CellType¶
lamindb provides access to the following public CellType ontologies through bionty:
Here we show how to access and search CellType 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:
celltypes = bt.CellType.public(organism="all")
celltypes
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: CellType
Organism: all
Source: cl, 2024-05-15
#terms: 2931
As for registries, you can export the ontology as a DataFrame:
df = celltypes.df()
df.head()
| name | definition | synonyms | parents | |
|---|---|---|---|---|
| ontology_id | ||||
| CL:0000000 | cell | A Material Entity Of Anatomical Origin (Part O... | None | [] |
| CL:0000001 | primary cultured cell | A Cultured Cell That Is Freshly Isolated From ... | primary cell culture cell|unpassaged cultured ... | [CL:0000010] |
| CL:0000002 | obsolete immortal cell line cell | Obsolete: A Cell Line Cell That Is Expected To... | permanent cell line cell|continuous cell line ... | [] |
| CL:0000003 | obsolete native cell | Obsolete. A Cell That Is Found In A Natural Se... | None | [] |
| CL:0000004 | obsolete cell by organism | Obsolete: A Classification Of Cells By The Org... | None | [] |
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 = celltypes.lookup()
The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):
lookup.cd8_positive_alpha_beta_t_cell
CellType(ontology_id='CL:0000625', name='CD8-positive, alpha-beta T cell', definition='A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor.', synonyms='CD8-positive, alpha-beta T lymphocyte|CD8-positive, alpha-beta T-cell|CD8-positive, alpha-beta T-lymphocyte', parents=array(['CL:0000791'], 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["CD8-positive, alpha-beta T cell"]
CellType(ontology_id='CL:0000625', name='CD8-positive, alpha-beta T cell', definition='A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor.', synonyms='CD8-positive, alpha-beta T lymphocyte|CD8-positive, alpha-beta T-cell|CD8-positive, alpha-beta T-lymphocyte', parents=array(['CL:0000791'], dtype=object))
By default, the name field is used to generate lookup keys. You can specify another field to look up:
lookup = celltypes.lookup(celltypes.ontology_id)
lookup.cl_0000625
CellType(ontology_id='CL:0000625', name='CD8-positive, alpha-beta T cell', definition='A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor.', synonyms='CD8-positive, alpha-beta T lymphocyte|CD8-positive, alpha-beta T-cell|CD8-positive, alpha-beta T-lymphocyte', parents=array(['CL:0000791'], dtype=object))
Search terms¶
Search behaves in the same way as it does for registries:
celltypes.search("CD8 positive T cell").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Tc2 cell | CL:0000918 | A Cd8-Positive, Alpha-Beta Positive T Cell Exp... | Th2 non-TFH CD8-positive T cell|Tc2 T-cell|T-c... | [CL:0000908, CL:0001052] | 95.000000 |
| Tc1 cell | CL:0000917 | A Cd8-Positive, Alpha-Beta Positive T Cell Tha... | Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... | [CL:0000908] | 95.000000 |
| Tc17 cell | CL:0002128 | A Cd8-Positive, Alpha-Beta T Cell That Has The... | Th17 CD8-positive T cell|Tc17 T-cell|CD8-posit... | [CL:0000908] | 92.682927 |
By default, search also covers synonyms:
celltypes.search("Tc1 T lymphocyte").head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Tc1 cell | CL:0000917 | A Cd8-Positive, Alpha-Beta Positive T Cell Tha... | Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8... | [CL:0000908] | 100.000000 |
| Tc17 cell | CL:0002128 | A Cd8-Positive, Alpha-Beta T Cell That Has The... | Th17 CD8-positive T cell|Tc17 T-cell|CD8-posit... | [CL:0000908] | 96.969697 |
| Tr1 cell | CL:0000901 | Cd4-Positive Alpha-Beta T Cell With Regulatory... | Tr1 T-lymphocyte|T-regulatory T cell type 1|Tr... | [CL:0000492, CL:0000815] | 93.750000 |
You can turn this off synonym by passing synonyms_field=None:
celltypes.search("Tc1 T lymphocyte", synonyms_field=None).head(3)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| lymphocyte | CL:0000542 | A Lymphocyte Is A Leukocyte Commonly Found In ... | None | [CL:0000842] | 76.923077 |
| blood lymphocyte | CL:4030029 | A Lymphocyte Located In Blood. | None | [CL:2000001, CL:0000542] | 68.750000 |
| obsolete null lymphocyte | CL:0002245 | Obsolete: A Lymphocyte That Lacks T Or B Cell ... | None | [] | 65.000000 |
Search another field (default is .name):
celltypes.search(
"CD8 positive alpha beta T cell",
field=celltypes.definition,
).head()
| ontology_id | name | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| definition | |||||
| A T Cell Expressing An Alpha-Beta T Cell Receptor And The Cd8 Coreceptor. | CL:0000625 | CD8-positive, alpha-beta T cell | CD8-positive, alpha-beta T lymphocyte|CD8-posi... | [CL:0000791] | 98.360656 |
| A Mature Alpha-Beta T Cell That Expresses An Alpha-Beta T Cell Receptor And The Cd4 Coreceptor. | CL:0000624 | CD4-positive, alpha-beta T cell | CD4-positive, alpha-beta T lymphocyte|CD4-posi... | [CL:0000791] | 95.081967 |
| A Cd8-Positive, Alpha-Beta T Cell That Has Differentiated Into A Memory T Cell. | CL:0000909 | CD8-positive, alpha-beta memory T cell | CD8-positive, alpha-beta memory T-cell|CD8-pos... | [CL:0000625, CL:0000813] | 88.235294 |
| A Cd8-Positive, Alpha-Beta T Cell That Regulates Overall Immune Responses As Well As The Responses Of Other T Cell Subsets Through Direct Cell-Cell Contact And Cytokine Release. | CL:0000795 | CD8-positive, alpha-beta regulatory T cell | CD8-positive Treg|CD8-positive, alpha-beta Tre... | [CL:0000815, CL:0000625] | 88.135593 |
| An Immature Alpha-Beta T Cell That Is Located In The Thymus And Is Cd8-Positive And Cd4-Negative. | CL:0000811 | CD8-positive, alpha-beta thymocyte | CD8-positive, alpha-beta immature T-cell|CD8-p... | [CL:0000893, CL:0000790] | 85.714286 |
Standardize CellType identifiers¶
Let us generate a DataFrame that stores a number of CellType identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"Boettcher cell",
"bone marrow cell",
"interstitial cell of ovary",
"pancreatic ductal cell",
"This celltype does not exist",
]
)
df_orig
| Boettcher cell |
|---|
| bone marrow cell |
| interstitial cell of ovary |
| pancreatic ductal cell |
| This celltype does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = celltypes.validate(df_orig.index, celltypes.name)
df_orig.index[~validated]
! 1 term (20.00%) is not validated: This celltype does not exist
Index(['This celltype does not exist'], dtype='object')
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.CellType.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 | |||||||||||||||
| 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 | 2024-08-30 11:11:49.282828+00:00 |
| 33 | FxPV | bionty.CellType | all | cl | 2024-02-13 | False | False | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | d6d962b58c48f372c2c98b71e0833242 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-30 11:11:49.282864+00:00 |
| 34 | 1Mek | bionty.CellType | all | cl | 2024-01-04 | False | False | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | 46203f72ef94479f69ea9f03982b3c94 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-30 11:11:49.282902+00:00 |
| 35 | 4YVk | bionty.CellType | all | cl | 2023-08-24 | False | False | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | 46e7dd89421f1255cf0191eca1548f73 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-30 11:11:49.282940+00:00 |
| 36 | 56Kg | bionty.CellType | all | cl | 2023-04-20 | False | False | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | 58cdc1545f0d35e6fce76a65331b00fb | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-30 11:11:49.282976+00:00 |
| 37 | 5Xrg | bionty.CellType | all | cl | 2023-02-15 | False | False | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | 9331a6a029cb1863bd0584ab41508df7 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-30 11:11:49.283013+00:00 |
| 38 | 32df | bionty.CellType | all | cl | 2022-08-16 | False | False | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | d0655766574e63f3fe5ed56d3c030880 | https://obophenotype.github.io/cell-ontology | None | None | 1 | 2024-08-30 11:11:49.283049+00:00 |
# only lists the sources that are currently used
bt.CellType.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 | |||||||||||||||
| 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 | 2024-08-30 11:11:49.282828+00:00 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.filter(
name="cl", version="2023-04-20", organism="all"
).one()
celltypes= bt.CellType.public(source=source)
celltypes
PublicOntology
Entity: CellType
Organism: all
Source: cl, 2023-04-20
#terms: 2862
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 | 2024-08-30 11:11:49.281648+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 | 2024-08-30 11:11:49.281849+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 | 2024-08-30 11:11:49.281886+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 | 2024-08-30 11:11:49.281922+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 | 2024-08-30 11:11:49.281958+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 | 2024-08-30 11:11:49.281995+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 | 2024-08-30 11:11:49.282057+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 | 2024-08-30 11:11:49.282206+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 | 2024-08-30 11:11:49.282354+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 | 2024-08-30 11:11:49.282465+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 | 2024-08-30 11:11:49.282575+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 | 2024-08-30 11:11:49.282683+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 | 2024-08-30 11:11:49.282720+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 | 2024-08-30 11:11:49.282756+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 | 2024-08-30 11:11:49.282828+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 | 2024-08-30 11:11:49.283086+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 | 2024-08-30 11:11:49.283376+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 | 2024-08-30 11:11:49.283631+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 | 2024-08-30 11:11:49.283925+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 | 2024-08-30 11:11:49.286184+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 | 2024-08-30 11:11:49.286365+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 | 2024-08-30 11:11:49.286471+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 | 2024-08-30 11:11:49.286608+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 | 2024-08-30 11:11:49.286676+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 | 2024-08-30 11:11:49.286849+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 | 2024-08-30 11:11:49.286884+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 | 2024-08-30 11:11:49.287020+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 | 2024-08-30 11:11:49.287096+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 | 2024-08-30 11:11:49.287166+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 | 2024-08-30 11:11:49.287201+00:00 |