Look up records of Bionty entities#

Entities and ontologies can be complex with many different identifiers.

Here we show Bionty’s lookup model for species, genes, proteins and cell markers. You’ll see how to

access the reference table via .df()
look up an entity term via .lookup()
look up an entity term via .fuzzy_match()

import bionty as bt

✅ Created /home/runner/.lamin/bionty/versions/sources_local.yaml!

.fields: fields of an ontology reference#

gene_bionty = bt.Gene()

gene_bionty

Gene
Species: human
Source: ensembl, release-108

📖 Gene.df(): ontology reference table
🔎 Gene.lookup(): autocompletion of ontology terms
🎯 Gene.fuzzy_match(): fuzzy match against ontology terms
🧐 Gene.inspect(): check if identifiers are mappable
👽 Gene.map_synonyms(): map synonyms to standardized names
🔗 Gene.ontology: Pronto.Ontology object

gene_bionty.fields

{'description',
 'ensembl_gene_id',
 'gene_type',
 'hgnc_id',
 'id',
 'ncbi_gene_id',
 'omim_id',
 'symbol',
 'synonyms'}

Fields can be accessed as attributes for autocompletion:

(You can pass them to the field parameter in any bionty function instead of strings.)

gene_bionty.ncbi_gene_id

ncbi_gene_id

`.df()`: reference table#

Data scientists love DataFrames, and every entity has a reference table containing all the fields.

df = gene_bionty.df()

df.head()

	id	ensembl_gene_id	symbol	gene_type	description	ncbi_gene_id	hgnc_id	omim_id	synonyms	version
0	Lzl9xt	ENSG00000210049	MT-TF	Mt_tRNA	mitochondrially encoded tRNA-Phe (UUU/C) [Sour...	None	HGNC:7481	None	MTTF\|trnF	Ens107
1	ILAWa7	ENSG00000211459	MT-RNR1	Mt_rRNA	mitochondrially encoded 12S rRNA [Source:HGNC ...	None	HGNC:7470	None	12S\|MOTS-c\|MTRNR1	Ens107
2	XkyeQz	ENSG00000210077	MT-TV	Mt_tRNA	mitochondrially encoded tRNA-Val (GUN) [Source...	None	HGNC:7500	None	MTTV\|trnV	Ens107
3	jDD2jW	ENSG00000210082	MT-RNR2	Mt_rRNA	mitochondrially encoded 16S rRNA [Source:HGNC ...	None	HGNC:7471	None	16S\|HN\|MTRNR2	Ens107
4	J58H9b	ENSG00000209082	MT-TL1	Mt_tRNA	mitochondrially encoded tRNA-Leu (UUA/G) 1 [So...	None	HGNC:7490	None	MTTL1\|TRNL1	Ens107

To access the information of, for example the multiple gene symbols, we select the corresponding species through Pandas:

df.set_index("symbol").loc[["LMNA", "TCF7", "BRCA1"]]

	id	ensembl_gene_id	gene_type	description	ncbi_gene_id	hgnc_id	omim_id	synonyms	version
symbol
LMNA	96RlDv	ENSG00000160789	protein_coding	lamin A/C [Source:HGNC Symbol;Acc:HGNC:6636]	4000	HGNC:6636	150330	CMD1A\|HGPS\|LGMD1B\|LMN1\|LMNL1\|MADA\|PRO1	Ens107
TCF7	sXCrmQ	ENSG00000081059	protein_coding	transcription factor 7 [Source:HGNC Symbol;Acc...	6932	HGNC:11639	189908	TCF-1	Ens107
BRCA1	9FY8yO	ENSG00000012048	protein_coding	BRCA1 DNA repair associated [Source:HGNC Symbo...	672	HGNC:1100	113705	BRCC1\|FANCS\|PPP1R53\|RNF53	Ens107

.lookup(): Lookup terms and records with autocompletion#

Terms can be searched with auto-complete using a lookup object.

lookup = gene_bionty.lookup()

Pythonic terms can be directly fetched via dot . accessor:

lookup.TCF7

Gene(id='sXCrmQ', ensembl_gene_id='ENSG00000081059', symbol='TCF7', gene_type='protein_coding', description='transcription factor 7 [Source:HGNC Symbol;Acc:HGNC:11639]', ncbi_gene_id='6932', hgnc_id='HGNC:11639', omim_id='189908', synonyms='TCF-1', version='Ens107')

For non-pythonic string, use bracket [] for autocompletion:

lookup["ADGRL1-AS1"]

Gene(id='v68LyZ', ensembl_gene_id='ENSG00000267169', symbol='ADGRL1-AS1', gene_type='lncRNA', description='ADGRL1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:55309]', ncbi_gene_id='100507373', hgnc_id='HGNC:55309', omim_id=None, synonyms=None, version='Ens107')

By default, the name field is used to generate lookup keys.

You can specify another field to look up:

lookup = gene_bionty.lookup(gene_bionty.hgnc_id)

lookup["HGNC:10478"]

Gene(id='AdmgUK', ensembl_gene_id='ENSG00000204231', symbol='RXRB', gene_type='protein_coding', description='retinoid X receptor beta [Source:HGNC Symbol;Acc:HGNC:10478]', ncbi_gene_id='6257', hgnc_id='HGNC:10478', omim_id='180246', synonyms='H-2RIIBP|NR2B2|RCoR-1|RXR-beta|RXRbeta', version='Ens107')

`.fuzzy_match`: Look up a term via fuzzy matching#

celltype_bionty = bt.CellType()

celltype_bionty.fuzzy_match("cytotoxic T cells")

	ontology_id	definition	synonyms	children	__ratio__
name
cytotoxic T cell	CL:0000910	A Mature T Cell That Differentiated And Acquir...	cytotoxic T lymphocyte\|cytotoxic T-lymphocyte\|...	[]	96.969697

By default, fuzzy_match also matches against synonyms:

celltype_bionty.fuzzy_match("P cell")

	ontology_id	definition	synonyms	children	__ratio__
name
nodal myocyte	CL:0002072	A Specialized Cardiac Myocyte In The Sinoatria...	cardiac pacemaker cell\|myocytus nodalis\|P cell	[CL:1000409, CL:1000410]	100.0

You can turn off synonym matching with synonyms_field=None:

celltype_bionty.fuzzy_match("P cell", synonyms_field=None)

	ontology_id	definition	synonyms	children	__ratio__
name
PP cell	CL:0000696	A Cell That Stores And Secretes Pancreatic Pol...	type F enteroendocrine cell	[CL:0002680]	92.307692

Match against another field (default is “name”):

celltype_bionty.fuzzy_match("CD8+ alpha beta T cells", field=celltype_bionty.definition)

	ontology_id	name	synonyms	children	__ratio__
definition
A T Cell That Expresses An Alpha-Beta T Cell Receptor Complex.	CL:0000789	alpha-beta T cell	alpha-beta T-cell\|alpha-beta T-lymphocyte\|alph...	[CL:0000790, CL:0000791]	75.0

Return all results ranked by matching ratios:

celltype_bionty.fuzzy_match("P cell", return_ranked_results=True).head()

	ontology_id	definition	synonyms	children	__ratio__
name
nodal myocyte	CL:0002072	A Specialized Cardiac Myocyte In The Sinoatria...	cardiac pacemaker cell\|myocytus nodalis\|P cell	[CL:1000409, CL:1000410]	100.000000
double-positive, alpha-beta thymocyte	CL:0000809	A Thymocyte Expressing The Alpha-Beta T Cell R...	DP cell\|DP thymocyte\|double-positive, alpha-be...	[CL:0002430, CL:0002427, CL:0002431, CL:000242...	92.307692
PP cell	CL:0000696	A Cell That Stores And Secretes Pancreatic Pol...	type F enteroendocrine cell	[CL:0002680]	92.307692
pigmented ciliary epithelial cell	CL:0002303	A Cell That Is Part Of Pigmented Ciliary Epith...	PE cell	[]	92.307692
GIP cell	CL:0002278	An Enteroendocrine Cell Of Duodenum And Jejunu...	type K enteroendocrine cell	[]	85.714286

Tied results will all be returns:

celltype_bionty.fuzzy_match("A cell", synonyms_field=None)

	ontology_id	definition	synonyms	children	__ratio__
name
T cell	CL:0000084	A Type Of Lymphocyte Whose Defining Characteri...	T-cell\|T lymphocyte\|T-lymphocyte	[CL:0000798, CL:0002420, CL:0002419, CL:0000789]	83.333333
B cell	CL:0000236	A Lymphocyte Of B Lineage That Is Capable Of B...	B lymphocyte\|B-lymphocyte\|B-cell	[CL:0009114, CL:0001201]	83.333333

Look up records of Bionty entities#

.fields: fields of an ontology reference#

.df(): reference table#

.lookup(): Lookup terms and records with autocompletion#

.fuzzy_match: Look up a term via fuzzy matching#

`.df()`: reference table#

`.fuzzy_match`: Look up a term via fuzzy matching#