontology https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None None 1 2024-09-04 11:37:26.400392+00:00
83 40Jk bionty.Pathway all pw 7.84 False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... d7d7fc41833dff97910863ca429eb769 https://www.ebi.ac.uk/ols/ontologies/pw None None 1 2024-09-04 11:37:26.400427+00:00
84 3xjF bionty.Pathway all pw 7.82 False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... 392eb131d0513f9a186128ea4935edc9 https://www.ebi.ac.uk/ols/ontologies/pw None None 1 2024-09-04 11:37:26.400461+00:00
85 5cYE bionty.Pathway all pw 7.79 False False Pathway Ontology https://data.bioontology.org/ontologies/PW/sub... 02e2337bb1ab7cc4332ef6acc4cbdfa6 https://www.ebi.ac.uk/ols/ontologies/pw None None 1 2024-09-04 11:37:26.400496+00:00 
# only lists the sources that are currently used
bt.Pathway.list_source(currently_used=True).df()
uid entity organism name version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_by_id updated_at
id
81 7Ent bionty.Pathway all go 2024-06-17 False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None None 1 2024-09-04 11:37:26.400358+00:00

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 version in_db currently_used description url md5 source_website dataframe_artifact_id run_id created_by_id updated_at
id
1 33TU bionty.Organism vertebrates ensembl release-112 False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None None 1 2024-09-04 11:37:26.394877+00:00
6 6bbV bionty.Organism bacteria ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None None 1 2024-09-04 11:37:26.395087+00:00
7 6s9n bionty.Organism fungi ensembl release-57 False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None None 1 2024-09-04 11:37:26.395125+00:00
8 2PmT bionty.Organism metazoa ensembl release-57 False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None None 1 2024-09-04 11:37:26.395163+00:00
9 7GPH bionty.Organism plants ensembl release-57 False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None None 1 2024-09-04 11:37:26.395201+00:00
10 4tsk bionty.Organism all ncbitaxon 2023-06-20 False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None None 1 2024-09-04 11:37:26.395239+00:00
11 4UGN bionty.Gene human ensembl release-112 False True Ensembl s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None None 1 2024-09-04 11:37:26.395276+00:00
15 4r4f bionty.Gene mouse ensembl release-112 False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None None 1 2024-09-04 11:37:26.395425+00:00
19 4RPA bionty.Gene saccharomyces cerevisiae ensembl release-112 False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None None 1 2024-09-04 11:37:26.395582+00:00
22 3EYy bionty.Protein human uniprot 2024-03 False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... b5b9e7645065b4b3187114f07e3f402f https://www.uniprot.org None None 1 2024-09-04 11:37:26.395721+00:00
25 01RW bionty.Protein mouse uniprot 2024-03 False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... b1b6a196eb853088d36198d8e3749ec4 https://www.uniprot.org None None 1 2024-09-04 11:37:26.395834+00:00
28 3kDh bionty.CellMarker human cellmarker 2.0 False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None None 1 2024-09-04 11:37:26.395947+00:00
29 7bV5 bionty.CellMarker mouse cellmarker 2.0 False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None None 1 2024-09-04 11:37:26.395984+00:00
30 6LyR bionty.CellLine all clo 2022-03-21 False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO None None 1 2024-09-04 11:37:26.396021+00:00
32 1Lhf bionty.CellType all cl 2024-05-15 False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... 8a8638a9e79567935793e5007704c650 https://obophenotype.github.io/cell-ontology None None 1 2024-09-04 11:37:26.396095+00:00
39 MUtA bionty.Tissue all uberon 2024-08-07 False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... http://obophenotype.github.io/uberon None None 1 2024-09-04 11:37:26.396400+00:00
47 2L2r bionty.Disease all mondo 2024-06-04 False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... c47e8edb894c01f2511dfe0751fbc428 https://mondo.monarchinitiative.org None None 1 2024-09-04 11:37:26.396695+00:00
54 4ksw bionty.Disease human doid 2024-05-29 False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... bbefd72247d638edfcd31ec699947407 https://disease-ontology.org None None 1 2024-09-04 11:37:26.396955+00:00
62 69Xc bionty.ExperimentalFactor all efo 3.66.0 False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.66.0/efo.owl 6bd24217c740af7e1e771c1dabc9680b https://bioportal.bioontology.org/ontologies/EFO None None 1 2024-09-04 11:37:26.397252+00:00
67 48fB bionty.Phenotype human hp 2024-04-26 False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... e0f2e534eb2ad44a4d45573ef27b508f https://hpo.jax.org None None 1 2024-09-04 11:37:26.399862+00:00
72 4t7Q bionty.Phenotype mammalian mp 2024-06-18 False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... 795d8378fe48ec13b41d01a86dd1c86c https://github.com/mgijax/mammalian-phenotype-... None None 1 2024-09-04 11:37:26.400044+00:00
75 sqPX bionty.Phenotype zebrafish zp 2024-04-18 False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... 2231ebaa95becf8ff34a33c95a8d4350 https://github.com/obophenotype/zebrafish-phen... None None 1 2024-09-04 11:37:26.400150+00:00
79 6S4q bionty.Phenotype all pato 2024-03-28 False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... 6b1eaacd3d453b34375ce2e31c16328a https://github.com/pato-ontology/pato None None 1 2024-09-04 11:37:26.400289+00:00
81 7Ent bionty.Pathway all go 2024-06-17 False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... 7fa7ade5e3e26eab3959a7e4bc89ad4f http://geneontology.org None None 1 2024-09-04 11:37:26.400358+00:00
86 3rm9 BFXPipeline all lamin 1.0.0 False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... https://lamin.ai None None 1 2024-09-04 11:37:26.400530+00:00
87 ugaI Drug all dron 2024-08-05 False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... https://bioportal.bioontology.org/ontologies/DRON None None 1 2024-09-04 11:37:26.400565+00:00
91 1GbF bionty.DevelopmentalStage human hsapdv 2024-05-28 False True Human Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None None 1 2024-09-04 11:37:26.400703+00:00
93 10va bionty.DevelopmentalStage mouse mmusdv 2024-05-28 False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... https://github.com/obophenotype/developmental-... None None 1 2024-09-04 11:37:26.400771+00:00
95 MJRq bionty.Ethnicity human hancestro 3.0 False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro None None 1 2024-09-04 11:37:26.400840+00:00
96 5JnV BioSample all ncbi 2023-09 False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... 918db9bd1734b97c596c67d9654a4126 https://www.ncbi.nlm.nih.gov/biosample/docs/at... None None 1 2024-09-04 11:37:26.400874+00:00