CellMarker¶
lamindb provides access to the following public cell marker ontologies through bionty:
Here we show how to access and search cell marker ontologies to standardize new data.
import bionty as bt
import pandas as pd
PublicOntology objects¶
Let us create a public ontology accessor with public(), which chooses a default public ontology source from Source. It’s a PublicOntology object, which you can think about as a public registry:
public = bt.CellMarker.public(organism="human")
public
→ connected lamindb: testuser1/test-public-ontologies
PublicOntology
Entity: CellMarker
Organism: human
Source: cellmarker, 2.0
#terms: 15466
As for registries, you can export the ontology as a DataFrame:
df = public.df()
df.head()
| name | synonyms | gene_symbol | ncbi_gene_id | uniprotkb_id | |
|---|---|---|---|---|---|
| 0 | A1BG | A1BG | 1 | P04217 | |
| 1 | A2M | A2M | 3494 | None | |
| 2 | A2ML1 | A2ML1 | 144568 | A8K2U0 | |
| 3 | A4GALT | A4GALT | 53947 | A0A0S2Z5J1 | |
| 4 | AADAC | AADAC | 13 | P22760 |
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.immp1l
CellMarker(name='IMMP1L', synonyms='', gene_symbol='IMMP1L', ncbi_gene_id='196294', uniprotkb_id='Q96LU5')
To look up the exact original strings, convert the lookup object to dict and use the [] accessor:
lookup_dict = lookup.dict()
lookup_dict["IMMP1L"]
CellMarker(name='IMMP1L', synonyms='', gene_symbol='IMMP1L', ncbi_gene_id='196294', uniprotkb_id='Q96LU5')
Search terms¶
Search behaves in the same way as it does for registries:
public.search("CD4").head(5)
| name | synonyms | gene_symbol | ncbi_gene_id | uniprotkb_id | |
|---|---|---|---|---|---|
| 1900 | Cd4 | CD4 | 920 | B4DT49 | |
| 1901 | CD40 | CD40 | 958 | A0A0S2Z3C7 | |
| 1905 | CD40LG | CD40LG | 959 | P29965 | |
| 1908 | CD46 | CD46 | 4179 | P15529 | |
| 1907 | Cd44 | CD44 | 960 | P16070 |
Search another field (default is .name):
public.search("CD4", field=public.gene_symbol).head(1)
| name | synonyms | gene_symbol | ncbi_gene_id | uniprotkb_id | |
|---|---|---|---|---|---|
| 1900 | Cd4 | CD4 | 920 | B4DT49 |
Standardize cell marker identifiers¶
Let us generate a DataFrame that stores a number of cell markers identifiers, some of which corrupted:
markers = pd.DataFrame(
index=[
"KI67",
"CCR7",
"CD14",
"CD8",
"CD45RA",
"CD4",
"CD3",
"CD127a",
"PD1",
"Invalid-1",
"Invalid-2",
"CD66b",
"Siglec8",
"Time",
]
)
Now let’s check which cell markers can be found in the reference:
public.inspect(markers.index, public.name);
! 8 unique terms (57.10%) are not validated for name: 'KI67', 'CCR7', 'CD14', 'CD4', 'CD127a', 'Invalid-1', 'Invalid-2', 'Time'
detected 4 unique terms with inconsistent casing/synonyms: KI67, CCR7, CD14, CD4
→ standardize terms via .standardize()
Logging suggests to map synonyms:
synonyms_mapper = public.standardize(markers.index, return_mapper=True)
synonyms_mapper
{'KI67': 'Ki67', 'CCR7': 'Ccr7', 'CD14': 'Cd14', 'CD4': 'Cd4'}
Let’s replace the synonyms with standardized names in the DataFrame:
markers.rename(index=synonyms_mapper, inplace=True)
The Time, Invalid-1 and Invalid-2 are non-marker channels which won’t be curated by cell marker:
public.inspect(markers.index, public.name);
! 4 unique terms (28.60%) are not validated for name: 'CD127a', 'Invalid-1', 'Invalid-2', 'Time'
We don’t find CD127a, let’s check in the lookup with auto-completion:
lookup = public.lookup()
lookup.cd127
CellMarker(name='CD127', synonyms='', gene_symbol='IL7R', ncbi_gene_id='3575', uniprotkb_id='P16871', _5='cd127')
It should be cd127, we had a typo there with cd127a:
curated_df = markers.rename(index={"CD127a": lookup.cd127.name})
Optionally, search:
public.search("CD127a").head()
| name | synonyms | gene_symbol | ncbi_gene_id | uniprotkb_id | __agg__ |
|---|
Now we see that all cell marker candidates validate:
public.validate(curated_df.index, public.name);
! 3 unique terms (21.40%) are not validated: 'Invalid-1', 'Invalid-2', 'Time'
Ontology source versions¶
For any given entity, we can choose from a number of versions:
bt.Source.filter(entity="bionty.CellMarker").df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
# only lists the sources that are currently used
bt.Source.filter(entity="bionty.CellMarker", currently_used=True).df()
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
When instantiating a Bionty object, we can choose a source or version:
source = bt.Source.get(name="cellmarker", version="2.0", organism="human")
public = bt.CellMarker.public(source=source)
public
PublicOntology
Entity: CellMarker
Organism: human
Source: cellmarker, 2.0
#terms: 15466
The currently used ontologies can be displayed using:
bt.Source.filter(currently_used=True).df()
Show code cell output
| uid | entity | organism | name | in_db | currently_used | description | url | md5 | source_website | space_id | dataframe_artifact_id | version | run_id | created_at | created_by_id | _aux | _branch_code | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||||||||
| 1 | 33TU | bionty.Organism | vertebrates | ensembl | False | True | Ensembl | https://ftp.ensembl.org/pub/release-112/specie... | 0ec37e77f4bc2d0b0b47c6c62b9f122d | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 6 | 6bbV | bionty.Organism | bacteria | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... | ee28510ed5586ea7ab4495717c96efc8 | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 7 | 6s9n | bionty.Organism | fungi | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/fungi/releas... | dbcde58f4396ab8b2480f7fe9f83df8a | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 8 | 2PmT | bionty.Organism | metazoa | ensembl | False | True | Ensembl | http://ftp.ensemblgenomes.org/pub/metazoa/rele... | 424636a574fec078a61cbdddb05f9132 | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 9 | 7GPH | bionty.Organism | plants | ensembl | False | True | Ensembl | https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... | eadaa1f3e527e4c3940c90c7fa5c8bf4 | https://www.ensembl.org | 1 | None | release-57 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 10 | 4tsk | bionty.Organism | all | ncbitaxon | False | True | NCBItaxon Ontology | s3://bionty-assets/df_all__ncbitaxon__2023-06-... | 00d97ba65627f1cd65636d2df22ea76c | https://github.com/obophenotype/ncbitaxon | 1 | None | 2023-06-20 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 11 | 4UGN | bionty.Gene | human | ensembl | False | True | Ensembl | s3://bionty-assets/df_human__ensembl__release-... | 4ccda4d88720a326737376c534e8446b | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 15 | 4r4f | bionty.Gene | mouse | ensembl | False | True | Ensembl | s3://bionty-assets/df_mouse__ensembl__release-... | 519cf7b8acc3c948274f66f3155a3210 | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 19 | 4RPA | bionty.Gene | saccharomyces cerevisiae | ensembl | False | True | Ensembl | s3://bionty-assets/df_saccharomyces cerevisiae... | 11775126b101233525a0a9e2dd64edae | https://www.ensembl.org | 1 | None | release-112 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 22 | 3EYy | bionty.Protein | human | uniprot | False | True | Uniprot | s3://bionty-assets/df_human__uniprot__2024-03_... | b5b9e7645065b4b3187114f07e3f402f | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 25 | 01RW | bionty.Protein | mouse | uniprot | False | True | Uniprot | s3://bionty-assets/df_mouse__uniprot__2024-03_... | b1b6a196eb853088d36198d8e3749ec4 | https://www.uniprot.org | 1 | None | 2024-03 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 28 | 3kDh | bionty.CellMarker | human | cellmarker | False | True | CellMarker | s3://bionty-assets/human_cellmarker_2.0_CellMa... | d565d4a542a5c7e7a06255975358e4f4 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 29 | 7bV5 | bionty.CellMarker | mouse | cellmarker | False | True | CellMarker | s3://bionty-assets/mouse_cellmarker_2.0_CellMa... | 189586732c63be949e40dfa6a3636105 | http://bio-bigdata.hrbmu.edu.cn/CellMarker | 1 | None | 2.0 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 30 | 6LyR | bionty.CellLine | all | clo | False | True | Cell Line Ontology | https://data.bioontology.org/ontologies/CLO/su... | ea58a1010b7e745702a8397a526b3a33 | https://bioportal.bioontology.org/ontologies/CLO | 1 | None | 2022-03-21 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 |
| 32 | 3Uw2 | bionty.CellType | all | cl | False | True | Cell Ontology | http://purl.obolibrary.org/obo/cl/releases/202... | https://obophenotype.github.io/cell-ontology | 1 | None | 2024-08-16 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 | |
| 41 | MUtA | bionty.Tissue | all | uberon | False | True | Uberon multi-species anatomy ontology | http://purl.obolibrary.org/obo/uberon/releases... | http://obophenotype.github.io/uberon | 1 | None | 2024-08-07 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 | |
| 50 | 4a3e | bionty.Disease | all | mondo | False | True | Mondo Disease Ontology | http://purl.obolibrary.org/obo/mondo/releases/... | https://mondo.monarchinitiative.org | 1 | None | 2024-08-06 | None | 2025-01-20 07:34:38.666000+00:00 | 1 | None | 1 | |
| 59 | 4ksw | bionty.Disease | human | doid | False | True | Human Disease Ontology | http://purl.obolibrary.org/obo/doid/releases/2... | bbefd72247d638edfcd31ec699947407 | https://disease-ontology.org | 1 | None | 2024-05-29 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 67 | 2a1H | bionty.ExperimentalFactor | all | efo | False | True | The Experimental Factor Ontology | http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl | https://bioportal.bioontology.org/ontologies/EFO | 1 | None | 3.70.0 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 | |
| 74 | 48fB | bionty.Phenotype | human | hp | False | True | Human Phenotype Ontology | https://github.com/obophenotype/human-phenotyp... | e0f2e534eb2ad44a4d45573ef27b508f | https://hpo.jax.org | 1 | None | 2024-04-26 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 79 | 4t7Q | bionty.Phenotype | mammalian | mp | False | True | Mammalian Phenotype Ontology | https://github.com/mgijax/mammalian-phenotype-... | 795d8378fe48ec13b41d01a86dd1c86c | https://github.com/mgijax/mammalian-phenotype-... | 1 | None | 2024-06-18 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 82 | sqPX | bionty.Phenotype | zebrafish | zp | False | True | Zebrafish Phenotype Ontology | https://github.com/obophenotype/zebrafish-phen... | 2231ebaa95becf8ff34a33c95a8d4350 | https://github.com/obophenotype/zebrafish-phen... | 1 | None | 2024-04-18 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 86 | 6S4q | bionty.Phenotype | all | pato | False | True | Phenotype And Trait Ontology | http://purl.obolibrary.org/obo/pato/releases/2... | 6b1eaacd3d453b34375ce2e31c16328a | https://github.com/pato-ontology/pato | 1 | None | 2024-03-28 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 88 | 7Ent | bionty.Pathway | all | go | False | True | Gene Ontology | https://data.bioontology.org/ontologies/GO/sub... | 7fa7ade5e3e26eab3959a7e4bc89ad4f | http://geneontology.org | 1 | None | 2024-06-17 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 93 | 3rm9 | BFXPipeline | all | lamin | False | True | Bioinformatics Pipeline | s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... | https://lamin.ai | 1 | None | 1.0.0 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 | |
| 94 | ugaI | Drug | all | dron | False | True | Drug Ontology | https://data.bioontology.org/ontologies/DRON/s... | https://bioportal.bioontology.org/ontologies/DRON | 1 | None | 2024-08-05 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 | |
| 98 | 1GbF | bionty.DevelopmentalStage | human | hsapdv | False | True | Human Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 | |
| 100 | 10va | bionty.DevelopmentalStage | mouse | mmusdv | False | True | Mouse Developmental Stages | https://github.com/obophenotype/developmental-... | https://github.com/obophenotype/developmental-... | 1 | None | 2024-05-28 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 | |
| 102 | MJRq | bionty.Ethnicity | human | hancestro | False | True | Human Ancestry Ontology | https://github.com/EBISPOT/hancestro/raw/3.0/h... | 76dd9efda9c2abd4bc32fc57c0b755dd | https://github.com/EBISPOT/hancestro | 1 | None | 3.0 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |
| 103 | 5JnV | BioSample | all | ncbi | False | True | NCBI BioSample attributes | s3://bionty-assets/df_all__ncbi__2023-09__BioS... | 918db9bd1734b97c596c67d9654a4126 | https://www.ncbi.nlm.nih.gov/biosample/docs/at... | 1 | None | 2023-09 | None | 2025-01-20 07:34:38.670000+00:00 | 1 | None | 1 |