Pathway ontologies#
lamindb provides access to the following public protein ontologies through lnschema-bionty:
Here we show how to access and search pathway ontologies to standardize new data.
Setup#
!lamin init --storage ./test-pathway --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-22 11:25:19 UTC)
✅ saved: Storage(uid='2yqrXYZH', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-pathway', type='local', updated_at=2023-12-22 11:25:19 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-pathway
💡 did not register local instance on hub
import lnschema_bionty as lb
import pandas as pd
# adds an entry "human" into an empty instance
lb.settings.organism = "human"
💡 loaded instance: testuser1/test-pathway
Bionty objects#
Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:
pathway_bt = lb.Pathway.bionty()
pathway_bt
Pathway
Organism: all
Source: go, 2023-05-10
#terms: 47514
📖 Pathway.df(): ontology reference table
🔎 Pathway.lookup(): autocompletion of terms
🎯 Pathway.search(): free text search of terms
✅ Pathway.validate(): strictly validate values
🧐 Pathway.inspect(): full inspection of values
👽 Pathway.standardize(): convert to standardized names
🪜 Pathway.diff(): difference between two versions
🔗 Pathway.ontology: Pronto.Ontology object
As for registries, you can export the ontology as a DataFrame:
df = pathway_bt.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 pathway_bt.ontology.
Look up terms#
As for registries, terms can be looked up with auto-complete:
lookup = pathway_bt.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 = pathway_bt.lookup(pathway_bt.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:
pathway_bt = lb.Pathway.bionty()
pathway_bt.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:
pathway_bt.search("acetyl-CoA catabolism").head(1)
| 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... | 100.0 |
Search another field (default is .name):
pathway_bt.search(
"Chemical reactions and pathways resulting in the breakdown of Cinnamic Acid,"
" 3-Phenyl-2-Propenoic Acid.",
field=pathway_bt.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] | 98.076923 |
| 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] | 93.269231 |
| 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] | 86.607143 |
| 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] | 84.507042 |
| 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] | 82.828283 |
Standardize pathway identifiers#
Let us generate a DataFrame that stores a number of pathway identifiers, some of which are 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 = pathway_bt.validate(df_orig.index, pathway_bt.ontology_id)
df_orig.index[~validated]
❗ 1 term (20.00%) is not validated: This pathway does not exist
Index(['This pathway does not exist'], dtype='object')
Ontology source versions#
For any given entity, we can choose from a number of versions:
lb.BiontySource.filter(entity="Pathway").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 44 | h0rU | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2023-12-22 11:25:19.179627+00:00 | 1 |
| 45 | DiJI | Pathway | all | False | pw | Pathway Ontology | 7.79 | https://data.bioontology.org/ontologies/PW/sub... | 02e2337bb1ab7cc4332ef6acc4cbdfa6 | https://www.ebi.ac.uk/ols/ontologies/pw | 2023-12-22 11:25:19.179660+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
bionty_source = lb.BiontySource.filter(
source="go", version="2023-05-10", organism="all"
).one()
pathway_bt = lb.Pathway.bionty(bionty_source=bionty_source)
pathway_bt
Pathway
Organism: all
Source: go, 2023-05-10
#terms: 47514
📖 Pathway.df(): ontology reference table
🔎 Pathway.lookup(): autocompletion of terms
🎯 Pathway.search(): free text search of terms
✅ Pathway.validate(): strictly validate values
🧐 Pathway.inspect(): full inspection of values
👽 Pathway.standardize(): convert to standardized names
🪜 Pathway.diff(): difference between two versions
🔗 Pathway.ontology: Pronto.Ontology object
The currently used ontologies can be displayed using:
lb.BiontySource.filter(currently_used=True).df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | zvGR | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2023-12-22 11:25:19.178158+00:00 | 1 |
| 4 | TE9h | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2023-12-22 11:25:19.178287+00:00 | 1 |
| 5 | OZIG | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2023-12-22 11:25:19.178322+00:00 | 1 |
| 6 | W07m | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2023-12-22 11:25:19.178356+00:00 | 1 |
| 7 | AVh3 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2023-12-22 11:25:19.178390+00:00 | 1 |
| 8 | MdBu | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2023-12-22 11:25:19.178424+00:00 | 1 |
| 9 | o36k | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2023-12-22 11:25:19.178457+00:00 | 1 |
| 11 | VTEw | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2023-12-22 11:25:19.178525+00:00 | 1 |
| 13 | Uhnp | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2023-12-22 11:25:19.178592+00:00 | 1 |
| 14 | 000Q | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2023-12-22 11:25:19.178625+00:00 | 1 |
| 16 | tD7O | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2023-12-22 11:25:19.178692+00:00 | 1 |
| 18 | vqWI | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2023-12-22 11:25:19.178758+00:00 | 1 |
| 19 | ypPK | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2023-12-22 11:25:19.178791+00:00 | 1 |
| 20 | 2Zjk | CellLine | all | True | clo | Cell Line Ontology | 2022-03-21 | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 2023-12-22 11:25:19.178824+00:00 | 1 |
| 21 | 4shh | CellType | all | True | cl | Cell Ontology | 2023-08-24 | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | 2023-12-22 11:25:19.178857+00:00 | 1 |
| 25 | LmWQ | 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 | 2023-12-22 11:25:19.178998+00:00 | 1 |
| 29 | zMWv | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2023-12-22 11:25:19.179132+00:00 | 1 |
| 33 | cxPr | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2023-12-22 11:25:19.179264+00:00 | 1 |
| 35 | 2wto | 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 | 2023-12-22 11:25:19.179330+00:00 | 1 |
| 37 | 3SSF | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2023-12-22 11:25:19.179395+00:00 | 1 |
| 40 | nwdt | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2023-12-22 11:25:19.179494+00:00 | 1 |
| 41 | zAfB | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2023-12-22 11:25:19.179527+00:00 | 1 |
| 43 | p1co | 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 | 2023-12-22 11:25:19.179594+00:00 | 1 |
| 44 | h0rU | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2023-12-22 11:25:19.179627+00:00 | 1 |
| 46 | fxHJ | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2023-12-22 11:25:19.179693+00:00 | 1 |
| 47 | chfO | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2023-12-22 11:25:19.179726+00:00 | 1 |
| 48 | 7JhT | DevelopmentalStage | human | True | hsapdv | Human Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/HSAPDV/11... | 52181d59df84578ed69214a5cb614036 | https://github.com/obophenotype/developmental-... | 2023-12-22 11:25:19.179759+00:00 | 1 |
| 49 | JIKv | DevelopmentalStage | mouse | True | mmusdv | Mouse Developmental Stages | 2020-03-10 | http://aber-owl.net/media/ontologies/MMUSDV/9/... | 5bef72395d853c7f65450e6c2a1fc653 | https://github.com/obophenotype/developmental-... | 2023-12-22 11:25:19.179791+00:00 | 1 |
| 50 | clid | Ethnicity | human | True | hancestro | Human Ancestry Ontology | 3.0 | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 2023-12-22 11:25:19.179825+00:00 | 1 |
| 51 | rsbG | 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... | 2023-12-22 11:25:19.179860+00:00 | 1 |
Show code cell content
!lamin delete --force test-pathway
!rm -r test-pathway
💡 deleting instance testuser1/test-pathway
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-pathway.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-pathway