Benchmark search

from laminci.db import setup_local_test_postgres

pgurl = setup_local_test_postgres()

• Created Postgres test instance: 'postgresql://postgres:pwd@0.0.0.0:5432/pgtest'
It runs in docker container 'pgtest'

!lamin init --name benchmark_search --db {pgurl} --schema bionty --storage ./benchmark_search

→ connected lamindb: testuser1/benchmark_search

import lamindb as ln
import bionty as bt
import pandas as pd
import rbo
from django.test import modify_settings
from django.contrib.postgres.search import SearchQuery, SearchVector, SearchRank

→ connected lamindb: testuser1/benchmark_search

postgres = {"append": "django.contrib.postgres"}

@modify_settings(INSTALLED_APPS=postgres)
def rank_fulltext_postgres(cls, search_str, fields=None):
    if fields is None:
        fields = [field.name for field in cls._meta.fields if field.get_internal_type() in {"CharField", "TextField"}]
    vector = SearchVector(*fields)
    query = SearchQuery(search_str)
    qs = cls.objects.annotate(rank=SearchRank(vector, query)).filter()
    if "ontology_id" not in fields:
        fields.append("ontology_id")
    ls = qs.values(*fields, "rank").list()
    df = pd.DataFrame(ls)[["rank"] + fields]
    return df.set_index("ontology_id").sort_values("rank", ascending=False)

bt.CellType.import_from_source()

SEARCH_QUERIES = ("t cell", "stem cell", "b cell", "regulatory B cell", "Be2 cell", "neural", "adipocyte")
TOP_N = 20

postgres fulltext search vs bionty search

ct_public = bt.CellType.public()

for query in SEARCH_QUERIES:
    print("Query:", query)
    print("postgres search:")
    df_ps = rank_fulltext_postgres(bt.CellType, query, ["name"]).head(TOP_N)
    display(df_ps)
    df_bt = ct_public.search(query)
    df_bt["name"] = df_bt.index
    df_bt = df_bt[["ontology_id", "name"]].set_index("ontology_id").head(TOP_N)
    print("bionty search:")
    display(df_bt)
    rbo_score = rbo.RankingSimilarity(df_ps.index.to_list(), df_bt.index.to_list()).rbo(p=0.9)
    print("RBO:", rbo_score)

Query: t cell
postgres search:

	rank	name
ontology_id
CL:0000002	0.075991	obsolete immortal cell line cell
CL:2000020	0.075991	inner cell mass cell
CL:0007015	0.075991	obsolete mortal cell line cell
CL:0007014	0.075991	obsolete cell line cell
CL:0000892	0.075991	smooth muscle cell derived foam cell
CL:0009104	0.075991	B cell zone reticular cell
CL:0009105	0.075991	T cell zone reticular cell
CL:0000000	0.060793	cell
CL:0002658	0.060793	glandular cell of the large intestine
CL:0002654	0.060793	epithelial cell of stratum corneum of esophage...
CL:0002655	0.060793	epithelial cell of stratum spinosum of esophag...
CL:0002656	0.060793	glandular cell of endometrium
CL:0002657	0.060793	glandular cell of esophagus
CL:0002661	0.060793	luminal cell of lactiferous terminal ductal lo...
CL:0002659	0.060793	glandular cell of stomach
CL:0002660	0.060793	luminal cell of acinus of lactiferous gland
CL:0002652	0.060793	endothelial cell of high endothelial venule
CL:0002662	0.060793	luminal cell of lactiferous duct
CL:0002663	0.060793	myocardial endocrine cell of atrium
CL:0002671	0.060793	endothelial stalk cell

bionty search:

	name
ontology_id
CL:0000084	T cell
CL:0000806	DN2 thymocyte
CL:0000136	adipocyte
CL:0000545	T-helper 1 cell
CL:0000632	hepatic stellate cell
CL:0000901	Tr1 cell
CL:0000807	DN3 thymocyte
CL:0000546	T-helper 2 cell
CL:0000918	Tc2 cell
CL:0000423	tip cell
CL:0000917	Tc1 cell
CL:0011025	exhausted T cell
CL:0000682	M cell of gut
CL:0002280	type N enteroendocrine cell
CL:0000570	parafollicular cell
CL:0002072	nodal myocyte
CL:4023187	koniocellular cell
CL:0000508	type G enteroendocrine cell
CL:0000502	type D enteroendocrine cell
CL:0000236	B cell

RBO: 0.0
Query: stem cell
postgres search:

	rank	name
ontology_id
CL:4030035	0.099103	dental pulp stem cell
CL:0002569	0.099103	mesenchymal stem cell of umbilical cord
CL:0009028	0.099103	intestinal crypt stem cell of appendix
CL:0000723	0.099103	somatic stem cell
CL:0002339	0.099103	prostate stem cell
CL:0002337	0.099103	keratinocyte stem cell
CL:0009043	0.099103	intestinal crypt stem cell of colon
CL:0002259	0.099103	neuroepithelial stem cell
CL:2000095	0.099103	cord blood hematopoietic stem cell
CL:0002183	0.099103	stem cell of gastric gland
CL:0009017	0.099103	intestinal crypt stem cell of small intestine
CL:0002250	0.099103	intestinal crypt stem cell
CL:0000052	0.099103	totipotent stem cell
CL:0009016	0.099103	intestinal crypt stem cell of large intestine
CL:0002248	0.099103	pluripotent stem cell
CL:0000383	0.099103	nephrogenic mesenchyme stem cell
CL:0000047	0.099103	neural stem cell
CL:0000046	0.099103	obsolete bursa processed stem cell
CL:0000045	0.099103	obsolete thymus processed stem cell
CL:0002568	0.099103	mesenchymal stem cell of Wharton's jelly

bionty search:

	name
ontology_id
CL:0000034	stem cell
CL:0000419	seam cell
CL:0002033	short term hematopoietic stem cell
CL:0002034	long term hematopoietic stem cell
CL:0002651	endothelial cell of venous sinus of spleen
CL:4030002	effector memory CD45RA-positive, alpha-beta T ...
CL:0000019	sperm
CL:0011025	exhausted T cell
CL:0001008	Kit and Sca1-positive hematopoietic stem cell
CL:0000354	blastemal cell
CL:0000718	compound eye cone cell
CL:0000682	M cell of gut
CL:0000084	T cell
CL:0000097	mast cell
CL:0000583	alveolar macrophage
CL:0000586	germ cell
CL:0002085	tanycyte
CL:0000499	stromal cell
CL:0000629	storage cell
CL:0002303	pigmented ciliary epithelial cell

RBO: 0.0
Query: b cell
postgres search:

	rank	name
ontology_id
CL:0000819	0.186813	B-1 B cell
CL:0000820	0.186813	B-1a B cell
CL:0000822	0.186813	B-2 B cell
CL:0002047	0.186813	fraction B precursor B cell
CL:0000821	0.186813	B-1b B cell
CL:0009104	0.184907	B cell zone reticular cell
CL:0001053	0.099103	IgD-negative memory B cell
CL:0000275	0.099103	obsolete prestalk B cell
CL:0009032	0.099103	B cell of appendix
CL:0000981	0.099103	double negative memory B cell
CL:0004115	0.099103	retinal ganglion cell B
CL:0000302	0.099103	obsolete IgM B cell
CL:0000303	0.099103	obsolete IgG B cell
CL:0009037	0.099103	lymph node mantle zone B cell
CL:0009045	0.099103	B cell of medullary sinus of lymph node
CL:0009050	0.099103	B cell of anorectum
CL:0000236	0.099103	B cell
CL:0009060	0.099103	marginal zone B cell of lymph node
CL:0000979	0.099103	IgG memory B cell
CL:0000305	0.099103	obsolete IgE B cell

bionty search:

	name
ontology_id
CL:0000236	B cell
CL:0000819	B-1 B cell
CL:0000968	Be cell
CL:0000822	B-2 B cell
CL:0000969	regulatory B cell
CL:0000944	Be2 cell
CL:0000943	Be1 Cell
CL:0000821	B-1b B cell
CL:0000820	B-1a B cell
CL:0000570	parafollicular cell
CL:4023187	koniocellular cell
CL:0002280	type N enteroendocrine cell
CL:0000508	type G enteroendocrine cell
CL:0000502	type D enteroendocrine cell
CL:0000682	M cell of gut
CL:0002072	nodal myocyte
CL:0000084	T cell
CL:0000844	germinal center B cell
CL:0000958	T1 B cell
CL:0002155	echinocyte

RBO: 0.2898753947265706
Query: regulatory B cell
postgres search:

	rank	name
ontology_id
CL:0000969	0.268330	regulatory B cell
CL:0000819	0.186813	B-1 B cell
CL:0000822	0.186813	B-2 B cell
CL:0000821	0.186813	B-1b B cell
CL:0002047	0.186813	fraction B precursor B cell
CL:0000820	0.186813	B-1a B cell
CL:0009104	0.184907	B cell zone reticular cell
CL:0002052	0.099103	fraction D precursor B cell
CL:0002111	0.099103	CD38-negative unswitched memory B cell
CL:0002113	0.099103	B220-low CD38-negative unswitched memory B cell
CL:0002112	0.099103	B220-positive CD38-negative unswitched memory ...
CL:0002109	0.099103	B220-positive CD38-positive naive B cell
CL:0002114	0.099103	CD38-positive unswitched memory B cell
CL:0002115	0.099103	B220-positive CD38-positive unswitched memory ...
CL:0002116	0.099103	B220-low CD38-positive unswitched memory B cell
CL:0002117	0.099103	IgG-negative class switched memory B cell
CL:0002110	0.099103	B220-low CD38-positive naive B cell
CL:0002107	0.099103	IgD-negative CD38-positive IgG memory B cell
CL:0002108	0.099103	CD38-negative IgG memory B cell
CL:0002119	0.099103	CD38-positive IgG-negative class switched memo...

bionty search:

	name
ontology_id
CL:0000969	regulatory B cell
CL:0000815	regulatory T cell
CL:0000795	CD8-positive, alpha-beta regulatory T cell
CL:0002677	naive regulatory T cell
CL:0002678	memory regulatory T cell
CL:0000902	induced T-regulatory cell
CL:0000903	natural T-regulatory cell
CL:0000493	obsolete regulatory T cell
CL:0000901	Tr1 cell
CL:0000787	memory B cell
CL:0000817	precursor B cell
CL:0002633	respiratory basal cell
CL:0009113	T follicular regulatory cell
CL:0000424	excretory cell
CL:0000432	reticular cell
CL:0000151	secretory cell
CL:0000973	IgA memory B cell
CL:0000826	pro-B cell
CL:0002370	respiratory goblet cell
CL:0002048	late pro-B cell

RBO: 0.2514833037385551
Query: Be2 cell
postgres search:

	rank	name
ontology_id
CL:0000944	9.910322e-02	Be2 cell
CL:0000000	1.000000e-20	cell
CL:0009019	1.000000e-20	nephrogenic zone cell
CL:0009011	1.000000e-20	transit amplifying cell of colon
CL:0009012	1.000000e-20	transit amplifying cell of small intestine
CL:0009013	1.000000e-20	fetal hepatobiliary progenitor cell
CL:0009014	1.000000e-20	Peyer's patch lymphocyte
CL:0009015	1.000000e-20	Peyer's patch follicular dendritic cell
CL:0009016	1.000000e-20	intestinal crypt stem cell of large intestine
CL:0009017	1.000000e-20	intestinal crypt stem cell of small intestine
CL:0009018	1.000000e-20	lymphocyte of large intestine lamina propria
CL:0009020	1.000000e-20	tuft cell of appendix
CL:0009009	1.000000e-20	paneth cell of colon
CL:0009021	1.000000e-20	stromal cell of lamina propria of large intestine
CL:0009022	1.000000e-20	stromal cell of lamina propria of small intestine
CL:0009023	1.000000e-20	small intestine Peyer's patch T cell
CL:0009024	1.000000e-20	mesothelial cell of small intestine
CL:0009025	1.000000e-20	mesothelial cell of colon
CL:0009026	1.000000e-20	enterocyte of appendix
CL:0009027	1.000000e-20	transit amplifying cell of appendix

bionty search:

	name
ontology_id
CL:0000944	Be2 cell
CL:0000968	Be cell
CL:0000822	B-2 B cell
CL:0000943	Be1 Cell
CL:0000236	B cell
CL:0008049	Betz cell
CL:0001035	bone cell
CL:0000690	R2 photoreceptor cell
CL:0000819	B-1 B cell
CL:0002303	pigmented ciliary epithelial cell
CL:0000962	Bm2 B cell
CL:0001070	beige adipocyte
CL:0002652	endothelial cell of high endothelial venule
CL:4033014	peg cell
CL:0011025	exhausted T cell
CL:0002304	non-pigmented ciliary epithelial cell
CL:0000546	T-helper 2 cell
CL:0000806	DN2 thymocyte
CL:0000025	egg cell
CL:0000820	B-1a B cell

RBO: 0.2514833037385551
Query: neural
postgres search:

	rank	name
ontology_id
CL:0000047	0.060793	neural stem cell
CL:0002607	0.060793	migratory enteric neural crest cell
CL:0011012	0.060793	neural crest cell
CL:0002676	0.060793	neural crest derived neuroblast
CL:0007004	0.060793	premigratory neural crest cell
CL:0000027	0.060793	smooth muscle cell neural crest derived
CL:0002319	0.060793	neural cell
CL:0011017	0.060793	vagal neural crest cell
CL:2000073	0.060793	migratory cardiac neural crest cell
CL:0000011	0.060793	migratory trunk neural crest cell
CL:0000029	0.060793	neural crest derived neuron
CL:0000008	0.060793	migratory cranial neural crest cell
CL:0011020	0.060793	neural progenitor cell
CL:0000005	0.060793	neural crest derived fibroblast
CL:0002333	0.060793	neural crest derived adipocyte
CL:0000333	0.060793	migratory neural crest cell
CL:0009015	0.000000	Peyer's patch follicular dendritic cell
CL:0009014	0.000000	Peyer's patch lymphocyte
CL:0009016	0.000000	intestinal crypt stem cell of large intestine
CL:0009013	0.000000	fetal hepatobiliary progenitor cell

bionty search:

	name
ontology_id
CL:0007004	premigratory neural crest cell
CL:0000029	neural crest derived neuron
CL:0002607	migratory enteric neural crest cell
CL:0011012	neural crest cell
CL:0000027	smooth muscle cell neural crest derived
CL:0002333	neural crest derived adipocyte
CL:0000005	neural crest derived fibroblast
CL:0011020	neural progenitor cell
CL:0000333	migratory neural crest cell
CL:0000516	perineuronal satellite cell
CL:0000047	neural stem cell
CL:0000008	migratory cranial neural crest cell
CL:0000032	neuroplacodal cell
CL:2000073	migratory cardiac neural crest cell
CL:0002676	neural crest derived neuroblast
CL:0002319	neural cell
CL:0000011	migratory trunk neural crest cell
CL:0011017	vagal neural crest cell
CL:0002247	pleural macrophage
CL:1000491	mesothelial cell of pleura

RBO: 0.39489211311660155
Query: adipocyte
postgres search:

	rank	name
ontology_id
CL:0002615	0.060793	adipocyte of omentum tissue
CL:0000449	0.060793	brown adipocyte
CL:0000448	0.060793	white adipocyte
CL:0001070	0.060793	beige adipocyte
CL:1001583	0.060793	obsolete breast adipocyte
CL:0000136	0.060793	adipocyte
CL:0002333	0.060793	neural crest derived adipocyte
CL:1000311	0.060793	adipocyte of epicardial fat of left ventricle
CL:1000310	0.060793	adipocyte of epicardial fat of right ventricle
CL:1000309	0.060793	epicardial adipocyte
CL:0002521	0.060793	subcutaneous adipocyte
CL:0002617	0.060793	adipocyte of breast
CL:0002616	0.060793	perirenal adipocyte
CL:0000000	0.000000	cell
CL:0009014	0.000000	Peyer's patch lymphocyte
CL:0009015	0.000000	Peyer's patch follicular dendritic cell
CL:0009016	0.000000	intestinal crypt stem cell of large intestine
CL:0009012	0.000000	transit amplifying cell of small intestine
CL:0009017	0.000000	intestinal crypt stem cell of small intestine
CL:0009018	0.000000	lymphocyte of large intestine lamina propria

bionty search:

	name
ontology_id
CL:0000136	adipocyte
CL:0002579	omentum preadipocyte
CL:0002521	subcutaneous adipocyte
CL:0002335	brown preadipocyte
CL:0002615	adipocyte of omentum tissue
CL:1000309	epicardial adipocyte
CL:1000310	adipocyte of epicardial fat of right ventricle
CL:1000311	adipocyte of epicardial fat of left ventricle
CL:0002617	adipocyte of breast
CL:0002583	subcutaneous preadipocyte
CL:0001070	beige adipocyte
CL:0000449	brown adipocyte
CL:0002582	visceral preadipocyte
CL:1001583	obsolete breast adipocyte
CL:0002581	perirenal preadipocyte
CL:0002333	neural crest derived adipocyte
CL:0002580	preadipocyte of the breast
CL:0002616	perirenal adipocyte
CL:0000448	white adipocyte
CL:0002578	mesenteric preadipocyte

RBO: 0.2594261152112632

postgres fulltext search vs lamindb search

for query in SEARCH_QUERIES:
    print("Query:", query)
    print("postgres search:")
    df_ps = rank_fulltext_postgres(bt.CellType, query).head(TOP_N)
    display(df_ps)
    df_ln = bt.CellType.search(query).df()[["name", "ontology_id", "description", "synonyms"]]
    df_ln = df_ln.set_index("ontology_id").head(TOP_N)
    print("lamindb search:")
    display(df_ln)
    rbo_score = rbo.RankingSimilarity(df_ps.index.to_list(), df_ln.index.to_list()).rbo(p=0.9)
    print("RBO:", rbo_score)

Query: t cell
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0009011	0.096079	5leYvtE4	transit amplifying cell of colon	None	transient amplifying cell of colon|transient a...	A Rapidly Proliferating Population Of Cells Th...
CL:0009012	0.096079	5aWDzEsw	transit amplifying cell of small intestine	None	small intestine transit amplifying cell|transi...	A Rapidly Proliferating Population Of Cells Th...
CL:0002535	0.095499	42lVKL3k	epithelial cell of cervix	None	epithelial cell of cervical canal of uterus|ep...	An Epithelial Cell Of The Cervix.
CL:0002293	0.095139	5LP2vtZ7	epithelial cell of thymus	None	thymic epithelial cell|epithelial reticular ce...	An Epithelial Cell Of The Thymus. Epithelial R...
CL:0000037	0.094717	2U8xapxu	hematopoietic stem cell	None	blood forming stem cell|hemopoietic stem cell	A Stem Cell From Which All Cells Of The Lympho...
CL:0000568	0.094717	1qJ2DpdL	amine precursor uptake and decarboxylation cell	None	APUD cell	A Cell That Originates In The Neural Crest, Th...
CL:0002084	0.094717	3u1juPtN	Boettcher cell	None	Bottcher cell|Bottcher's cell|Boettcher's cell	A Boettcher Cell Is A Polyhedral Cells On The ...
CL:0000960	0.094215	6wMDn1pw	T3 B cell	None	T3 B-lymphocyte|T3 B-cell|T3 B lymphocyte|An1 ...	A Transitional Stage B Cell That Expresses Sur...
CL:0007015	0.094215	5ZvFiznj	obsolete mortal cell line cell	None	finite cell line cell	Obsolete: A Cell Line Cell That Is Expected To...
CL:0000711	0.094215	5SnzkbSG	cumulus cell	None	None	Cumulus Cell Is A Specialized Granulosa Cell T...
CL:0000939	0.094215	2rJgf4sI	CD16-positive, CD56-dim natural killer cell, h...	None	CD16-positive, CD56-positive natural killer ce...	A Mature Natural Killer Cell That Has The Phen...
CL:4030056	0.094215	7mYcRDsu	umbrella cell of urothelium	None	facet cell of urothelium|superficial cell of u...	A Urothelial Cell That Is Terminally Different...
CL:0002103	0.094215	2n1cdAd9	IgG-positive double negative memory B cell	None	IgG-positive double negative memory B-cell|IgG...	An Igg-Positive Double Negative Memory B Cell ...
CL:0002104	0.094215	2CPm1x2L	IgG-negative double negative memory B cell	None	IgG-negative dn memory B-cell|IgG-negative dou...	An Igg-Negative Double Negative Memory B Cell ...
CL:0009096	0.094215	4MIgrcWm	esophagus non-keratinized squamous epithelial ...	None	nonkeratinized squamous epithelial cell of eso...	Any Cell That Is Part Of The Esophageal Non-Ke...
CL:0009028	0.094215	5aMQ7VXC	intestinal crypt stem cell of appendix	None	intestinal crypt stem cell of vermiform append...	An Intestinal Crypt Stem Cell That Is Located ...
CL:0002289	0.093607	9Lrirtls	type I taste bud cell	None	type I taste cell|dark tongue cell|type taste ...	A Densely Staining Taste Receptor Cell That Co...
CL:0000432	0.093607	3JxaRgdH	reticular cell	None	reticulum cell	A Fibroblast That Synthesizes Collagen And Use...
CL:0000002	0.093607	2GqGKpwD	obsolete immortal cell line cell	None	permanent cell line cell|continuous cell line ...	Obsolete: A Cell Line Cell That Is Expected To...
CL:0000173	0.093607	4Urf8PQD	pancreatic D cell	None	pancreatic D-cell|delta cell of pancreatic isl...	A D Cell Located In The Pancreas. Peripherally...

lamindb search:

	name	description	synonyms
ontology_id
CL:0000084	T cell	A Type Of Lymphocyte Whose Defining Characteri...	T lymphocyte|T-lymphocyte|T-cell
CL:0009031	T cell of appendix	A T Cell That Is Located In A Vermiform Appendix.	appendix T cell|T cell of appendix vermiformis...
CL:0009051	T cell of anorectum	A T Cell That Is Located In The Anorectum.	None
CL:4030058	TCR-positive macrophage	A Macrophage That Expresses The T Cell Recepto...	T cell receptor positive macrophage|TCR+ macro...
CL:0009105	T cell zone reticular cell	A Fibroblastic Reticular Cell Found In The Lym...	lymph node T cell domain fibroblastic reticula...
CL:0009064	lymph node paracortex T cell	A T Cell Located In The Lymph Node Paracortex,...	T cell of lymph node paracortex
CL:0009023	small intestine Peyer's patch T cell	A T Cell Which Resides In The Peyer'S Patch Of...	T cell of Peyer's patch of small intestine|T c...
CL:0009046	T cell of medullary sinus of lymph node	A T Cell Found In The Lymph Node Medullary Sinus.	None
CL:0000968	Be cell	A Mature B Cell That Produces Cytokines That C...	effector B-lymphocyte|effector B cell|effector...
CL:0000943	Be1 Cell	A Be Cell That Facilitates Development Of T-He...	B effector 1 cell
CL:0000918	Tc2 cell	A Cd8-Positive, Alpha-Beta Positive T Cell Exp...	Th2 non-TFH CD8-positive T cell|Tc2 T-cell|T-c...
CL:0000917	Tc1 cell	A Cd8-Positive, Alpha-Beta Positive T Cell Tha...	Tc1 T cell|Th1 non-TFH CD8-positive T cell|CD8...
CL:0000901	Tr1 cell	Cd4-Positive Alpha-Beta T Cell With Regulatory...	Tr1 T-lymphocyte|T-regulatory T cell type 1|Tr...
CL:0000944	Be2 cell	A Be Cell That Facilitates Development Of T-He...	B effector 2 cell
CL:0002128	Tc17 cell	A Cd8-Positive, Alpha-Beta T Cell That Has The...	Th17 CD8-positive T cell|Tc17 T-cell|CD8-posit...
CL:0000893	thymocyte	An Immature T Cell Located In The Thymus.	thymic lymphocyte
CL:0000962	Bm2 B cell	A Follicular B Cell That Is Igd-Positive And C...	Bm2 B-cell|Bm2 B lymphocyte|Bm2 B-lymphocyte
CL:0000961	Bm1 B cell	A Follicular B Cell That Is Igd-Positive, Cd23...	Bm1 B-cell|Bm1 B-lymphocyte|Bm1 B lymphocyte
CL:0000827	pro-T cell	A Lymphoid Progenitor Cell Of The T Cell Linea...	progenitor T cell|pro-T lymphocyte
CL:0000822	B-2 B cell	A Conventional B Cell Subject To Antigenic Sti...	B2 B lymphocyte|B-2 B-cell|B2 B-lymphocyte|B-2...

RBO: 0.0
Query: stem cell
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0000048	0.887745	5AU7hMOa	multi fate stem cell	None	multi-fate stem cell|multipotent cell|multifat...	A Stem Cell That Can Give Rise To Multiple Lin...
CL:0000037	0.863547	2U8xapxu	hematopoietic stem cell	None	blood forming stem cell|hemopoietic stem cell	A Stem Cell From Which All Cells Of The Lympho...
CL:0009028	0.861798	5aMQ7VXC	intestinal crypt stem cell of appendix	None	intestinal crypt stem cell of vermiform append...	An Intestinal Crypt Stem Cell That Is Located ...
CL:0000035	0.752624	58RHatFb	single fate stem cell	None	unipotent stem cell|unipotential stem cell	A Stem Cell That Self-Renews As Well As Give R...
CL:0008011	0.700412	6Mas2FLu	skeletal muscle satellite stem cell	None	None	A Skeletal Muscle Satellite Cell That Divides ...
CL:1001610	0.692528	2cR2YcLf	bone marrow hematopoietic cell	None	None	Hematopoietic Cells Resident In The Bone Marro...
CL:0001008	0.681246	1yjJyVS8	Kit and Sca1-positive hematopoietic stem cell	None	LSK stem cell|Sca1-positive hematopoietic stem...	A Hematopoietic Stem Cell That Has Plasma Memb...
CL:0000052	0.638292	6Z8jsYOX	totipotent stem cell	None	totipotential stem cell	A Stem Cell From Which All Cells Of The Body C...
CL:0001024	0.634096	5NOO2SHF	CD34-positive, CD38-negative hematopoietic ste...	None	CD133-positive hematopoietic stem cell	Cd133-Positive Hematopoietic Stem Cell Is A He...
CL:0009017	0.581894	5S7LEcUj	intestinal crypt stem cell of small intestine	None	stem cell of small intestine crypt of Lieberkuhn	An Intestinal Stem Cell That Is Located In The...
CL:0009016	0.581894	66xlGEYm	intestinal crypt stem cell of large intestine	None	stem cell of large intestine crypt of Lieberkuhn	An Intestinal Stem Cell That Is Located In The...
CL:0000014	0.567623	3dsBAMM1	germ line stem cell	None	germline stem cell	A Stem Cell That Is The Precursor Of Gametes.
CL:0009091	0.566885	71i37vTD	Leydig stem cell	None	stem Leydig cell	A Stem Cell Found In The Interstitial Compartm...
CL:0002639	0.539257	4Hk94xax	amniotic stem cell	None	None	An Amniotic Stem Cell Is A Mesenchymalstem Cel...
CL:0002537	0.536928	4cuSaXq3	amnion mesenchymal stem cell	None	amniotic membrane stem cell	A Mesenchymal Stem Cell Of The Amnion Membrane.
CL:0002034	0.534312	fQaazBGV	long term hematopoietic stem cell	None	LT stem cell|LT-HSC	A Hematopoietic Stem Cell With Long Term Self ...
CL:0002248	0.531966	2nQapnO0	pluripotent stem cell	None	None	A Pluripotent Stem Cell Has The Ability To For...
CL:1000428	0.518002	1n840sKH	stem cell of epidermis	None	epidermal stem cell	A Somatic Stem Cell That Is Part Of The Epider...
CL:0002033	0.509959	2WPBsduL	short term hematopoietic stem cell	None	ST stem cell|ST-HSC	A Hematopoietic Stem Cell Capable Of Rapid Rep...
CL:0002359	0.492534	1ssZY3nR	placental hematopoietic stem cell	None	None	A Hematopoietic Stem Cell Of The Placenta. Thi...

lamindb search:

	name	description	synonyms
ontology_id
CL:0000034	stem cell	A Relatively Undifferentiated Cell That Retain...	animal stem cell
CL:4023129	retinoblast	A Retinal Cell That Is Immature Or Undifferent...	retinal stem cell
CL:0000047	neural stem cell	An Undifferentiated Neural Cell That Originate...	neuronal stem cell|NSC
CL:0009091	Leydig stem cell	A Stem Cell Found In The Interstitial Compartm...	stem Leydig cell
CL:0002451	mammary stem cell	A Multi-Fate Stem Cell That Is The Source Of C...	None
CL:0000723	somatic stem cell	A Stem Cell That Can Give Rise To Cell Types O...	None
CL:0002195	hepatic stem cell	A Stem Cell That Can Give Rise To The Cells Of...	None
CL:0002639	amniotic stem cell	An Amniotic Stem Cell Is A Mesenchymalstem Cel...	None
CL:0002339	prostate stem cell	A Prostate Epithelial Cell That Is Cd133-Posit...	CD133-positive prostate epithelial cell
CL:0002322	embryonic stem cell	A Stem Cell Of Embryonic Origin.	ESC
CL:0000014	germ line stem cell	A Stem Cell That Is The Precursor Of Gametes.	germline stem cell
CL:0000048	multi fate stem cell	A Stem Cell That Can Give Rise To Multiple Lin...	multi-fate stem cell|multipotent cell|multifat...
CL:0000052	totipotent stem cell	A Stem Cell From Which All Cells Of The Body C...	totipotential stem cell
CL:0000356	hair matrix stem cell	None	None
CL:0000134	mesenchymal stem cell	A Connective Tissue Cell That Normally Gives R...	None
CL:0002248	pluripotent stem cell	A Pluripotent Stem Cell Has The Ability To For...	None
CL:4030035	dental pulp stem cell	A Dental Pulp Cell That Possesses Stem-Cell-Li...	DPSC
CL:0000035	single fate stem cell	A Stem Cell That Self-Renews As Well As Give R...	unipotent stem cell|unipotential stem cell
CL:0002196	hepatic oval stem cell	A Transient Hepatic Stem Cell Observed After L...	hepatic progenitor cell|liver progenitor cell|...
CL:1000428	stem cell of epidermis	A Somatic Stem Cell That Is Part Of The Epider...	epidermal stem cell

RBO: 0.06101695493199965
Query: b cell
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0000819	0.987156	3VMOKHg2	B-1 B cell	None	B1 B-cell|B-1 B-lymphocyte|B-1 B-cell|B1 cell|...	A B Cell Of Distinct Lineage And Surface Marke...
CL:0000820	0.969263	3fXg2Aru	B-1a B cell	None	B1a B lymphocyte|B-1a B-lymphocyte|B1a B-cell|...	A B-1 B Cell That Has The Phenotype Cd5-Positive.
CL:0000822	0.968621	1jrUVVsT	B-2 B cell	None	B2 B lymphocyte|B-2 B-cell|B2 B-lymphocyte|B-2...	A Conventional B Cell Subject To Antigenic Sti...
CL:0000821	0.963643	26E9jKKt	B-1b B cell	None	B1b B-lymphocyte|B-1b B-lymphocyte|B1b B cell|...	A B-1 B Cell That Has The Phenotype Cd5-Negati...
CL:0002103	0.924735	2n1cdAd9	IgG-positive double negative memory B cell	None	IgG-positive double negative memory B-cell|IgG...	An Igg-Positive Double Negative Memory B Cell ...
CL:0000826	0.920337	1gKQ0rC2	pro-B cell	None	progenitor B cell|pro-B lymphocyte|progenitor ...	A Progenitor Cell Of The B Cell Lineage, With ...
CL:0002104	0.917375	2CPm1x2L	IgG-negative double negative memory B cell	None	IgG-negative dn memory B-cell|IgG-negative dou...	An Igg-Negative Double Negative Memory B Cell ...
CL:0002109	0.891143	3wzkSBms	B220-positive CD38-positive naive B cell	None	B220-positive CD38-positive naive B-lymphocyte...	A B220-Positive Cd38-Positive Naive B Cell Is ...
CL:0000960	0.875140	6wMDn1pw	T3 B cell	None	T3 B-lymphocyte|T3 B-cell|T3 B lymphocyte|An1 ...	A Transitional Stage B Cell That Expresses Sur...
CL:0000979	0.868853	74TtdefA	IgG memory B cell	None	IgG memory B-lymphocyte|memory IgG B-cell|memo...	An Igg Memory B Cell Is A Class Switched Memor...
CL:0000843	0.868138	2EhFTUoZ	follicular B cell	None	follicular B lymphocyte|Fo B-cell|Fo B cell|fo...	A Resting Mature B Cell That Has The Phenotype...
CL:0000971	0.860784	5QR8GcfH	IgM memory B cell	None	memory IgM B cell|memory IgM B-lymphocyte|IgM ...	An Igm Memory B Cell Is An Unswitched Memory B...
CL:0000844	0.859277	4IowPafD	germinal center B cell	None	GC B-lymphocyte|germinal center B-cell|GC B ce...	A Rapidly Cycling Mature B Cell That Has Disti...
CL:0000968	0.854689	3UQgan3n	Be cell	None	effector B-lymphocyte|effector B cell|effector...	A Mature B Cell That Produces Cytokines That C...
CL:0000818	0.854054	75GaqGOI	transitional stage B cell	None	transitional B cell|transitional stage B-cell|...	An Immature B Cell Of An Intermediate Stage Be...
CL:0000816	0.845462	6VBn74jE	immature B cell	None	immature B lymphocyte|immature B-cell|immature...	An Immature B Cell Is A B Cell That Has The Ph...
CL:0000169	0.839823	Z7G1oH1k	type B pancreatic cell	None	pancreatic beta cell|pancreatic B-cell|B-cell ...	A Cell That Secretes Insulin And Is Located To...
CL:0002102	0.832719	6uy4Hmew	CD38-negative naive B cell	None	CD38- naive B-lymphocyte|CD38-negative naive B...	A Cd38-Negative Naive B Cell Is A Mature B Cel...
CL:0002101	0.830476	1jDSA7Vg	CD38-positive naive B cell	None	CD38+ naive B-cell|CD38-positive naive B lymph...	A Cd38-Positive Naive B Cell Is A Mature B Cel...
CL:0000948	0.824372	vUMLrFZL	IgE memory B cell	None	IgE memory B lymphocyte|IgE memory B-cell|memo...	A Class Switched Memory B Cell That Expresses ...

lamindb search:

	name	description	synonyms
ontology_id
CL:0000236	B cell	A Lymphocyte Of B Lineage That Is Capable Of B...	B lymphocyte|B-cell|B-lymphocyte
CL:0009032	B cell of appendix	A B Cell That Is Located In A Vermiform Appendix.	appendix B cell|B cell of vermiform appendix|B...
CL:0009050	B cell of anorectum	A B Cell That Is Located In The Anorectum.	None
CL:0001201	B cell, CD19-positive	A B Cell That Is Cd19-Positive.	CD19-positive B cell|B-cell, CD19-positive|CD1...
CL:0009104	B cell zone reticular cell	A Fibroblastic Reticular Cell Found In The Lym...	lymph node germinal center dark zone fibroblas...
CL:0000845	marginal zone B cell of spleen	A Mature B Cell That Is Located In The Margina...	B cell of marginal zone of spleen|marginal zon...
CL:0009045	B cell of medullary sinus of lymph node	A B Cell Found In The Lymph Node Medullary Sinus.	None
CL:0000968	Be cell	A Mature B Cell That Produces Cytokines That C...	effector B-lymphocyte|effector B cell|effector...
CL:0000958	T1 B cell	A Transitional Stage B Cell That Migrates From...	T1 B lymphocyte|T1 B-cell|T1 B-lymphocyte|tran...
CL:0000959	T2 B cell	A Transitional Stage B Cell That Has The Pheno...	T2 B lymphocyte|T2 B-cell|transitional stage 2...
CL:0000960	T3 B cell	A Transitional Stage B Cell That Expresses Sur...	T3 B-lymphocyte|T3 B-cell|T3 B lymphocyte|An1 ...
CL:0000966	Bm4 B cell	A Germinal Center B Cell That Has The Phenotyp...	Bm4 B-lymphocyte|Bm4 B lymphocyte|Bm4 B-cell
CL:0000819	B-1 B cell	A B Cell Of Distinct Lineage And Surface Marke...	B1 B-cell|B-1 B-lymphocyte|B-1 B-cell|B1 cell|...
CL:0000822	B-2 B cell	A Conventional B Cell Subject To Antigenic Sti...	B2 B lymphocyte|B-2 B-cell|B2 B-lymphocyte|B-2...
CL:0000962	Bm2 B cell	A Follicular B Cell That Is Igd-Positive And C...	Bm2 B-cell|Bm2 B lymphocyte|Bm2 B-lymphocyte
CL:0000965	Bm3 B cell	A Germinal Center B Cell That Is Rapidly Divid...	Bm3 B lymphocyte|Bm3 B-cell|Bm3 B-lymphocyte
CL:0000826	pro-B cell	A Progenitor Cell Of The B Cell Lineage, With ...	progenitor B cell|pro-B lymphocyte|progenitor ...
CL:0000967	Bm5 B cell	A Memory B Cell Arising In The Germinal Center...	Bm5 B-lymphocyte|Bm5 B-cell|Bm5 B lymphocyte
CL:0009111	centrocyte	A Germinal Center B Cell Found In A Lymph Node...	lymph node centrocyte
CL:0000961	Bm1 B cell	A Follicular B Cell That Is Igd-Positive, Cd23...	Bm1 B-cell|Bm1 B-lymphocyte|Bm1 B lymphocyte

RBO: 0.04604979014814935
Query: regulatory B cell
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0000819	0.987156	3VMOKHg2	B-1 B cell	None	B1 B-cell|B-1 B-lymphocyte|B-1 B-cell|B1 cell|...	A B Cell Of Distinct Lineage And Surface Marke...
CL:0000969	0.978899	5b0DoJIx	regulatory B cell	None	B(reg)|regulatory B lymphocyte|B10 cell|regula...	A Mature B Cell That Has The Phenotype Cd1D-Po...
CL:0000820	0.969263	3fXg2Aru	B-1a B cell	None	B1a B lymphocyte|B-1a B-lymphocyte|B1a B-cell|...	A B-1 B Cell That Has The Phenotype Cd5-Positive.
CL:0000822	0.968621	1jrUVVsT	B-2 B cell	None	B2 B lymphocyte|B-2 B-cell|B2 B-lymphocyte|B-2...	A Conventional B Cell Subject To Antigenic Sti...
CL:0000821	0.963643	26E9jKKt	B-1b B cell	None	B1b B-lymphocyte|B-1b B-lymphocyte|B1b B cell|...	A B-1 B Cell That Has The Phenotype Cd5-Negati...
CL:0002103	0.924735	2n1cdAd9	IgG-positive double negative memory B cell	None	IgG-positive double negative memory B-cell|IgG...	An Igg-Positive Double Negative Memory B Cell ...
CL:0000826	0.920337	1gKQ0rC2	pro-B cell	None	progenitor B cell|pro-B lymphocyte|progenitor ...	A Progenitor Cell Of The B Cell Lineage, With ...
CL:0002104	0.917375	2CPm1x2L	IgG-negative double negative memory B cell	None	IgG-negative dn memory B-cell|IgG-negative dou...	An Igg-Negative Double Negative Memory B Cell ...
CL:0002109	0.891143	3wzkSBms	B220-positive CD38-positive naive B cell	None	B220-positive CD38-positive naive B-lymphocyte...	A B220-Positive Cd38-Positive Naive B Cell Is ...
CL:0000960	0.875140	6wMDn1pw	T3 B cell	None	T3 B-lymphocyte|T3 B-cell|T3 B lymphocyte|An1 ...	A Transitional Stage B Cell That Expresses Sur...
CL:0000979	0.868853	74TtdefA	IgG memory B cell	None	IgG memory B-lymphocyte|memory IgG B-cell|memo...	An Igg Memory B Cell Is A Class Switched Memor...
CL:0000843	0.868138	2EhFTUoZ	follicular B cell	None	follicular B lymphocyte|Fo B-cell|Fo B cell|fo...	A Resting Mature B Cell That Has The Phenotype...
CL:0000971	0.860784	5QR8GcfH	IgM memory B cell	None	memory IgM B cell|memory IgM B-lymphocyte|IgM ...	An Igm Memory B Cell Is An Unswitched Memory B...
CL:0000844	0.859277	4IowPafD	germinal center B cell	None	GC B-lymphocyte|germinal center B-cell|GC B ce...	A Rapidly Cycling Mature B Cell That Has Disti...
CL:0000968	0.854689	3UQgan3n	Be cell	None	effector B-lymphocyte|effector B cell|effector...	A Mature B Cell That Produces Cytokines That C...
CL:0000818	0.854054	75GaqGOI	transitional stage B cell	None	transitional B cell|transitional stage B-cell|...	An Immature B Cell Of An Intermediate Stage Be...
CL:0000816	0.845462	6VBn74jE	immature B cell	None	immature B lymphocyte|immature B-cell|immature...	An Immature B Cell Is A B Cell That Has The Ph...
CL:0000169	0.839823	Z7G1oH1k	type B pancreatic cell	None	pancreatic beta cell|pancreatic B-cell|B-cell ...	A Cell That Secretes Insulin And Is Located To...
CL:0002102	0.832719	6uy4Hmew	CD38-negative naive B cell	None	CD38- naive B-lymphocyte|CD38-negative naive B...	A Cd38-Negative Naive B Cell Is A Mature B Cel...
CL:0002101	0.830476	1jDSA7Vg	CD38-positive naive B cell	None	CD38+ naive B-cell|CD38-positive naive B lymph...	A Cd38-Positive Naive B Cell Is A Mature B Cel...

lamindb search:

	name	description	synonyms
ontology_id
CL:0000969	regulatory B cell	A Mature B Cell That Has The Phenotype Cd1D-Po...	B(reg)|regulatory B lymphocyte|B10 cell|regula...
CL:0000000	cell	A Material Entity Of Anatomical Origin (Part O...	None
CL:0001068	ILC1	A Group 1 Innate Lymphoid Cell That Is Non-Cyt...	None
CL:0000019	sperm	A Mature Male Germ Cell That Develops From A S...	spermatozoid|sperm cell|spermatozoon
CL:0000023	oocyte	A Female Germ Cell That Has Entered Meiosis.	None
CL:0000300	gamete	A Mature Sexual Reproductive Cell Having A Sin...	haploid nucleated cell
CL:0002675	H plus	A S. Pombe Cell Type Determined By Mat1-Pc And...	None
CL:0000236	B cell	A Lymphocyte Of B Lineage That Is Capable Of B...	B lymphocyte|B-cell|B-lymphocyte
CL:0000084	T cell	A Type Of Lymphocyte Whose Defining Characteri...	T lymphocyte|T-lymphocyte|T-cell
CL:0000540	neuron	The Basic Cellular Unit Of Nervous Tissue. Eac...	nerve cell
CL:0002674	H minus	A S. Pombe Mating Type Determined By The Mat1-...	H- cell
CL:0002239	ooblast	A Primordial Cell From Which An Oocyte (Ovum) ...	ovary primordial germ cell|ovigerm
CL:0002380	oospore	An Asexual Spore Formed By Oomycetes; Formed U...	None
CL:0002372	myotube	A Transversely Striated, Synctial Muscle Cell,...	single cell sarcomere|myotubule
CL:0000696	PP cell	A Cell That Stores And Secretes Pancreatic Pol...	type F enteroendocrine cell
CL:0000968	Be cell	A Mature B Cell That Produces Cytokines That C...	effector B-lymphocyte|effector B cell|effector...
CL:0000767	basophil	Any Of The Immature Or Mature Forms Of A Granu...	basophilic leukocyte|basophilic leucocyte
CL:0000427	GLR cell	A Scaffolding Cell Type Found In C. Elegans, T...	None
CL:0000669	pericyte	An Elongated, Contractile Cell Found Wrapped A...	pericyte of Rouget|cell of Rouget|ARC|adventit...
CL:0000918	Tc2 cell	A Cd8-Positive, Alpha-Beta Positive T Cell Exp...	Th2 non-TFH CD8-positive T cell|Tc2 T-cell|T-c...

RBO: 0.15625204290792533
Query: Be2 cell
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0000944	2.014405e-01	7Hxc3PWU	Be2 cell	None	B effector 2 cell	A Be Cell That Facilitates Development Of T-He...
CL:0000000	1.000000e-20	4bKGljt0	cell	None	None	A Material Entity Of Anatomical Origin (Part O...
CL:0009019	1.000000e-20	3kvooQIQ	nephrogenic zone cell	None	cortical nephrogenic zone cell|cortical nephro...	A Kidney Cortical Cell That Is Part Of The Nep...
CL:0009011	1.000000e-20	5leYvtE4	transit amplifying cell of colon	None	transient amplifying cell of colon|transient a...	A Rapidly Proliferating Population Of Cells Th...
CL:0009012	1.000000e-20	5aWDzEsw	transit amplifying cell of small intestine	None	small intestine transit amplifying cell|transi...	A Rapidly Proliferating Population Of Cells Th...
CL:0009013	1.000000e-20	6kPthzrt	fetal hepatobiliary progenitor cell	None	fetal hepatobiliary hybrid progenitor cell|HHy...	A Progenitor Cell With Hepatic And Biliary Lin...
CL:0009014	1.000000e-20	6lkkXGSf	Peyer's patch lymphocyte	None	Peyer's patch resident lymphocyte	A Lymphocyte That Is Part Of A Peyer'S Patch. ...
CL:0009015	1.000000e-20	3pdV7BH8	Peyer's patch follicular dendritic cell	None	None	A Follicular Dendritic Cell Located In The Pey...
CL:0009016	1.000000e-20	66xlGEYm	intestinal crypt stem cell of large intestine	None	stem cell of large intestine crypt of Lieberkuhn	An Intestinal Stem Cell That Is Located In The...
CL:0009017	1.000000e-20	5S7LEcUj	intestinal crypt stem cell of small intestine	None	stem cell of small intestine crypt of Lieberkuhn	An Intestinal Stem Cell That Is Located In The...
CL:0009018	1.000000e-20	4arKrgYT	lymphocyte of large intestine lamina propria	None	lamina propria lymphocyte of large intestine	A Lymphocyte That Resides In The Lamina Propri...
CL:0009020	1.000000e-20	5h9OF2q1	tuft cell of appendix	None	appendix tuft cell|tuft cell of vermiform appe...	An Intestinal Tuft Cell That Is A Part Of A Ve...
CL:0009009	1.000000e-20	hA3U5CHJ	paneth cell of colon	None	paneth-like cell|paneth cell of epithelium of ...	A Paneth Cell That Is Located In The Epitheliu...
CL:0009021	1.000000e-20	5lwok37s	stromal cell of lamina propria of large intestine	None	None	A Stromal Cell Found In The Lamina Propria Of ...
CL:0009022	1.000000e-20	12a8qokb	stromal cell of lamina propria of small intestine	None	None	A Stromal Cell Found In The Lamina Propria Of ...
CL:0009023	1.000000e-20	78mumrXE	small intestine Peyer's patch T cell	None	T cell of Peyer's patch of small intestine|T c...	A T Cell Which Resides In The Peyer'S Patch Of...
CL:0009024	1.000000e-20	2j3nNHI6	mesothelial cell of small intestine	None	None	A Mesothelial Cell That Is Part Of The Small I...
CL:0009025	1.000000e-20	1oOu6qlM	mesothelial cell of colon	None	None	A Mesothelial Cell That Is Part Of The Colon.
CL:0009026	1.000000e-20	2dSeoVtK	enterocyte of appendix	None	enterocyte of vermiform appendix|appendix ente...	An Enterocyte That Is A Part Of A Vermiform Ap...
CL:0009027	1.000000e-20	1UFo19Bl	transit amplifying cell of appendix	None	transit amplifying cell of vermiform appendix|...	A Transit Amplifying Cell That Is Part Of A Cr...

lamindb search:

	name	description	synonyms
ontology_id
CL:0000944	Be2 cell	A Be Cell That Facilitates Development Of T-He...	B effector 2 cell
CL:0001068	ILC1	A Group 1 Innate Lymphoid Cell That Is Non-Cyt...	None
CL:0000000	cell	A Material Entity Of Anatomical Origin (Part O...	None
CL:0000019	sperm	A Mature Male Germ Cell That Develops From A S...	spermatozoid|sperm cell|spermatozoon
CL:0002675	H plus	A S. Pombe Cell Type Determined By Mat1-Pc And...	None
CL:0000236	B cell	A Lymphocyte Of B Lineage That Is Capable Of B...	B lymphocyte|B-cell|B-lymphocyte
CL:0000023	oocyte	A Female Germ Cell That Has Entered Meiosis.	None
CL:0000300	gamete	A Mature Sexual Reproductive Cell Having A Sin...	haploid nucleated cell
CL:0000540	neuron	The Basic Cellular Unit Of Nervous Tissue. Eac...	nerve cell
CL:0000084	T cell	A Type Of Lymphocyte Whose Defining Characteri...	T lymphocyte|T-lymphocyte|T-cell
CL:0000696	PP cell	A Cell That Stores And Secretes Pancreatic Pol...	type F enteroendocrine cell
CL:0002372	myotube	A Transversely Striated, Synctial Muscle Cell,...	single cell sarcomere|myotubule
CL:0002674	H minus	A S. Pombe Mating Type Determined By The Mat1-...	H- cell
CL:0002239	ooblast	A Primordial Cell From Which An Oocyte (Ovum) ...	ovary primordial germ cell|ovigerm
CL:0000968	Be cell	A Mature B Cell That Produces Cytokines That C...	effector B-lymphocyte|effector B cell|effector...
CL:0000918	Tc2 cell	A Cd8-Positive, Alpha-Beta Positive T Cell Exp...	Th2 non-TFH CD8-positive T cell|Tc2 T-cell|T-c...
CL:0002198	oncocyte	A Large Epithelial Cell With An Extremely Acid...	oxyphil
CL:0000427	GLR cell	A Scaffolding Cell Type Found In C. Elegans, T...	None
CL:0000653	podocyte	A Specialized Kidney Epithelial Cell, Containe...	glomerular podocyte|renal podocyte|glomerular ...
CL:0000669	pericyte	An Elongated, Contractile Cell Found Wrapped A...	pericyte of Rouget|cell of Rouget|ARC|adventit...

RBO: 0.35796660747711023
Query: neural
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0011012	0.090666	1g7Tg3bV	neural crest cell	None	None	A Cell Of The Neural Crest. Neural Crest Cells...
CL:0000333	0.086545	17PFT8np	migratory neural crest cell	None	None	A Cell Derived From The Specialized Ectoderm F...
CL:0007004	0.086545	vcVrFvwF	premigratory neural crest cell	None	None	Cell That Is Part Of The Neural Crest Region O...
CL:2000073	0.086545	6GETDXmI	migratory cardiac neural crest cell	None	cardiac neural crest cell	Any Migratory Neural Crest Cell That Is Part O...
CL:0000008	0.086545	uzxSEqax	migratory cranial neural crest cell	None	None	Cell That Is Part Of The Migratory Cranial Neu...
CL:0000011	0.086545	3YAM45TD	migratory trunk neural crest cell	None	None	Cell That Is Part Of The Migratory Trunk Neura...
CL:0000029	0.082746	2K4t7Szl	neural crest derived neuron	None	neuron neural crest derived	Any Neuron That Develops From Some Migratory N...
CL:0000005	0.082746	2ANSKgCO	neural crest derived fibroblast	None	fibroblast neural crest derived	Any Fibroblast That Is Derived From The Neural...
CL:0011017	0.082746	2osXrTI3	vagal neural crest cell	None	None	Cell That Is Part Of The Vagal Neural Crest Po...
CL:0000047	0.075991	1Fbr1GYr	neural stem cell	None	neuronal stem cell|NSC	An Undifferentiated Neural Cell That Originate...
CL:0000027	0.075991	3iHAmhkV	smooth muscle cell neural crest derived	None	None	A Smooth Muscle Cell Derived From The Neural C...
CL:0000339	0.075991	iHIaVIeB	glioblast (sensu Vertebrata)	None	spongioblast	An Early Neural Cell Developing From The Early...
CL:0000710	0.075991	5PtXS7Ii	neurecto-epithelial cell	None	None	Epithelial Cells Derived From Neural Plate And...
CL:0002607	0.075991	2Cgzp1mO	migratory enteric neural crest cell	None	None	A Neural Crest Cell That Gives Rise To Cells O...
CL:0002333	0.075991	12Qj99kX	neural crest derived adipocyte	None	None	An Adipocyte Derived From A Neural Crest Cell.
CL:0002676	0.075991	2700Dq8O	neural crest derived neuroblast	None	None	A Neuroblast Derived From A Neural Crest Cell.
CL:0011020	0.075991	6whcJUgV	neural progenitor cell	None	None	An Undifferentiated Cell That Originates From ...
CL:0000469	0.060793	3z8DXWpY	ganglion mother cell	None	None	A Neural Progenitor Cell That Is The Daughter ...
CL:0002375	0.060793	nP9CqqA7	Schwann cell precursor	None	Schwann cell precursor cell	A Giioblast Cell That Develops From A Migrator...
CL:0000740	0.060793	4g244Aw3	retinal ganglion cell	None	ganglion cell of retina|gangliocyte	The Set Of Neurons That Receives Neural Inputs...

lamindb search:

	name	description	synonyms
ontology_id
CL:0002319	neural cell	A Cell That Is Part Of The Nervous System.	None
CL:0000047	neural stem cell	An Undifferentiated Neural Cell That Originate...	neuronal stem cell|NSC
CL:0011012	neural crest cell	A Cell Of The Neural Crest. Neural Crest Cells...	None
CL:0000032	neuroplacodal cell	A Cell Of A Platelike Structure, Especially A ...	neural placode cell
CL:0011020	neural progenitor cell	An Undifferentiated Cell That Originates From ...	None
CL:0000029	neural crest derived neuron	Any Neuron That Develops From Some Migratory N...	neuron neural crest derived
CL:0002333	neural crest derived adipocyte	An Adipocyte Derived From A Neural Crest Cell.	None
CL:0000005	neural crest derived fibroblast	Any Fibroblast That Is Derived From The Neural...	fibroblast neural crest derived
CL:0002676	neural crest derived neuroblast	A Neuroblast Derived From A Neural Crest Cell.	None
CL:0000747	cyanophore	A Pigment Cell Derived From The Neural Crest. ...	None
CL:0005001	iridoblast	A Non-Terminally Differentiated Cell That Orig...	None
CL:0000571	leucophore	A Pigment Cell Derived From The Neural Crest. ...	None
CL:0005003	leucoblast	A Non-Terminally Differentiated Cell That Orig...	None
CL:0000431	iridophore	A Pigment Cell Derived From The Neural Crest. ...	None
CL:0000148	melanocyte	A Pigment Cell Derived From The Neural Crest. ...	None
CL:0005005	cyanoblast	A Non-Terminally Differentiated Cell That Orig...	None
CL:0000541	melanoblast	A Cell That Originates From The Neural Crest A...	None
CL:0000574	erythrophore	A Pigment Cell Derived From The Neural Crest. ...	None
CL:0011007	paraxial cell	A Cell In The Area Of Mesoderm In The Neurulat...	paraxial mesoderm cell|somitic mesoderm cell
CL:0007010	preosteoblast	Skeletogenic Cell That Has The Potential To Tr...	osteoprogenitor cell

RBO: 0.2099665235623084
Query: adipocyte
postgres search:

	rank	uid	name	abbr	synonyms	description
ontology_id
CL:0001070	0.088977	3ccnEzNw	beige adipocyte	None	brite cell|beige/brite adipocyte|brite fat cel...	An Adipocyte That Is Beige In Color, Thermogen...
CL:0002616	0.082746	5IngQdBq	perirenal adipocyte	None	perirenal fat cell|perirenal adipocyte cell	An Adipocyte Of Perirenal Fat Tissue.
CL:1000309	0.082746	6GvX8eJQ	epicardial adipocyte	None	epicardial fat cell|adipocyte of epicardial fat	An Adipocyte That Is Part Of The Epicardial Fat.
CL:1000310	0.082746	5KdaaofT	adipocyte of epicardial fat of right ventricle	None	epicardial adipocyte of right ventricle|epicar...	An Adipocyte That Is Part Of The Epicardial Fa...
CL:0002617	0.082746	4ruvHG7A	adipocyte of breast	None	breast adipocyte|fat cell of breast	An Adipocyte That Is Part Of The Breast.
CL:1000311	0.082746	3zeirA0G	adipocyte of epicardial fat of left ventricle	None	epicardial fat cell of left ventricle|epicardi...	An Adipocyte That Is Part Of The Epicardial Fa...
CL:0002615	0.082746	5ikCt2mr	adipocyte of omentum tissue	None	omental fat cell|omental adipocyte	An Adipocyte That Is Part Of Omentum Tissue.
CL:1001583	0.075991	6bv1KRQr	obsolete breast adipocyte	None	None	Obsolete: Adipocytes Found In The Subcutaneous...
CL:0000448	0.075991	34sV4lgF	white adipocyte	None	white adipose cell	An Adipocyte With Light Coloration And Few Mit...
CL:0002521	0.075991	17EZdnrz	subcutaneous adipocyte	None	subcutaneous fat cell	An Adipocyte That Is Part Of Subcutaneous Adip...
CL:0002333	0.075991	12Qj99kX	neural crest derived adipocyte	None	None	An Adipocyte Derived From A Neural Crest Cell.
CL:0002092	0.060793	DdpLURjA	bone marrow cell	None	None	A Cell Found In The Bone Marrow. This Can Incl...
CL:0000134	0.060793	y0lNgtJm	mesenchymal stem cell	None	None	A Connective Tissue Cell That Normally Gives R...
CL:0000136	0.060793	wdLgwUXo	adipocyte	None	fat cell|adipose cell	A Fat-Storing Cell Found Mostly In The Abdomin...
CL:0000449	0.060793	1tWDTF2O	brown adipocyte	None	brown adipose cell|brown fat cell	A Cell From The Thermogenic Form Of Adipose Ti...
CL:0009099	0.060793	2QRRh8EM	fibro/adipogenic progenitor cell	None	fibro/adipogenic progenitor	A Progenitor Cell That Is A Tissue-Resident Me...
CL:0002335	0.060793	8dEt6lpw	brown preadipocyte	None	None	A Preadipocyte That Is Capable Of Differentiat...
CL:0009018	0.000000	4arKrgYT	lymphocyte of large intestine lamina propria	None	lamina propria lymphocyte of large intestine	A Lymphocyte That Resides In The Lamina Propri...
CL:0009017	0.000000	5S7LEcUj	intestinal crypt stem cell of small intestine	None	stem cell of small intestine crypt of Lieberkuhn	An Intestinal Stem Cell That Is Located In The...
CL:0009016	0.000000	66xlGEYm	intestinal crypt stem cell of large intestine	None	stem cell of large intestine crypt of Lieberkuhn	An Intestinal Stem Cell That Is Located In The...

lamindb search:

	name	description	synonyms
ontology_id
CL:0000136	adipocyte	A Fat-Storing Cell Found Mostly In The Abdomin...	fat cell|adipose cell
CL:0000448	white adipocyte	An Adipocyte With Light Coloration And Few Mit...	white adipose cell
CL:0000449	brown adipocyte	A Cell From The Thermogenic Form Of Adipose Ti...	brown adipose cell|brown fat cell
CL:0001070	beige adipocyte	An Adipocyte That Is Beige In Color, Thermogen...	brite cell|beige/brite adipocyte|brite fat cel...
CL:0002617	adipocyte of breast	An Adipocyte That Is Part Of The Breast.	breast adipocyte|fat cell of breast
CL:0002616	perirenal adipocyte	An Adipocyte Of Perirenal Fat Tissue.	perirenal fat cell|perirenal adipocyte cell
CL:1000309	epicardial adipocyte	An Adipocyte That Is Part Of The Epicardial Fat.	epicardial fat cell|adipocyte of epicardial fat
CL:0002521	subcutaneous adipocyte	An Adipocyte That Is Part Of Subcutaneous Adip...	subcutaneous fat cell
CL:1001583	obsolete breast adipocyte	Obsolete: Adipocytes Found In The Subcutaneous...	None
CL:0002615	adipocyte of omentum tissue	An Adipocyte That Is Part Of Omentum Tissue.	omental fat cell|omental adipocyte
CL:0002333	neural crest derived adipocyte	An Adipocyte Derived From A Neural Crest Cell.	None
CL:1000311	adipocyte of epicardial fat of left ventricle	An Adipocyte That Is Part Of The Epicardial Fa...	epicardial fat cell of left ventricle|epicardi...
CL:1000310	adipocyte of epicardial fat of right ventricle	An Adipocyte That Is Part Of The Epicardial Fa...	epicardial adipocyte of right ventricle|epicar...
CL:0002092	bone marrow cell	A Cell Found In The Bone Marrow. This Can Incl...	None
CL:0002335	brown preadipocyte	A Preadipocyte That Is Capable Of Differentiat...	None
CL:0000134	mesenchymal stem cell	A Connective Tissue Cell That Normally Gives R...	None
CL:0009099	fibro/adipogenic progenitor cell	A Progenitor Cell That Is A Tissue-Resident Me...	fibro/adipogenic progenitor
CL:0002334	preadipocyte	An Undifferentiated Fibroblast That Can Be Sti...	None
CL:0002579	omentum preadipocyte	A Preadipocyte That Is Part Of An Omentum.	None
CL:0002582	visceral preadipocyte	A Preadipocyte That Is Part Of Visceral Tissue.	None

RBO: 0.38999449765518135

!docker stop pgtest && docker rm pgtest
!lamin delete --force benchmark_search
!rm -r ./benchmark_search

pgtest

pgtest

! delete() does not yet affect your Postgres database at postgresql://postgres:pwd@0.0.0.0:5432/pgtest

• deleting instance testuser1/benchmark_search

rm: cannot remove './benchmark_search': No such file or directory