Access ontologies: cell type, tissue, disease, phenotype#
When it comes to ontology defined vocabularies, such as cell type, tissue, disease, and phenotype, the entity class extends to have the ontology accessible via {entity}.ontology
import bionty as bt
All available ontologies and their versions can be printed with:
bt.display_available_versions()
Available versions ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┓ ┃ Ontology ┃ URL ┃ Bionty … ┃ Databas… ┃ All ve… ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━┩ │ Ensembl │ https://www.ensembl.org/index.html │ Species │ ensembl │ releas… │ │ │ │ │ │ │ │ Ensembl │ https://www.ensembl.org/index.html │ Gene │ ensembl │ releas… │ │ │ │ │ │ releas… │ │ │ │ │ │ │ │ Uniprot │ https://www.uniprot.org/ │ Protein │ uniprot │ 2022-04 │ │ │ │ │ │ 2022-03 │ │ │ │ │ │ │ │ CellMarker │ http://bio-bigdata.hrbmu.edu.cn/CellMarker/ │ CellMar… │ cellmar… │ 2.0 │ │ │ │ │ │ │ │ Cell Line Ontology │ https://bioportal.bioontology.org/ontologie… │ CellLine │ clo │ 2022-0… │ │ │ │ │ │ │ │ Cell Ontology │ https://obophenotype.github.io/cell-ontolog… │ CellType │ cl │ 2023-0… │ │ │ │ │ │ 2022-0… │ │ │ │ │ │ │ │ Human Cell Atlas Ontology │ https://github.com/HumanCellAtlas/ontology │ CellType │ ca │ 2022-1… │ │ │ │ │ │ │ │ Uberon multi-species anatomy on… │ http://obophenotype.github.io/uberon/ │ Tissue │ uberon │ 2023-0… │ │ │ │ │ │ 2022-0… │ │ │ │ │ │ │ │ Mondo Disease Ontology │ https://mondo.monarchinitiative.org/ │ Disease │ mondo │ 2023-0… │ │ │ │ │ │ 2022-1… │ │ │ │ │ │ │ │ Human Disease Ontology │ https://disease-ontology.org/ │ Disease │ doid │ 2023-0… │ │ │ │ │ │ │ │ The Experimental Factor Ontology │ https://bioportal.bioontology.org/ontologie… │ Readout │ efo │ 3.48.0 │ │ │ │ │ │ │ │ Human Phenotype Ontology │ https://hpo.jax.org/ │ Phenoty… │ hp │ 2023-0… │ │ │ │ │ │ │ │ Pathway Ontology │ https://www.ebi.ac.uk/ols/ontologies/pw │ Pathway │ pw │ 7.78 │ │ │ │ │ │ 7.74 │ │ │ │ │ │ │ │ Bioinformatics Pipeline │ https://lamin.ai │ BFXPipe… │ lamin │ 1.0.0 │ │ │ │ │ │ │ └──────────────────────────────────┴──────────────────────────────────────────────┴──────────┴──────────┴─────────┘
The currently used versions can be shown with:
bt.display_active_versions()
Currently used versions in ._current.yaml ┏━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ ┃ Entity ┃ Database ┃ Version ┃ ┡━━━━━━━━━━━━━╇━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ │ Species │ ensembl │ release-108 │ │ Gene │ ensembl │ release-108 │ │ Protein │ uniprot │ 2022-04 │ │ CellMarker │ cellmarker │ 2.0 │ │ CellLine │ clo │ 2022-03-21 │ │ CellType │ cl │ 2023-02-15 │ │ Tissue │ uberon │ 2023-02-14 │ │ Disease │ mondo │ 2023-02-06 │ │ Readout │ efo │ 3.48.0 │ │ Phenotype │ hp │ 2023-01-27 │ │ Pathway │ pw │ 7.78 │ │ BFXPipeline │ lamin │ 1.0.0 │ └─────────────┴────────────┴─────────────┘
Cell Type#
Here we look at cell type as an example:
ct = bt.CellType()
df = ct.df()
df.head()
| name | |
|---|---|
| ontology_id | |
| CL:0000000 | cell |
| CL:0000001 | primary cultured cell |
| CL:0000002 | obsolete immortal cell line cell |
| CL:0000003 | native cell |
| CL:0000004 | obsolete cell by organism |
again you may look up the vocabulary using .lookup by tab completion
lookup = bt.CellType().lookup()
lookup.astrocyte
cell_type(ontology_id='CL:0000127', name='astrocyte')
Cell type ontology is accessible via pronto Ontology as .ontology
ct.ontology
Ontology('/home/runner/work/bionty/bionty/.nox/build-package-bionty/lib/python3.9/site-packages/bionty/_dynamic/human___cl___2023-02-15___CellType', timeout=100)
len(ct.ontology.terms())
4168
term = ct.ontology["CL:0000128"]
term.definition
Definition('A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system.', xrefs={Xref('MESH:D009836'), Xref('http://en.wikipedia.org/wiki/Oligodendrocyte')})
term.is_leaf()
True
tissue, disease, and phenotype work similary
Tissue#
tissue = bt.Tissue()
df = tissue.df()
df.head()
| name | |
|---|---|
| ontology_id | |
| UBERON:0000000 | processual entity |
| UBERON:0000002 | uterine cervix |
| UBERON:0000003 | naris |
| UBERON:0000004 | nose |
| UBERON:0000005 | chemosensory organ |
lookup = tissue.lookup()
lookup.kidney
tissue(ontology_id='UBERON:0002113', name='kidney')
Disease#
disease = bt.Disease()
df = disease.df()
df.head()
| name | |
|---|---|
| ontology_id | |
| http://identifiers.org/hgnc/10001 | RGS5 |
| http://identifiers.org/hgnc/10004 | RGS9 |
| http://identifiers.org/hgnc/10006 | RHAG |
| http://identifiers.org/hgnc/10012 | RHO |
| http://identifiers.org/hgnc/10013 | GRK1 |
lookup = disease.lookup()
lookup.chronic_kidney_disease
disease(ontology_id='MONDO:0005300', name='chronic kidney disease')
Phenotype#
phenotype = bt.Phenotype()
df = phenotype.df()
df.head()
/home/runner/work/bionty/bionty/.nox/build-package-bionty/lib/python3.9/site-packages/bionty/_ontology.py:32: UnicodeWarning: unsound encoding, assuming ISO-8859-1 (73% confidence)
super().__init__(
| name | |
|---|---|
| ontology_id | |
| BFO:0000001 | entity |
| BFO:0000002 | continuant |
| BFO:0000003 | occurrent |
| BFO:0000004 | independent continuant |
| BFO:0000006 | spatial region |
lookup = phenotype.lookup()
lookup.cerebral_nerve_fasciculus
phenotype(ontology_id='UBERON:0022248', name='cerebral nerve fasciculus')
Readout#
Readout parses Experimental Factor Ontology to the following categories for describing biological experiments:
efo_id
name
molecule
instrument
measurement
The columns are reflected in the readout table in lnschema-wetlab.
readout = bt.Readout()
df = readout.df()
df.head()
| ontology_id | name | |
|---|---|---|
| 0 | EFO:0000001 | experimental factor |
| 1 | EFO:0000002 | CS57511 |
| 2 | EFO:0000003 | CS57512 |
| 3 | EFO:0000004 | CS57515 |
| 4 | EFO:0000005 | CS57520 |
Search for a molecular readout:
readout.get("EFO:0010891")
{'ontology_id': 'EFO:0010891',
'name': 'scATAC-seq',
'molecule': 'DNA assay',
'instrument': 'assay by high throughput sequencer',
'measurement': None}
Searching for a non-molecular readout:
readout.get("EFO:0004134")
{'ontology_id': 'EFO:0004134',
'name': 'tumor size',
'molecule': None,
'instrument': None,
'measurement': 'tumor size'}