Pathway¶
lamindb provides access to the following public Pathway ontologies through bionty:
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, 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.Pathway.list_source().df()
Show 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 | |||||||||||||||
| 66 | 3RSX | bionty.Pathway | all | go | 2023-05-10 | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | None | None | 1 | 2024-08-05 13:21:58.386124+00:00 |
| 67 | 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 | 2024-08-05 13:21:58.386227+00:00 |
| 68 | 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 | 2024-08-05 13:21:58.386331+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 | |||||||||||||||
| 66 | 3RSX | bionty.Pathway | all | go | 2023-05-10 | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | None | None | 1 | 2024-08-05 13:21:58.386124+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()
Show 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 | 2024-08-05 13:21:58.375733+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 | 2024-08-05 13:21:58.376768+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 | 2024-08-05 13:21:58.376957+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 | 2024-08-05 13:21:58.377100+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 | 2024-08-05 13:21:58.377210+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 | 2024-08-05 13:21:58.377317+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 | 2024-08-05 13:21:58.377424+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 | 2024-08-05 13:21:58.377952+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 | 2024-08-05 13:21:58.378601+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 | 2024-08-05 13:21:58.378914+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 | 2024-08-05 13:21:58.379352+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 | 2024-08-05 13:21:58.379886+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 | 2024-08-05 13:21:58.380085+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 | 2024-08-05 13:21:58.380229+00:00 |
| 31 | FxPV | bionty.CellType | all | cl | 2024-02-13 | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | d6d962b58c48f372c2c98b71e0833242 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-05 13:21:58.380335+00:00 |
| 36 | Cwzj | bionty.Tissue | all | uberon | 2024-02-20 | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | 2048667b5fdf93192384bdf53cafba18 | http://obophenotype.github.io/uberon | None | None | 1 | 2024-08-05 13:21:58.380844+00:00 |
| 41 | 5Xov | bionty.Disease | all | mondo | 2024-02-06 | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | 78914fa236773c5ea6605f7570df6245 | https://mondo.monarchinitiative.org | None | None | 1 | 2024-08-05 13:21:58.381353+00:00 |
| 46 | 4Pd5 | bionty.Disease | human | doid | 2024-01-31 | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | b36c15a4610757094f8db64b78ae2693 | https://disease-ontology.org | None | None | 1 | 2024-08-05 13:21:58.381857+00:00 |
| 53 | 5Fi2 | bionty.ExperimentalFactor | all | efo | 3.63.0 | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl | 603e6f6981d53d501c5921aa3940b095 | https://bioportal.bioontology.org/ontologies/EFO | None | None | 1 | 2024-08-05 13:21:58.382569+00:00 |
| 56 | 3405 | bionty.Phenotype | human | hp | 2024-03-06 | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | 36b0d00c24a68edb9131707bc146a4c7 | https://hpo.jax.org | None | None | 1 | 2024-08-05 13:21:58.382873+00:00 |
| 60 | 3oMT | bionty.Phenotype | mammalian | mp | 2024-02-07 | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 31c27ed2c7d5774f8b20a77e4e1fd278 | https://github.com/mgijax/mammalian-phenotype-... | None | None | 1 | 2024-08-05 13:21:58.383288+00:00 |
| 62 | 2K58 | bionty.Phenotype | zebrafish | zp | 2024-01-22 | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 01600a5d392419b27fc567362d4cfff8 | https://github.com/obophenotype/zebrafish-phen... | None | None | 1 | 2024-08-05 13:21:58.383489+00:00 |
| 65 | 3ox8 | bionty.Phenotype | all | pato | 2023-05-18 | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | bd472f4971492109493d4ad8a779a8dd | https://github.com/pato-ontology/pato | None | None | 1 | 2024-08-05 13:21:58.386013+00:00 |
| 66 | 3RSX | bionty.Pathway | all | go | 2023-05-10 | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | None | None | 1 | 2024-08-05 13:21:58.386124+00:00 |
| 69 | 3rm9 | BFXPipeline | all | lamin | 1.0.0 | False | True | Bioinformatics Pipeline | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | None | None | 1 | 2024-08-05 13:21:58.386433+00:00 |
| 70 | 5alK | Drug | all | dron | 2024-03-02 | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | 84138459de4f65034e979f4e46783747 | https://bioportal.bioontology.org/ontologies/DRON | None | None | 1 | 2024-08-05 13:21:58.386533+00:00 |
| 72 | 7Zm9 | bionty.DevelopmentalStage | human | hsapdv | 2020-03-10 | False | True | Human Developmental Stages | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-05 13:21:58.386735+00:00 |
| 73 | 6vJm | bionty.DevelopmentalStage | mouse | mmusdv | 2020-03-10 | False | True | Mouse Developmental Stages | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | None | None | 1 | 2024-08-05 13:21:58.386837+00:00 |
| 74 | 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 | 2024-08-05 13:21:58.386946+00:00 |
| 75 | 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 | 2024-08-05 13:21:58.387049+00:00 |