Cell type#
lamindb provides access to the following public cell type ontologies:
Setup#
!lamin init --storage ./test-cell-type --schema bionty
✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-01-18 22:13:48 UTC)
✅ saved: Storage(uid='V6WvTHL7', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-cell-type', type='local', updated_at=2024-01-18 22:13:48 UTC, created_by_id=1)
💡 loaded instance: testuser1/test-cell-type
💡 did not register local instance on hub
import lnschema_bionty as lb
import pandas as pd
PublicOntology objects#
Let us create a public knowledge accessor with public(), which chooses a default public knowledge source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:
public = lb.CellType.public()
public
💡 loaded instance: testuser1/test-cell-type
PublicOntology
Entity: CellType
Organism: all
Source: cl, 2023-08-24
#terms: 2894
📖 .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 = public.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 ... | unpassaged cultured cell|primary cell culture ... | [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 | native cell | A Cell That Is Found In A Natural Setting, Whi... | None | [CL:0000000] |
| 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 = public.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-cell|CD8-positive, alpha-beta T lymphocyte|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-cell|CD8-positive, alpha-beta T lymphocyte|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:
public.search("CD8 positive T cell").head(5)
| ontology_id | definition | synonyms | parents | __ratio__ | |
|---|---|---|---|---|---|
| name | |||||
| Tc1 cell | CL:0000917 | A Cd8-Positive, Alpha-Beta Positive T Cell Tha... | Tc1 T lymphocyte|Tc1 T-cell|Tc1 T cell|T-cytot... | [CL:0000908] | 95.000000 |
| Tc2 cell | CL:0000918 | A Cd8-Positive, Alpha-Beta Positive T Cell Exp... | Th2 non-TFH CD8-positive T cell|Tc2 T lymphocy... | [CL:0000908, CL:0001052] | 95.000000 |
| Tc17 cell | CL:0002128 | A Cd8-Positive, Alpha-Beta T Cell That Has The... | Th17 CD8-positive T cell|Tc17 T lymphocyte|Tc1... | [CL:0000908] | 92.682927 |
| mature T cell | CL:0002419 | A T Cell That Expresses A T Cell Receptor Comp... | mature T-cell|CD3e-positive T cell | [CL:0000084] | 92.307692 |
| B cell, CD19-positive | CL:0001201 | A B Cell That Is Cd19-Positive. | B-cell, CD19-positive|B lymphocyte, CD19-posit... | [CL:0001200, CL:0000236] | 87.179487 |
Search another field (default is .name):
public.search("CD8 positive alpha beta T cell", field=public.definition).head(5)
| 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-cell|CD8-positive, ... | [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 lymphocyte|C... | [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, alpha-beta regulatory T-cell|CD8... | [CL:0000625, CL:0000815] | 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-lymphocyte... | [CL:0000893, CL:0000790] | 85.714286 |
Standardize cell type identifiers#
Let us generate a DataFrame that stores a number of cell type identifiers, some of which corrupted:
df_orig = pd.DataFrame(
index=[
"Boettcher cell",
"bone marrow cell",
"interstitial cell of ovary",
"pancreatic ductal cell",
"This cell type does not exist",
]
)
df_orig
| Boettcher cell |
|---|
| bone marrow cell |
| interstitial cell of ovary |
| pancreatic ductal cell |
| This cell type does not exist |
We can check whether any of our values are validated against the ontology reference:
validated = public.validate(df_orig.index, public.name)
df_orig.index[~validated]
✅ 4 terms (80.00%) are validated
❗ 1 term (20.00%) is not validated: This cell type does not exist
Index(['This cell type does not exist'], dtype='object')
Ontology source versions#
For any given entity, we can choose from a number of versions:
lb.PublicSource.filter(entity="CellType").df()
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 21 | 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 | 2024-01-18 22:13:48.379262+00:00 | 2024-01-18 22:13:48.379271+00:00 | 1 |
| 22 | 1oXM | CellType | all | False | cl | Cell Ontology | 2023-04-20 | http://purl.obolibrary.org/obo/cl/releases/202... | 58cdc1545f0d35e6fce76a65331b00fb | https://obophenotype.github.io/cell-ontology | 2024-01-18 22:13:48.379361+00:00 | 2024-01-18 22:13:48.379370+00:00 | 1 |
| 23 | 419m | CellType | all | False | cl | Cell Ontology | 2023-02-15 | http://purl.obolibrary.org/obo/cl/releases/202... | 9331a6a029cb1863bd0584ab41508df7 | https://obophenotype.github.io/cell-ontology | 2024-01-18 22:13:48.379460+00:00 | 2024-01-18 22:13:48.379469+00:00 | 1 |
| 24 | a0ZY | CellType | all | False | cl | Cell Ontology | 2022-08-16 | http://purl.obolibrary.org/obo/cl/releases/202... | d0655766574e63f3fe5ed56d3c030880 | https://obophenotype.github.io/cell-ontology | 2024-01-18 22:13:48.379559+00:00 | 2024-01-18 22:13:48.379568+00:00 | 1 |
When instantiating a Bionty object, we can choose a source or version:
public_source = lb.PublicSource.filter(
source="cl", version="2023-04-20", organism="all"
).one()
public = lb.CellType.public(public_source=public_source)
public
❗ loading non-default source inside a LaminDB instance
PublicOntology
Entity: CellType
Organism: all
Source: cl, 2023-04-20
#terms: 2862
📖 .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:
lb.PublicSource.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | currently_used | source | source_name | version | url | md5 | source_website | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | 6IUo | Organism | vertebrates | True | ensembl | Ensembl | release-110 | https://ftp.ensembl.org/pub/release-110/specie... | f3faf95648d3a2b50fd3625456739706 | https://www.ensembl.org | 2024-01-18 22:13:48.377157+00:00 | 2024-01-18 22:13:48.377178+00:00 | 1 |
| 4 | 2Jzh | Organism | bacteria | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 2024-01-18 22:13:48.377504+00:00 | 2024-01-18 22:13:48.377514+00:00 | 1 |
| 5 | 1kdI | Organism | fungi | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 2024-01-18 22:13:48.377605+00:00 | 2024-01-18 22:13:48.377614+00:00 | 1 |
| 6 | 2mIM | Organism | metazoa | True | ensembl | Ensembl | release-57 | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 2024-01-18 22:13:48.377727+00:00 | 2024-01-18 22:13:48.377739+00:00 | 1 |
| 7 | 2XQ6 | Organism | plants | True | ensembl | Ensembl | release-57 | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 2024-01-18 22:13:48.377837+00:00 | 2024-01-18 22:13:48.377847+00:00 | 1 |
| 8 | 1Vzs | Organism | all | True | ncbitaxon | NCBItaxon Ontology | 2023-06-20 | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 2024-01-18 22:13:48.377939+00:00 | 2024-01-18 22:13:48.377949+00:00 | 1 |
| 9 | 4yVc | Gene | human | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_human__ensembl__release-... | 832f3947e83664588d419608a469b528 | https://www.ensembl.org | 2024-01-18 22:13:48.378042+00:00 | 2024-01-18 22:13:48.378051+00:00 | 1 |
| 11 | 2akp | Gene | mouse | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_mouse__ensembl__release-... | fa4ce130f2929aefd7ac3bc8eaf0c4de | https://www.ensembl.org | 2024-01-18 22:13:48.378249+00:00 | 2024-01-18 22:13:48.378259+00:00 | 1 |
| 13 | 2UvD | Gene | saccharomyces cerevisiae | True | ensembl | Ensembl | release-110 | s3://bionty-assets/df_saccharomyces cerevisiae... | 2e59495a3e87ea6575e408697dd73459 | https://www.ensembl.org | 2024-01-18 22:13:48.378454+00:00 | 2024-01-18 22:13:48.378463+00:00 | 1 |
| 14 | 7llW | Protein | human | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_human__uniprot__2023-03_... | 1c46e85c6faf5eff3de5b4e1e4edc4d3 | https://www.uniprot.org | 2024-01-18 22:13:48.378556+00:00 | 2024-01-18 22:13:48.378565+00:00 | 1 |
| 16 | 5U7J | Protein | mouse | True | uniprot | Uniprot | 2023-03 | s3://bionty-assets/df_mouse__uniprot__2023-03_... | 9d5e9a8225011d3218e10f9bbb96a46c | https://www.uniprot.org | 2024-01-18 22:13:48.378759+00:00 | 2024-01-18 22:13:48.378768+00:00 | 1 |
| 18 | 5nkB | CellMarker | human | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-18 22:13:48.378961+00:00 | 2024-01-18 22:13:48.378971+00:00 | 1 |
| 19 | 6AFz | CellMarker | mouse | True | cellmarker | CellMarker | 2.0 | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 2024-01-18 22:13:48.379063+00:00 | 2024-01-18 22:13:48.379072+00:00 | 1 |
| 20 | 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 | 2024-01-18 22:13:48.379163+00:00 | 2024-01-18 22:13:48.379172+00:00 | 1 |
| 21 | 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 | 2024-01-18 22:13:48.379262+00:00 | 2024-01-18 22:13:48.379271+00:00 | 1 |
| 25 | 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 | 2024-01-18 22:13:48.379659+00:00 | 2024-01-18 22:13:48.379668+00:00 | 1 |
| 29 | 6EOm | Disease | all | True | mondo | Mondo Disease Ontology | 2023-08-02 | http://purl.obolibrary.org/obo/mondo/releases/... | 7f33767422042eec29f08b501fc851db | https://mondo.monarchinitiative.org | 2024-01-18 22:13:48.380060+00:00 | 2024-01-18 22:13:48.380069+00:00 | 1 |
| 33 | 3V9D | Disease | human | True | doid | Human Disease Ontology | 2023-03-31 | http://purl.obolibrary.org/obo/doid/releases/2... | 64f083a1e47867c307c8eae308afc3bb | https://disease-ontology.org | 2024-01-18 22:13:48.380459+00:00 | 2024-01-18 22:13:48.380468+00:00 | 1 |
| 35 | 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 | 2024-01-18 22:13:48.380657+00:00 | 2024-01-18 22:13:48.380666+00:00 | 1 |
| 37 | 6jHz | Phenotype | human | True | hp | Human Phenotype Ontology | 2023-06-17 | https://github.com/obophenotype/human-phenotyp... | 65e8d96bc81deb893163927063b10c06 | https://hpo.jax.org | 2024-01-18 22:13:48.380857+00:00 | 2024-01-18 22:13:48.380866+00:00 | 1 |
| 40 | 4q5A | Phenotype | mammalian | True | mp | Mammalian Phenotype Ontology | 2023-05-31 | https://github.com/mgijax/mammalian-phenotype-... | be89052cf6d9c0b6197038fe347ef293 | https://github.com/mgijax/mammalian-phenotype-... | 2024-01-18 22:13:48.381154+00:00 | 2024-01-18 22:13:48.381163+00:00 | 1 |
| 41 | 6Czy | Phenotype | zebrafish | True | zp | Zebrafish Phenotype Ontology | 2022-12-17 | https://github.com/obophenotype/zebrafish-phen... | 03430b567bf153216c0fa4c3440b3b24 | https://github.com/obophenotype/zebrafish-phen... | 2024-01-18 22:13:48.381253+00:00 | 2024-01-18 22:13:48.381262+00:00 | 1 |
| 43 | 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 | 2024-01-18 22:13:48.381450+00:00 | 2024-01-18 22:13:48.381458+00:00 | 1 |
| 44 | 48aa | Pathway | all | True | go | Gene Ontology | 2023-05-10 | https://data.bioontology.org/ontologies/GO/sub... | e9845499eadaef2418f464cd7e9ac92e | http://geneontology.org | 2024-01-18 22:13:48.381548+00:00 | 2024-01-18 22:13:48.381556+00:00 | 1 |
| 46 | 3rm9 | BFXPipeline | all | True | lamin | Bioinformatics Pipeline | 1.0.0 | s3://bionty-assets/bfxpipelines.json | a7eff57a256994692fba46e0199ffc94 | https://lamin.ai | 2024-01-18 22:13:48.381764+00:00 | 2024-01-18 22:13:48.381775+00:00 | 1 |
| 47 | 3TI0 | Drug | all | True | dron | Drug Ontology | 2023-03-10 | https://data.bioontology.org/ontologies/DRON/s... | 75e86011158fae76bb46d96662a33ba3 | https://bioportal.bioontology.org/ontologies/DRON | 2024-01-18 22:13:48.381868+00:00 | 2024-01-18 22:13:48.381878+00:00 | 1 |
| 48 | 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-... | 2024-01-18 22:13:48.381969+00:00 | 2024-01-18 22:13:48.381978+00:00 | 1 |
| 49 | 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-... | 2024-01-18 22:13:48.382069+00:00 | 2024-01-18 22:13:48.382078+00:00 | 1 |
| 50 | 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 | 2024-01-18 22:13:48.382169+00:00 | 2024-01-18 22:13:48.382178+00:00 | 1 |
| 51 | 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... | 2024-01-18 22:13:48.382269+00:00 | 2024-01-18 22:13:48.382277+00:00 | 1 |
Show code cell content
!lamin delete --force test-cell-type
!rm -r test-cell-type
💡 deleting instance testuser1/test-cell-type
✅ deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-cell-type.env
✅ instance cache deleted
✅ deleted '.lndb' sqlite file
❗ consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-cell-type