Pathway¶
lamindb provides access to the following public protein 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
💡 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
📖 .df(): ontology reference table
🔎 .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
✅ .validate(): strictly validate values
🧐 .inspect(): full inspection of values
👽 .standardize(): convert to standardized names
🪜 .diff(): difference between two versions
🔗 .to_pronto(): Pronto.Ontology object
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()
| created_at | created_by_id | run_id | updated_at | uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 48 | 2024-05-20 08:30:49.154222+00:00 | 1 | None | 2024-05-20 08:30:49.154245+00:00 | 48aa | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org |
| 49 | 2024-05-20 08:30:49.154316+00:00 | 1 | None | 2024-05-20 08:30:49.154338+00:00 | 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 |
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
📖 .df(): ontology reference table
🔎 .lookup(): autocompletion of terms
🎯 .search(): free text search of terms
✅ .validate(): strictly validate values
🧐 .inspect(): full inspection of values
👽 .standardize(): convert to standardized names
🪜 .diff(): difference between two versions
🔗 .to_pronto(): Pronto.Ontology object
The currently used ontologies can be displayed using:
bt.PublicSource.filter(currently_used=True).df()
Show code cell output
| created_at | created_by_id | run_id | updated_at | uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||
| 1 | 2024-05-20 08:30:49.149639+00:00 | 1 | None | 2024-05-20 08:30:49.149711+00:00 | 6IUo | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org |
| 4 | 2024-05-20 08:30:49.149991+00:00 | 1 | None | 2024-05-20 08:30:49.150015+00:00 | 2Jzh | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org |
| 5 | 2024-05-20 08:30:49.150087+00:00 | 1 | None | 2024-05-20 08:30:49.150110+00:00 | 1kdI | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org |
| 6 | 2024-05-20 08:30:49.150182+00:00 | 1 | None | 2024-05-20 08:30:49.150205+00:00 | 2mIM | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org |
| 7 | 2024-05-20 08:30:49.150275+00:00 | 1 | None | 2024-05-20 08:30:49.150298+00:00 | 2XQ6 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org |
| 8 | 2024-05-20 08:30:49.150368+00:00 | 1 | None | 2024-05-20 08:30:49.150392+00:00 | 1Vzs | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon |
| 9 | 2024-05-20 08:30:49.150462+00:00 | 1 | None | 2024-05-20 08:30:49.150486+00:00 | 4yVc | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org |
| 11 | 2024-05-20 08:30:49.150652+00:00 | 1 | None | 2024-05-20 08:30:49.150676+00:00 | 2akp | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org |
| 13 | 2024-05-20 08:30:49.150844+00:00 | 1 | None | 2024-05-20 08:30:49.150869+00:00 | 2UvD | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org |
| 14 | 2024-05-20 08:30:49.150941+00:00 | 1 | None | 2024-05-20 08:30:49.150964+00:00 | 7llW | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org |
| 16 | 2024-05-20 08:30:49.151130+00:00 | 1 | None | 2024-05-20 08:30:49.151153+00:00 | 5U7J | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org |
| 18 | 2024-05-20 08:30:49.151317+00:00 | 1 | None | 2024-05-20 08:30:49.151340+00:00 | 5nkB | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker |
| 19 | 2024-05-20 08:30:49.151411+00:00 | 1 | None | 2024-05-20 08:30:49.151433+00:00 | 6AFz | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker |
| 20 | 2024-05-20 08:30:49.151504+00:00 | 1 | None | 2024-05-20 08:30:49.151526+00:00 | 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 |
| 21 | 2024-05-20 08:30:49.151597+00:00 | 1 | None | 2024-05-20 08:30:49.151619+00:00 | 6tvq | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology |
| 25 | 2024-05-20 08:30:49.151976+00:00 | 1 | None | 2024-05-20 08:30:49.151999+00:00 | 1PY3 | Tissue | all | True | uberon | Uberon multi-species anatomy ontology | 2023-09-05 | http://purl.obolibrary.org/obo/uberon/releases... | abcee3ede566d1311d758b853ccdf5aa | http://obophenotype.github.io/uberon |
| 29 | 2024-05-20 08:30:49.152350+00:00 | 1 | None | 2024-05-20 08:30:49.152373+00:00 | 6EOm | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org |
| 33 | 2024-05-20 08:30:49.152733+00:00 | 1 | None | 2024-05-20 08:30:49.152757+00:00 | 3V9D | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org |
| 39 | 2024-05-20 08:30:49.153325+00:00 | 1 | None | 2024-05-20 08:30:49.153350+00:00 | 6fKX | ExperimentalFactor | all | True | efo | The Experimental Factor Ontology | 3.57.0 | http://www.ebi.ac.uk/efo/releases/v3.57.0/efo.owl | 2ecafc69b3aba7bdb31ad99438505c05 | https://bioportal.bioontology.org/ontologies/EFO |
| 41 | 2024-05-20 08:30:49.153517+00:00 | 1 | None | 2024-05-20 08:30:49.153541+00:00 | 6jHz | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org |
| 44 | 2024-05-20 08:30:49.153800+00:00 | 1 | None | 2024-05-20 08:30:49.153823+00:00 | 4q5A | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... |
| 45 | 2024-05-20 08:30:49.153894+00:00 | 1 | None | 2024-05-20 08:30:49.153916+00:00 | 6Czy | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... |
| 47 | 2024-05-20 08:30:49.154126+00:00 | 1 | None | 2024-05-20 08:30:49.154150+00:00 | 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 |
| 48 | 2024-05-20 08:30:49.154222+00:00 | 1 | None | 2024-05-20 08:30:49.154245+00:00 | 48aa | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org |
| 50 | 2024-05-20 08:30:49.154409+00:00 | 1 | None | 2024-05-20 08:30:49.154431+00:00 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai |
| 51 | 2024-05-20 08:30:49.154502+00:00 | 1 | None | 2024-05-20 08:30:49.154524+00:00 | 3TI0 | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON |
| 52 | 2024-05-20 08:30:49.154594+00:00 | 1 | None | 2024-05-20 08:30:49.154616+00:00 | 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-... |
| 53 | 2024-05-20 08:30:49.154686+00:00 | 1 | None | 2024-05-20 08:30:49.154708+00:00 | 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-... |
| 54 | 2024-05-20 08:30:49.154778+00:00 | 1 | None | 2024-05-20 08:30:49.154800+00:00 | 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 |
| 55 | 2024-05-20 08:30:49.154870+00:00 | 1 | None | 2024-05-20 08:30:49.154892+00:00 | 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... |