Cell line#

lamindb provides access to the following public cell line ontologies through lnschema-bionty:

  1. Cell Line Ontology

Here we show how to access and search cell line ontologies to standardize new data.

Setup#

!lamin init --storage ./test-cell-line --schema bionty

✅ saved: User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2023-12-22 16:53:28 UTC)
✅ saved: Storage(uid='m59Uwofe', root='/home/runner/work/lamin-usecases/lamin-usecases/docs/test-cell-line', type='local', updated_at=2023-12-22 16:53:28 UTC, created_by_id=1)

💡 loaded instance: testuser1/test-cell-line
💡 did not register local instance on hub

import lnschema_bionty as lb
import pandas as pd

# adds an entry "human" into an empty instance
lb.settings.organism = "human"

💡 loaded instance: testuser1/test-cell-line

Bionty objects#

Let us create a public knowledge accessor with bionty(), which chooses a default public knowledge source from BiontySource. It’s a Bionty object, which you can think about as a less-capable registry:

cell_line_bt = lb.CellLine.bionty()
cell_line_bt

CellLine
Organism: all
Source: clo, 2022-03-21
#terms: 39037

📖 CellLine.df(): ontology reference table
🔎 CellLine.lookup(): autocompletion of terms
🎯 CellLine.search(): free text search of terms
✅ CellLine.validate(): strictly validate values
🧐 CellLine.inspect(): full inspection of values
👽 CellLine.standardize(): convert to standardized names
🪜 CellLine.diff(): difference between two versions
🔗 CellLine.ontology: Pronto.Ontology object

As for registries, you can export the ontology as a DataFrame:

df = cell_line_bt.df()
df.head()
name definition synonyms parents
ontology_id
CLO:0000000 cell line cell culturing a maintaining cell culture process that keeps ... None []
CLO:0000001 cell line cell A cultured cell that is part of a cell line - ... None []
CLO:0000002 suspension cell line culturing suspension cell line culturing is a cell line ... None [CLO:0000000]
CLO:0000003 adherent cell line culturing adherent cell line culturing is a cell line cu... None [CLO:0000000]
CLO:0000004 cell line cell modification a material processing that modifies an existin... None []

Unlike registries, you can also export it as a Pronto object via cell_line_bt.ontology.

Look up terms#

As for registries, terms can be looked up with auto-complete:

lookup = cell_line_bt.lookup()

The . accessor provides normalized terms (lower case, only contains alphanumeric characters and underscores):

lookup.hek293

CellLine(ontology_id='CLO:0001230', name='HEK293', definition=None, synonyms='293|HEK-293|293 HEK|293 cell|Human Embryonic Kidney 293|HEK 293', parents=array(['CLO:0037236'], 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["HEK293"]

CellLine(ontology_id='CLO:0001230', name='HEK293', definition=None, synonyms='293|HEK-293|293 HEK|293 cell|Human Embryonic Kidney 293|HEK 293', parents=array(['CLO:0037236'], dtype=object))

By default, the name field is used to generate lookup keys. You can specify another field to look up:

lookup = cell_line_bt.lookup(cell_line_bt.ontology_id)

lookup.CLO: 0000000

Search terms#

Search behaves in the same way as it does for registries:

cell_line_bt = lb.CellLine.bionty()
cell_line_bt.search("hek293").head(1)
ontology_id definition synonyms parents __ratio__
name
293-derived cell CLO:0037237 None 293|HEK-293|293 HEK|HEK293|HEK 293 [CLO:0037236] 100.0

Search another field (default is .name):

cell_line_bt.search("suspension cell line", field=cell_line_bt.definition).head(1)
ontology_id name synonyms parents __ratio__
definition
a cell line that requires suspension cell cuturing. CLO:0000026 suspension cell line cell suspension cell line [CLO:0000001] 100.0

Standardize cell line identifiers#

Let us generate a DataFrame that stores a number of cell line identifiers, some of which corrupted:

df_orig = pd.DataFrame(
    index=[
        "253D cell",
        "HEK293",
        "2C1H7 cell",
        "283TAg cell",
        "This cell line does not exist",
    ]
)
df_orig
253D cell
HEK293
2C1H7 cell
283TAg cell
This cell line does not exist

We can check whether any of our values are validated against the ontology reference:

validated = cell_line_bt.validate(df_orig.index, cell_line_bt.name)
df_orig.index[~validated]

❗ 1 term (20.00%) is not validated: This cell line does not exist

Index(['This cell line does not exist'], dtype='object')

Ontology source versions#

For any given entity, we can choose from a number of versions:

lb.BiontySource.filter(entity="CellLine").df()
uid entity organism currently_used source source_name version url md5 source_website updated_at created_by_id
id
20 2Zjk CellLine all True clo Cell Line Ontology 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO 2023-12-22 16:53:28.593394+00:00 1

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

bionty_source = lb.BiontySource.filter(
    source="clo", version="2022-03-21", organism="all"
).one()
cell_line_bt = lb.CellLine.bionty(bionty_source=bionty_source)
cell_line_bt

CellLine
Organism: all
Source: clo, 2022-03-21
#terms: 39037

📖 CellLine.df(): ontology reference table
🔎 CellLine.lookup(): autocompletion of terms
🎯 CellLine.search(): free text search of terms
✅ CellLine.validate(): strictly validate values
🧐 CellLine.inspect(): full inspection of values
👽 CellLine.standardize(): convert to standardized names
🪜 CellLine.diff(): difference between two versions
🔗 CellLine.ontology: Pronto.Ontology object

The currently used ontologies can be displayed using:

lb.BiontySource.filter(currently_used=True).df()
uid entity organism currently_used source source_name version url md5 source_website updated_at created_by_id
id
1 zvGR Organism vertebrates True ensembl Ensembl release-110 https://ftp.ensembl.org/pub/release-110/specie... f3faf95648d3a2b50fd3625456739706 https://www.ensembl.org 2023-12-22 16:53:28.592724+00:00 1
4 TE9h Organism bacteria True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacte... ee28510ed5586ea7ab4495717c96efc8 https://www.ensembl.org 2023-12-22 16:53:28.592852+00:00 1
5 OZIG Organism fungi True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/fungi/releas... dbcde58f4396ab8b2480f7fe9f83df8a https://www.ensembl.org 2023-12-22 16:53:28.592887+00:00 1
6 W07m Organism metazoa True ensembl Ensembl release-57 http://ftp.ensemblgenomes.org/pub/metazoa/rele... 424636a574fec078a61cbdddb05f9132 https://www.ensembl.org 2023-12-22 16:53:28.592922+00:00 1
7 AVh3 Organism plants True ensembl Ensembl release-57 https://ftp.ensemblgenomes.ebi.ac.uk/pub/plant... eadaa1f3e527e4c3940c90c7fa5c8bf4 https://www.ensembl.org 2023-12-22 16:53:28.592956+00:00 1
8 MdBu Organism all True ncbitaxon NCBItaxon Ontology 2023-06-20 s3://bionty-assets/df_all__ncbitaxon__2023-06-... 00d97ba65627f1cd65636d2df22ea76c https://github.com/obophenotype/ncbitaxon 2023-12-22 16:53:28.592989+00:00 1
9 o36k Gene human True ensembl Ensembl release-110 s3://bionty-assets/df_human__ensembl__release-... 832f3947e83664588d419608a469b528 https://www.ensembl.org 2023-12-22 16:53:28.593023+00:00 1
11 VTEw Gene mouse True ensembl Ensembl release-110 s3://bionty-assets/df_mouse__ensembl__release-... fa4ce130f2929aefd7ac3bc8eaf0c4de https://www.ensembl.org 2023-12-22 16:53:28.593092+00:00 1
13 Uhnp Gene saccharomyces cerevisiae True ensembl Ensembl release-110 s3://bionty-assets/df_saccharomyces cerevisiae... 2e59495a3e87ea6575e408697dd73459 https://www.ensembl.org 2023-12-22 16:53:28.593161+00:00 1
14 000Q Protein human True uniprot Uniprot 2023-03 s3://bionty-assets/df_human__uniprot__2023-03_... 1c46e85c6faf5eff3de5b4e1e4edc4d3 https://www.uniprot.org 2023-12-22 16:53:28.593195+00:00 1
16 tD7O Protein mouse True uniprot Uniprot 2023-03 s3://bionty-assets/df_mouse__uniprot__2023-03_... 9d5e9a8225011d3218e10f9bbb96a46c https://www.uniprot.org 2023-12-22 16:53:28.593262+00:00 1
18 vqWI CellMarker human True cellmarker CellMarker 2.0 s3://bionty-assets/human_cellmarker_2.0_CellMa... d565d4a542a5c7e7a06255975358e4f4 http://bio-bigdata.hrbmu.edu.cn/CellMarker 2023-12-22 16:53:28.593328+00:00 1
19 ypPK CellMarker mouse True cellmarker CellMarker 2.0 s3://bionty-assets/mouse_cellmarker_2.0_CellMa... 189586732c63be949e40dfa6a3636105 http://bio-bigdata.hrbmu.edu.cn/CellMarker 2023-12-22 16:53:28.593361+00:00 1
20 2Zjk CellLine all True clo Cell Line Ontology 2022-03-21 https://data.bioontology.org/ontologies/CLO/su... ea58a1010b7e745702a8397a526b3a33 https://bioportal.bioontology.org/ontologies/CLO 2023-12-22 16:53:28.593394+00:00 1
21 4shh CellType all True cl Cell Ontology 2023-08-24 http://purl.obolibrary.org/obo/cl/releases/202... 46e7dd89421f1255cf0191eca1548f73 https://obophenotype.github.io/cell-ontology 2023-12-22 16:53:28.593429+00:00 1
25 LmWQ 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 2023-12-22 16:53:28.593564+00:00 1
29 zMWv Disease all True mondo Mondo Disease Ontology 2023-08-02 http://purl.obolibrary.org/obo/mondo/releases/... 7f33767422042eec29f08b501fc851db https://mondo.monarchinitiative.org 2023-12-22 16:53:28.593697+00:00 1
33 cxPr Disease human True doid Human Disease Ontology 2023-03-31 http://purl.obolibrary.org/obo/doid/releases/2... 64f083a1e47867c307c8eae308afc3bb https://disease-ontology.org 2023-12-22 16:53:28.593829+00:00 1
35 2wto 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 2023-12-22 16:53:28.593896+00:00 1
37 3SSF Phenotype human True hp Human Phenotype Ontology 2023-06-17 https://github.com/obophenotype/human-phenotyp... 65e8d96bc81deb893163927063b10c06 https://hpo.jax.org 2023-12-22 16:53:28.593962+00:00 1
40 nwdt Phenotype mammalian True mp Mammalian Phenotype Ontology 2023-05-31 https://github.com/mgijax/mammalian-phenotype-... be89052cf6d9c0b6197038fe347ef293 https://github.com/mgijax/mammalian-phenotype-... 2023-12-22 16:53:28.594060+00:00 1
41 zAfB Phenotype zebrafish True zp Zebrafish Phenotype Ontology 2022-12-17 https://github.com/obophenotype/zebrafish-phen... 03430b567bf153216c0fa4c3440b3b24 https://github.com/obophenotype/zebrafish-phen... 2023-12-22 16:53:28.594094+00:00 1
43 p1co 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 2023-12-22 16:53:28.594160+00:00 1
44 h0rU Pathway all True go Gene Ontology 2023-05-10 https://data.bioontology.org/ontologies/GO/sub... e9845499eadaef2418f464cd7e9ac92e http://geneontology.org 2023-12-22 16:53:28.594194+00:00 1
46 fxHJ BFXPipeline all True lamin Bioinformatics Pipeline 1.0.0 s3://bionty-assets/bfxpipelines.json a7eff57a256994692fba46e0199ffc94 https://lamin.ai 2023-12-22 16:53:28.594260+00:00 1
47 chfO Drug all True dron Drug Ontology 2023-03-10 https://data.bioontology.org/ontologies/DRON/s... 75e86011158fae76bb46d96662a33ba3 https://bioportal.bioontology.org/ontologies/DRON 2023-12-22 16:53:28.594294+00:00 1
48 7JhT DevelopmentalStage human True hsapdv Human Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/HSAPDV/11... 52181d59df84578ed69214a5cb614036 https://github.com/obophenotype/developmental-... 2023-12-22 16:53:28.594327+00:00 1
49 JIKv DevelopmentalStage mouse True mmusdv Mouse Developmental Stages 2020-03-10 http://aber-owl.net/media/ontologies/MMUSDV/9/... 5bef72395d853c7f65450e6c2a1fc653 https://github.com/obophenotype/developmental-... 2023-12-22 16:53:28.594360+00:00 1
50 clid Ethnicity human True hancestro Human Ancestry Ontology 3.0 https://github.com/EBISPOT/hancestro/raw/3.0/h... 76dd9efda9c2abd4bc32fc57c0b755dd https://github.com/EBISPOT/hancestro 2023-12-22 16:53:28.594393+00:00 1
51 rsbG 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... 2023-12-22 16:53:28.594426+00:00 1
Hide code cell content 
!lamin delete --force test-cell-line
!rm -r test-cell-line

💡 deleting instance testuser1/test-cell-line
✅     deleted instance settings file: /home/runner/.lamin/instance--testuser1--test-cell-line.env

✅     instance cache deleted
✅     deleted '.lndb' sqlite file
❗     consider manually deleting your stored data: /home/runner/work/lamin-usecases/lamin-usecases/docs/test-cell-line