Cell marker

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

💡 connected lamindb: testuser1/test-public-ontologies

PublicOntology objects

Let us create a public ontology accessor with public(), which chooses a default public ontology source from PublicSource. It’s a PublicOntology object, which you can think about as a public registry:

public = bt.CellMarker.public(organism="human")
public

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)
synonyms gene_symbol ncbi_gene_id uniprotkb_id __ratio__
name
Cd4 CD4 920 B4DT49 100.0
CD4+ None None None 100.0
CD45RB None None None 90.0
CD45RO None None None 90.0
CD44R None None None 90.0

Search another field (default is .name):

public.search("CD4", field=public.gene_symbol).head(1)
name synonyms ncbi_gene_id uniprotkb_id __ratio__
gene_symbol
CD4 Cd4 920 B4DT49 100.0

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);

✅ 6 terms (42.90%) are validated for name

❗ 8 terms (57.10%) are not validated for name: KI67, CCR7, CD14, CD4, CD127a, Invalid-1, Invalid-2, Time

   detected 4 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

💡 standardized 10/14 terms

{'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);

✅ 10 terms (71.40%) are validated for name

❗ 4 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()
synonyms gene_symbol ncbi_gene_id uniprotkb_id __agg__ __ratio__
name
CD127 IL7R 3575 P16871 cd127 90.909091
CD1 CD1A 910 P29016 cd1 90.000000
CD172a None None None cd172a 83.333333
CD167a None None None cd167a 83.333333
CD121a None None None cd121a 83.333333

Now we see that all cell marker candidates validate:

public.validate(curated_df.index, public.name);

✅ 11 terms (78.60%) are validated

❗ 3 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.PublicSource.filter(entity="CellMarker").df()
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-05-29 09:56:16.485913+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-05-29 09:56:16.486005+00:00

When instantiating a Bionty object, we can choose a source or version:

public_source = bt.PublicSource.filter(
    source="cellmarker", version="2.0", organism="human"
).one()
public = bt.CellMarker.public(public_source=public_source)
public

PublicOntology
Entity: CellMarker
Organism: human
Source: cellmarker, 2.0
#terms: 15466

The currently used ontologies can be displayed using:

bt.PublicSource.filter(currently_used=True).df()
Hide code cell output
uid entity organism currently_used source source_name version url md5 source_website run_id created_by_id updated_at
id
1 5Dlc Organism vertebrates True ensembl Ensembl release-112 https://ftp.ensembl.org/pub/release-112/specie... 0ec37e77f4bc2d0b0b47c6c62b9f122d https://www.ensembl.org None 1 2024-05-29 09:56:16.483555+00:00
6 2Jzh Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org None 1 2024-05-29 09:56:16.484046+00:00
7 1kdI Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org None 1 2024-05-29 09:56:16.484138+00:00
8 2mIM Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org None 1 2024-05-29 09:56:16.484233+00:00
9 2XQ6 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org None 1 2024-05-29 09:56:16.484333+00:00
10 1Vzs Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon None 1 2024-05-29 09:56:16.484429+00:00
11 1hx4 Gene human True ensembl Ensembl release-112 s3://bionty-assets/df_human__ensembl__release-... 4ccda4d88720a326737376c534e8446b https://www.ensembl.org None 1 2024-05-29 09:56:16.484524+00:00
15 76FX Gene mouse True ensembl Ensembl release-112 s3://bionty-assets/df_mouse__ensembl__release-... 519cf7b8acc3c948274f66f3155a3210 https://www.ensembl.org None 1 2024-05-29 09:56:16.484895+00:00
19 7LW6 Gene saccharomyces cerevisiae True ensembl Ensembl release-112 s3://bionty-assets/df_saccharomyces cerevisiae... 11775126b101233525a0a9e2dd64edae https://www.ensembl.org None 1 2024-05-29 09:56:16.485271+00:00
22 7llW Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org None 1 2024-05-29 09:56:16.485547+00:00
24 5U7J Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org None 1 2024-05-29 09:56:16.485730+00:00
26 5nkB CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-05-29 09:56:16.485913+00:00
27 6AFz CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker None 1 2024-05-29 09:56:16.486005+00:00
28 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 None 1 2024-05-29 09:56:16.486097+00:00
29 3DeN CellType all True cl Cell Ontology 2024-02-13 http://purl.obolibrary.org/obo/cl/releases/202... https://obophenotype.github.io/cell-ontology None 1 2024-05-29 09:56:16.486189+00:00
34 1AyH Tissue all True uberon Uberon multi-species anatomy ontology 2024-02-20 http://purl.obolibrary.org/obo/uberon/releases... 2048667b5fdf93192384bdf53cafba18 http://obophenotype.github.io/uberon None 1 2024-05-29 09:56:16.486674+00:00
39 LoCG Disease all True mondo Mondo Disease Ontology 2024-02-06 http://purl.obolibrary.org/obo/mondo/releases/... 78914fa236773c5ea6605f7570df6245 https://mondo.monarchinitiative.org None 1 2024-05-29 09:56:16.487135+00:00
44 2mou Disease human True doid Human Disease Ontology 2024-01-31 http://purl.obolibrary.org/obo/doid/releases/2... b36c15a4610757094f8db64b78ae2693 https://disease-ontology.org None 1 2024-05-29 09:56:16.487603+00:00
51 4usY ExperimentalFactor all True efo The Experimental Factor Ontology 3.63.0 http://www.ebi.ac.uk/efo/releases/v3.63.0/efo.owl 603e6f6981d53d501c5921aa3940b095 https://bioportal.bioontology.org/ontologies/EFO None 1 2024-05-29 09:56:16.488253+00:00
54 2WLc Phenotype human True hp Human Phenotype Ontology 2024-03-06 https://github.com/obophenotype/human-phenotyp... 36b0d00c24a68edb9131707bc146a4c7 https://hpo.jax.org None 1 2024-05-29 09:56:16.488529+00:00
58 6zE1 Phenotype mammalian True mp Mammalian Phenotype Ontology 2024-02-07 https://github.com/mgijax/mammalian-phenotype-... 31c27ed2c7d5774f8b20a77e4e1fd278 https://github.com/mgijax/mammalian-phenotype-... None 1 2024-05-29 09:56:16.488896+00:00
60 7EnA Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2024-01-22 https://github.com/obophenotype/zebrafish-phen... 01600a5d392419b27fc567362d4cfff8 https://github.com/obophenotype/zebrafish-phen... None 1 2024-05-29 09:56:16.489080+00:00
63 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 None 1 2024-05-29 09:56:16.489354+00:00
64 48aa Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org None 1 2024-05-29 09:56:16.489445+00:00
67 3rm9 BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai None 1 2024-05-29 09:56:16.489724+00:00
68 5alK Drug all True dron Drug Ontology 2024-03-02 https://data.bioontology.org/ontologies/DRON/s... 84138459de4f65034e979f4e46783747 https://bioportal.bioontology.org/ontologies/DRON None 1 2024-05-29 09:56:16.489824+00:00
70 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-... None 1 2024-05-29 09:56:16.490012+00:00
71 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-... None 1 2024-05-29 09:56:16.490106+00:00
72 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 None 1 2024-05-29 09:56:16.492428+00:00
73 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... None 1 2024-05-29 09:56:16.492535+00:00