CellMarker

lamindb provides access to the following public cell marker ontologies through bionty:

  1. CellMarker

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()
Hide 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 3kDh8qAX bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+00:00 1 None 1
29 7bV5uJo3 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+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 3kDh8qAX bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+00:00 1 None 1
29 7bV5uJo3 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+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()
Hide 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 33TUF039 bionty.Organism vertebrates ensembl False True Ensembl https://ftp.ensembl.org/pub/release-112/specie... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
6 6bbVUTCS bionty.Organism bacteria ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
7 6s9nV6xh bionty.Organism fungi ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/fungi/releas... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
8 2PmTrc8x bionty.Organism metazoa ensembl False True Ensembl http://ftp.ensemblgenomes.org/pub/metazoa/rele... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
9 7GPHh16S bionty.Organism plants ensembl False True Ensembl https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... None https://www.ensembl.org 1 None release-57 None 2025-03-10 13:25:14.948000+00:00 1 None 1
10 4tsksCMX bionty.Organism all ncbitaxon False True NCBItaxon Ontology s3://bionty-assets/df_all__ncbitaxon__2023-06-... None https://github.com/obophenotype/ncbitaxon 1 None 2023-06-20 None 2025-03-10 13:25:14.948000+00:00 1 None 1
11 4UGNz3fr bionty.Gene human ensembl False True Ensembl s3://bionty-assets/df_human__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
15 4r4fvV0S bionty.Gene mouse ensembl False True Ensembl s3://bionty-assets/df_mouse__ensembl__release-... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
19 4RPA3Re0 bionty.Gene saccharomyces cerevisiae ensembl False True Ensembl s3://bionty-assets/df_saccharomyces cerevisiae... None https://www.ensembl.org 1 None release-112 None 2025-03-10 13:25:14.948000+00:00 1 None 1
22 3EYyGRYN bionty.Protein human uniprot False True Uniprot s3://bionty-assets/df_human__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-03-10 13:25:14.948000+00:00 1 None 1
25 01RWXN2V bionty.Protein mouse uniprot False True Uniprot s3://bionty-assets/df_mouse__uniprot__2024-03_... None https://www.uniprot.org 1 None 2024-03 None 2025-03-10 13:25:14.948000+00:00 1 None 1
28 3kDh8qAX bionty.CellMarker human cellmarker False True CellMarker s3://bionty-assets/human_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+00:00 1 None 1
29 7bV5uJo3 bionty.CellMarker mouse cellmarker False True CellMarker s3://bionty-assets/mouse_cellmarker_2.0_CellMa... None http://bio-bigdata.hrbmu.edu.cn/CellMarker 1 None 2.0 None 2025-03-10 13:25:14.948000+00:00 1 None 1
30 6LyRtvz8 bionty.CellLine all clo False True Cell Line Ontology https://data.bioontology.org/ontologies/CLO/su... None https://bioportal.bioontology.org/ontologies/CLO 1 None 2022-03-21 None 2025-03-10 13:25:14.948000+00:00 1 None 1
32 3Uw2Va7a bionty.CellType all cl False True Cell Ontology http://purl.obolibrary.org/obo/cl/releases/202... None https://obophenotype.github.io/cell-ontology 1 None 2024-08-16 None 2025-03-10 13:25:14.948000+00:00 1 None 1
41 MUtAGdL4 bionty.Tissue all uberon False True Uberon multi-species anatomy ontology http://purl.obolibrary.org/obo/uberon/releases... None http://obophenotype.github.io/uberon 1 None 2024-08-07 None 2025-03-10 13:25:14.948000+00:00 1 None 1
50 4a3ejKuf bionty.Disease all mondo False True Mondo Disease Ontology http://purl.obolibrary.org/obo/mondo/releases/... None https://mondo.monarchinitiative.org 1 None 2024-08-06 None 2025-03-10 13:25:14.948000+00:00 1 None 1
59 4kswnHVF bionty.Disease human doid False True Human Disease Ontology http://purl.obolibrary.org/obo/doid/releases/2... None https://disease-ontology.org 1 None 2024-05-29 None 2025-03-10 13:25:14.952000+00:00 1 None 1
67 2a1HvjdB bionty.ExperimentalFactor all efo False True The Experimental Factor Ontology http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl None https://bioportal.bioontology.org/ontologies/EFO 1 None 3.70.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
75 48fBFLmn bionty.Phenotype human hp False True Human Phenotype Ontology https://github.com/obophenotype/human-phenotyp... None https://hpo.jax.org 1 None 2024-04-26 None 2025-03-10 13:25:14.952000+00:00 1 None 1
80 4t7QibxO bionty.Phenotype mammalian mp False True Mammalian Phenotype Ontology https://github.com/mgijax/mammalian-phenotype-... None https://github.com/mgijax/mammalian-phenotype-... 1 None 2024-06-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
83 sqPX2b7b bionty.Phenotype zebrafish zp False True Zebrafish Phenotype Ontology https://github.com/obophenotype/zebrafish-phen... None https://github.com/obophenotype/zebrafish-phen... 1 None 2024-04-18 None 2025-03-10 13:25:14.952000+00:00 1 None 1
87 6S4qkDx1 bionty.Phenotype all pato False True Phenotype And Trait Ontology http://purl.obolibrary.org/obo/pato/releases/2... None https://github.com/pato-ontology/pato 1 None 2024-03-28 None 2025-03-10 13:25:14.952000+00:00 1 None 1
89 7Ent3V2y bionty.Pathway all go False True Gene Ontology https://data.bioontology.org/ontologies/GO/sub... None http://geneontology.org 1 None 2024-06-17 None 2025-03-10 13:25:14.952000+00:00 1 None 1
94 3rm9aOzL BFXPipeline all lamin False True Bioinformatics Pipeline s3://bionty-assets/df_all__lamin__1.0.0__BFXpi... None https://lamin.ai 1 None 1.0.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
95 ugaIoIlj Drug all dron False True Drug Ontology https://data.bioontology.org/ontologies/DRON/s... None https://bioportal.bioontology.org/ontologies/DRON 1 None 2024-08-05 None 2025-03-10 13:25:14.952000+00:00 1 None 1
99 1GbFkOdz bionty.DevelopmentalStage human hsapdv False True Human Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-03-10 13:25:14.952000+00:00 1 None 1
101 10va5JSt bionty.DevelopmentalStage mouse mmusdv False True Mouse Developmental Stages https://github.com/obophenotype/developmental-... None https://github.com/obophenotype/developmental-... 1 None 2024-05-28 None 2025-03-10 13:25:14.952000+00:00 1 None 1
103 MJRqduf9 bionty.Ethnicity human hancestro False True Human Ancestry Ontology https://github.com/EBISPOT/hancestro/raw/3.0/h... None https://github.com/EBISPOT/hancestro 1 None 3.0 None 2025-03-10 13:25:14.952000+00:00 1 None 1
104 5JnVODh4 BioSample all ncbi False True NCBI BioSample attributes s3://bionty-assets/df_all__ncbi__2023-09__BioS... None https://www.ncbi.nlm.nih.gov/biosample/docs/at... 1 None 2023-09 None 2025-03-10 13:25:14.952000+00:00 1 None 1