Datasets:

cxyzhang
/

OntologyBench

task_name stringclasses 8 values	tier_id int64 1 3	tier_name stringclasses 3 values	query_id stringlengths 2 259	query stringlengths 2 2.97k	target_id stringlengths 29 46	raw_target_id stringlengths 2 14	target stringlengths 7 3.58k	split stringclasses 1 value
1A-R_gene_document_retrieval	1	Concept Grounding	100	ADA	1A-R_gene_document_retrieval::100	100	The gene is a protein-coding gene located on chromosome 20q13.12. It belongs to the following gene groups: Adenosine deaminase family. Functionally, This gene encodes an enzyme that catalyzes the hydrolysis of adenosine to inosine in the purine catabolic pathway. Various mutations have been described for this gene and ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1000	CDH2	1A-R_gene_document_retrieval::1000	1000	The gene is a protein-coding gene located on chromosome 18q12.1. It belongs to the following gene groups: CD molecules and Type I classical cadherins. Functionally, This gene encodes a classical cadherin and member of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one o...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10000	AKT3	1A-R_gene_document_retrieval::10000	10000	The gene is a protein-coding gene located on chromosome 1q43-q44. It belongs to the following gene groups: Pleckstrin homology domain containing and AKT kinase family. Functionally, The protein encoded by this gene is a member of the AKT, also called PKB, serine/threonine protein kinase family. AKT kinases are known to...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10008	KCNE3	1A-R_gene_document_retrieval::10008	10008	The gene is a protein-coding gene located on chromosome 11q13.4. It belongs to the following gene groups: Potassium voltage-gated channel regulatory subunits. Functionally, Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoint...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1001	CDH3	1A-R_gene_document_retrieval::1001	1001	The gene is a protein-coding gene located on chromosome 16q22.1. It belongs to the following gene groups: Type I classical cadherins. Functionally, This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprot...	train
1A-R_gene_document_retrieval	1	Concept Grounding	100128908	CIROP	1A-R_gene_document_retrieval::100128908	100128908	The gene is a protein-coding gene located on chromosome 14q11.2. Functionally, Predicted to enable peptidase activity. Predicted to be involved in establishment of left/right asymmetry. Predicted to be located in membrane. Predicted to be active in cytoplasm. Implicated in visceral heterotaxy 12.	train
1A-R_gene_document_retrieval	1	Concept Grounding	100144748	KLLN	1A-R_gene_document_retrieval::100144748	100144748	The gene is a protein-coding gene located on chromosome 10q23. Functionally, The protein encoded by this intronless gene is found in the nucleus, where it can inhibit DNA synthesis and promote S phase arrest coupled to apoptosis. The expression of this DNA binding protein is upregulated by transcription factor p53.	train
1A-R_gene_document_retrieval	1	Concept Grounding	10020	GNE	1A-R_gene_document_retrieval::10020	10020	The gene is a protein-coding gene located on chromosome 9p13.3. Functionally, The protein encoded by this gene is a bifunctional enzyme that initiates and regulates the biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. It is a rate-limiting enzyme in the sialic acid biosynthetic pathway. Sia...	train
1A-R_gene_document_retrieval	1	Concept Grounding	100288687	DUX4	1A-R_gene_document_retrieval::100288687	100288687	The gene is a protein-coding gene located on chromosome 4q35.2. Functionally, This gene is located within a D4Z4 repeat array in the subtelomeric region of chromosome 4q. The D4Z4 repeat is polymorphic in length; a similar D4Z4 repeat array has been identified on chromosome 10. Each D4Z4 repeat unit has an open reading...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10058	ABCB6	1A-R_gene_document_retrieval::10058	10058	The gene is a protein-coding gene located on chromosome 2q35. It belongs to the following gene groups: Blood group antigens and ATP binding cassette subfamily B. Functionally, This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ABC proteins transport various molecules across extra- and...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10073	SNUPN	1A-R_gene_document_retrieval::10073	10073	The gene is a protein-coding gene located on chromosome 15q24.2. Functionally, The nuclear import of the spliceosomal snRNPs U1, U2, U4 and U5, is dependent on the presence of a complex nuclear localization signal. The latter is composed of the 5'-2,2,7-terminal trimethylguanosine (m3G) cap structure of the U snRNA and...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10075	HUWE1	1A-R_gene_document_retrieval::10075	10075	The gene is a protein-coding gene located on chromosome Xp11.22. It belongs to the following gene groups: Armadillo like helical domain containing, MicroRNA protein coding host genes, and HECT domain containing. Functionally, This gene encodes a protein containing a C-terminal HECT (E6AP type E3 ubiquitin protein ligas...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10079	ATP9A	1A-R_gene_document_retrieval::10079	10079	The gene is a protein-coding gene located on chromosome 20q13.2. It belongs to the following gene groups: ATPase phospholipid transporting. Functionally, Enables protease binding activity. Involved in negative regulation of exosomal secretion; regulation of endocytic recycling; and regulation of retrograde transport, e...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10082	GPC6	1A-R_gene_document_retrieval::10082	10082	The gene is a protein-coding gene located on chromosome 13q31.3-q32.1. It belongs to the following gene groups: Glypicans. Functionally, The glypicans comprise a family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans, and they have been implicated in the control of cell growth and cell division. ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	100820829	MYZAP	1A-R_gene_document_retrieval::100820829	100820829	The gene is a protein-coding gene located on chromosome 15q21.3. Functionally, This gene encodes a protein that is abundantly expressed in cardiac tissue. The encoded protein localizes to intercalated discs in cardiomyocytes and functions as an activator of Rho-dependent serum-response factor signaling. Alternative spl...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10092	ARPC5	1A-R_gene_document_retrieval::10092	10092	The gene is a protein-coding gene located on chromosome 1q25.3. It belongs to the following gene groups: Actin related protein 2/3 complex subunits. Functionally, This gene encodes one of seven subunits of the human Arp2/3 protein complex. The Arp2/3 protein complex has been implicated in the control of actin polymeriz...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10093	ARPC4	1A-R_gene_document_retrieval::10093	10093	The gene is a protein-coding gene located on chromosome 3p25.3. It belongs to the following gene groups: Actin related protein 2/3 complex subunits. Functionally, This gene encodes one of seven subunits of the human Arp2/3 protein complex. This complex controls actin polymerization in cells and has been conserved throu...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10095	ARPC1B	1A-R_gene_document_retrieval::10095	10095	The gene is a protein-coding gene located on chromosome 7q22.1. It belongs to the following gene groups: Actin related protein 2/3 complex subunits and WD repeat domain containing. Functionally, This gene encodes one of seven subunits of the human Arp2/3 protein complex. This subunit is a member of the SOP2 family of p...	train
1A-R_gene_document_retrieval	1	Concept Grounding	100996717	NOTCH2NLC	1A-R_gene_document_retrieval::100996717	100996717	The gene is a protein-coding gene located on chromosome 1q21.2. Functionally, Enables Notch binding activity. Involved in cerebral cortex development and positive regulation of Notch signaling pathway. Located in extracellular region. Implicated in essential tremor 6; neuronal intranuclear inclusion disease; and oculop...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10102	TSFM	1A-R_gene_document_retrieval::10102	10102	The gene is a protein-coding gene located on chromosome 12q14.1. Functionally, This gene encodes a mitochondrial translation elongation factor. The encoded protein is an enzyme that catalyzes the exchange of guanine nucleotides on the translation elongation factor Tu during the elongation step of mitchondrial protein t...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10112	KIF20A	1A-R_gene_document_retrieval::10112	10112	The gene is a protein-coding gene located on chromosome 5q31.2. It belongs to the following gene groups: Kinesins. Functionally, Enables protein kinase binding activity. Involved in microtubule bundle formation; midbody abscission; and regulation of cytokinesis. Located in several cellular components, including cleavag...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10128	LRPPRC	1A-R_gene_document_retrieval::10128	10128	The gene is a protein-coding gene located on chromosome 2p21. It belongs to the following gene groups: Mitochondrial respiratory chain complex assembly factors, Pentatricopeptide repeat containing, and Mitochondrial nucleoid associated proteins. Functionally, This gene encodes a leucine-rich protein that has multiple p...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10159	ATP6AP2	1A-R_gene_document_retrieval::10159	10159	The gene is a protein-coding gene located on chromosome Xp11.4. Functionally, This gene encodes a protein that is associated with adenosine triphosphatases (ATPases). Proton-translocating ATPases have fundamental roles in energy conservation, secondary active transport, acidification of intracellular compartments, and ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10165	SLC25A13	1A-R_gene_document_retrieval::10165	10165	The gene is a protein-coding gene located on chromosome 7q21.3. It belongs to the following gene groups: EF-hand domain containing, MicroRNA protein coding host genes, and Solute carrier family 25. Functionally, This gene is a member of the mitochondrial carrier family. The encoded protein contains four EF-hand Ca(2+) ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10166	SLC25A15	1A-R_gene_document_retrieval::10166	10166	The gene is a protein-coding gene located on chromosome 13q14.11. It belongs to the following gene groups: MicroRNA protein coding host genes and Solute carrier family 25. Functionally, This gene is a member of the mitochondrial carrier family. The encoded protein transports ornithine across the inner mitochondrial mem...	train
1A-R_gene_document_retrieval	1	Concept Grounding	101929726	MYMX	1A-R_gene_document_retrieval::101929726	101929726	The gene is a protein-coding gene located on chromosome 6p21.1. Functionally, Involved in myoblast fusion involved in skeletal muscle regeneration. Predicted to be active in Golgi membrane; endoplasmic reticulum membrane; and plasma membrane. Implicated in Carey-Fineman-Ziter syndrome.	train
1A-R_gene_document_retrieval	1	Concept Grounding	10195	ALG3	1A-R_gene_document_retrieval::10195	10195	The gene is a protein-coding gene located on chromosome 3q27.1. It belongs to the following gene groups: Dolichyl D-mannosyl phosphate dependent mannosyltransferases. Functionally, This gene encodes a member of the ALG3 family. The encoded protein catalyses the addition of the first dol-P-Man derived mannose in an alph...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1021	CDK6	1A-R_gene_document_retrieval::1021	1021	The gene is a protein-coding gene located on chromosome 7q21.2. It belongs to the following gene groups: Cyclin dependent kinases. Functionally, The protein encoded by this gene is a member of the CMGC family of serine/threonine protein kinases. This kinase is a catalytic subunit of the protein kinase complex that is i...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10216	PRG4	1A-R_gene_document_retrieval::10216	10216	The gene is a protein-coding gene located on chromosome 1q31.1. Functionally, The protein encoded by this gene is a large proteoglycan that is synthesized by chondrocytes located at the surface of articular cartilage and by some synovial lining cells. This protein contains both chondroitin sulfate and keratan sulfate g...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10225	CD96	1A-R_gene_document_retrieval::10225	10225	The gene is a protein-coding gene located on chromosome 3q13.13-q13.2. It belongs to the following gene groups: CD molecules, Immunoglobulin like domain containing, and Ig-like cell adhesion molecule family. Functionally, The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membran...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10253	SPRY2	1A-R_gene_document_retrieval::10253	10253	The gene is a protein-coding gene located on chromosome 13q31.1. It belongs to the following gene groups: Sprouty RTK signaling antagonist family. Functionally, This gene encodes a protein belonging to the sprouty family. The encoded protein contains a carboxyl-terminal cysteine-rich domain essential for the inhibitory...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10265	IRX5	1A-R_gene_document_retrieval::10265	10265	The gene is a protein-coding gene located on chromosome 16q12.2. It belongs to the following gene groups: TALE class homeoboxes and pseudogenes. Functionally, This gene encodes a member of the iroquois homeobox gene family, which are involved in several embryonic developmental processes. Knockout mice lacking this gene...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10269	ZMPSTE24	1A-R_gene_document_retrieval::10269	10269	The gene is a protein-coding gene located on chromosome 1p34.2. It belongs to the following gene groups: M48 metallopeptidase family. Functionally, This gene encodes a member of the peptidase M48A family. The encoded protein is a zinc metalloproteinase involved in the two step post-translational proteolytic cleavage of...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1027	CDKN1B	1A-R_gene_document_retrieval::1027	1027	The gene is a protein-coding gene located on chromosome 12p13.1. Functionally, This gene encodes a cyclin-dependent kinase inhibitor, which shares a limited similarity with CDK inhibitor CDKN1A/p21. The encoded protein binds to and prevents the activation of cyclin E-CDK2 or cyclin D-CDK4 complexes, and thus controls t...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1028	CDKN1C	1A-R_gene_document_retrieval::1028	1028	The gene is a protein-coding gene located on chromosome 11p15.4. Functionally, This gene is imprinted, with preferential expression of the maternal allele. The encoded protein is a tight-binding, strong inhibitor of several G1 cyclin/Cdk complexes and a negative regulator of cell proliferation. Mutations in this gene a...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10283	CWC27	1A-R_gene_document_retrieval::10283	10283	The gene is a protein-coding gene located on chromosome 5q12.3. It belongs to the following gene groups: Cyclophilin peptidylprolyl isomerases, NTC associated proteins, Spliceosomal Bact complex, Spliceosomal C complex, and Spliceosomal P complex. Functionally, Predicted to enable peptidyl-prolyl cis-trans isomerase ac...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1029	CDKN2A	1A-R_gene_document_retrieval::1029	1029	The gene is a protein-coding gene located on chromosome 9p21.3. Functionally, This gene generates several transcript variants which differ in their first exons. At least three alternatively spliced variants encoding distinct proteins have been reported, two of which encode structurally related isoforms known to functio...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10297	APC2	1A-R_gene_document_retrieval::10297	10297	The gene is a protein-coding gene located on chromosome 19p13.3. It belongs to the following gene groups: Armadillo repeat containing. Functionally, This gene encodes a strongly conserved protein that has an N-terminal coiled-coil domain followed by an armadillo domain, five 20-amino acid repeats, and two SAMP domains....	train
1A-R_gene_document_retrieval	1	Concept Grounding	10299	MARCHF6	1A-R_gene_document_retrieval::10299	10299	The gene is a protein-coding gene located on chromosome 5p15.2. It belongs to the following gene groups: Ring finger proteins and Membrane associated ring-CH-type fingers. Functionally, This gene encodes a member of a family of membrane-associated E3 ubiquitin ligases containing RING-CH-type zinc finger motifs. Ubiquit...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1031	CDKN2C	1A-R_gene_document_retrieval::1031	1031	The gene is a protein-coding gene located on chromosome 1p32.3. It belongs to the following gene groups: Ankyrin repeat domain containing. Functionally, The protein encoded by this gene is a member of the INK4 family of cyclin-dependent kinase inhibitors. This protein has been shown to interact with CDK4 or CDK6, and p...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10319	LAMC3	1A-R_gene_document_retrieval::10319	10319	The gene is a protein-coding gene located on chromosome 9q34.12. It belongs to the following gene groups: Laminin subunits. Functionally, Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological pr...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10342	TFG	1A-R_gene_document_retrieval::10342	10342	The gene is a protein-coding gene located on chromosome 3q12.2. Functionally, There are several documented fusion oncoproteins encoded partially by this gene. This gene also participates in several oncogenic rearrangements resulting in anaplastic lymphoma and mixoid chondrosarcoma, and may play a role in the NF-kappaB ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10347	ABCA7	1A-R_gene_document_retrieval::10347	10347	The gene is a protein-coding gene located on chromosome 19p13.3. It belongs to the following gene groups: ATP binding cassette subfamily A and ATPase phospholipid transporting. Functionally, The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transpor...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10367	MICU1	1A-R_gene_document_retrieval::10367	10367	The gene is a protein-coding gene located on chromosome 10q22.1. It belongs to the following gene groups: EF-hand domain containing and MCU complex subunits. Functionally, This gene encodes an essential regulator of mitochondrial Ca2+ uptake under basal conditions. The encoded protein interacts with the mitochondrial c...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10370	CITED2	1A-R_gene_document_retrieval::10370	10370	The gene is a protein-coding gene located on chromosome 6q24.1. Functionally, The protein encoded by this gene inhibits transactivation of HIF1A-induced genes by competing with binding of hypoxia-inducible factor 1-alpha to p300-CH1. Mutations in this gene are a cause of cardiac septal defects. Alternatively spliced tr...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10381	TUBB3	1A-R_gene_document_retrieval::10381	10381	The gene is a protein-coding gene located on chromosome 16q24.3. It belongs to the following gene groups: Tubulins. Functionally, This gene encodes a class III member of the beta tubulin protein family. Beta tubulins are one of two core protein families (alpha and beta tubulins) that heterodimerize and assemble to form...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1041	CDSN	1A-R_gene_document_retrieval::1041	1041	The gene is a protein-coding gene located on chromosome 6p21.33. Functionally, This gene encodes a protein found in corneodesmosomes, which localize to human epidermis and other cornified squamous epithelia. The encoded protein undergoes a series of cleavages during corneocyte maturation. This gene is highly polymorphi...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10430	TMEM147	1A-R_gene_document_retrieval::10430	10430	The gene is a protein-coding gene located on chromosome 19q13.12. Functionally, Enables ribosome binding activity. Involved in multi-pass transmembrane protein insertion into ER membrane and protein localization to nuclear inner membrane. Located in nuclear membrane. Part of multi-pass translocon complex. Is active in ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10456	HAX1	1A-R_gene_document_retrieval::10456	10456	The gene is a protein-coding gene located on chromosome 1q21.3. Functionally, The protein encoded by this gene is known to associate with hematopoietic cell-specific Lyn substrate 1, a substrate of Src family tyrosine kinases. It also interacts with the product of the polycystic kidney disease 2 gene, mutations in whic...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10463	SLC30A9	1A-R_gene_document_retrieval::10463	10463	The gene is a protein-coding gene located on chromosome 4p13. It belongs to the following gene groups: Solute carrier family 30. Functionally, Enables zinc ion transmembrane transporter activity. Involved in intracellular zinc ion homeostasis; regulation of mitochondrion organization; and zinc ion transport. Located in...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10484	SEC23A	1A-R_gene_document_retrieval::10484	10484	The gene is a protein-coding gene located on chromosome 14q21.1. It belongs to the following gene groups: Coat protein complex II. Functionally, The protein encoded by this gene is a member of the SEC23 subfamily of the SEC23/SEC24 family. It is part of a protein complex and found in the ribosome-free transitional face...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10486	CAP2	1A-R_gene_document_retrieval::10486	10486	The gene is a protein-coding gene located on chromosome 6p22.3. Functionally, This gene was identified by its similarity to the gene for human adenylyl cyclase-associated protein. The function of the protein encoded by this gene is unknown. However, the protein appears to be able to interact with adenylyl cyclase-assoc...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10491	CRTAP	1A-R_gene_document_retrieval::10491	10491	The gene is a protein-coding gene located on chromosome 3p22.3. It belongs to the following gene groups: Prolyl 3-hydroxylase family. Functionally, The protein encoded by this gene is similar to the chicken and mouse CRTAP genes. The encoded protein is a scaffolding protein that may influence the activity of at least o...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10501	SEMA6B	1A-R_gene_document_retrieval::10501	10501	The gene is a protein-coding gene located on chromosome 19p13.3. It belongs to the following gene groups: Semaphorins. Functionally, This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10522	DEAF1	1A-R_gene_document_retrieval::10522	10522	The gene is a protein-coding gene located on chromosome 11p15.5. It belongs to the following gene groups: Zinc fingers MYND-type and SAND domain containing. Functionally, This gene encodes a zinc finger domain-containing protein that functions as a regulator of transcription. The encoded proteins binds to its own promo...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10524	KAT5	1A-R_gene_document_retrieval::10524	10524	The gene is a protein-coding gene located on chromosome 11q13.1. It belongs to the following gene groups: Zinc fingers C2HC-type, MYST type domain containing lysine acetyltransferases, and Tip60/Nua4 histone acetyltransferase complex subunits. Functionally, The protein encoded by this gene belongs to the MYST family of...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10526	IPO8	1A-R_gene_document_retrieval::10526	10526	The gene is a protein-coding gene located on chromosome 12p11.21. It belongs to the following gene groups: Importins. Functionally, The importin-alpha/beta complex and the GTPase Ran mediate nuclear import of proteins with a classical nuclear localization signal. The protein encoded by this gene is a member of a class ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10528	NOP56	1A-R_gene_document_retrieval::10528	10528	The gene is a protein-coding gene located on chromosome 20p13. It belongs to the following gene groups: U3 small nucleolar ribonucleoprotein, MicroRNA protein coding host genes, and Small nucleolar RNA protein coding host genes. Functionally, Nop56p is a yeast nucleolar protein that is part of a complex with the nucleo...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1053	CEBPE	1A-R_gene_document_retrieval::1053	1053	The gene is a protein-coding gene located on chromosome 14q11.2. It belongs to the following gene groups: Basic leucine zipper proteins and CCAAT/enhancer binding proteins. Functionally, The protein encoded by this gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It c...	train
1A-R_gene_document_retrieval	1	Concept Grounding	105371045	PERCC1	1A-R_gene_document_retrieval::105371045	105371045	The gene is a protein-coding gene located on chromosome 16p13.3. Functionally, Predicted to be involved in digestive tract morphogenesis and enteroendocrine cell differentiation. Implicated in congenital diarrhea.	train
1A-R_gene_document_retrieval	1	Concept Grounding	10551	AGR2	1A-R_gene_document_retrieval::10551	10551	The gene is a protein-coding gene located on chromosome 7p21.1. It belongs to the following gene groups: Protein disulfide isomerases. Functionally, This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange rea...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10555	AGPAT2	1A-R_gene_document_retrieval::10555	10555	The gene is a protein-coding gene located on chromosome 9q34.3. It belongs to the following gene groups: 1-acylglycerol-3-phosphate O-acyltransferases and Lysophospholipid acyltransferases. Functionally, This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. The protein is located within...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10559	SLC35A1	1A-R_gene_document_retrieval::10559	10559	The gene is a protein-coding gene located on chromosome 6q15. It belongs to the following gene groups: Solute carrier family 35. Functionally, The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic a...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10560	SLC19A2	1A-R_gene_document_retrieval::10560	10560	The gene is a protein-coding gene located on chromosome 1q24.2. It belongs to the following gene groups: Solute carrier family 19. Functionally, This gene encodes the thiamin transporter protein. Mutations in this gene cause thiamin-responsive megaloblastic anemia syndrome (TRMA), which is an autosomal recessive disord...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10568	SLC34A2	1A-R_gene_document_retrieval::10568	10568	The gene is a protein-coding gene located on chromosome 4p15.2. It belongs to the following gene groups: Solute carrier family 34. Functionally, The protein encoded by this gene is a pH-sensitive sodium-dependent phosphate transporter. Phosphate uptake is increased at lower pH. Defects in this gene are a cause of pulmo...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10584	COLEC10	1A-R_gene_document_retrieval::10584	10584	The gene is a protein-coding gene located on chromosome 8q24.12. It belongs to the following gene groups: Collectins, C-type lectin domain containing, and Complement system activation components. Functionally, This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydr...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10585	POMT1	1A-R_gene_document_retrieval::10585	10585	The gene is a protein-coding gene located on chromosome 9q34.13. It belongs to the following gene groups: Dolichyl D-mannosyl phosphate dependent mannosyltransferases. Functionally, The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT2 gene for enzymatic fu...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10587	TXNRD2	1A-R_gene_document_retrieval::10587	10587	The gene is a protein-coding gene located on chromosome 22q11.21. It belongs to the following gene groups: Selenoproteins and Flavoproteins. Functionally, The protein encoded by this gene belongs to the pyridine nucleotide-disulfide oxidoreductase family, and is a member of the thioredoxin (Trx) system. Three thioredox...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10621	POLR3F	1A-R_gene_document_retrieval::10621	10621	The gene is a protein-coding gene located on chromosome 20p11.23. It belongs to the following gene groups: RNA polymerase subunits and MicroRNA protein coding host genes. Functionally, The protein encoded by this gene is one of more than a dozen subunits forming eukaryotic RNA polymerase III (RNA Pol III), which transc...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10641	NPRL2	1A-R_gene_document_retrieval::10641	10641	The gene is a protein-coding gene located on chromosome 3p21.31. It belongs to the following gene groups: GATOR1 subcomplex. Functionally, Enables GTPase activator activity. Involved in cellular response to amino acid starvation; negative regulation of TORC1 signaling; and negative regulation of kinase activity. Part o...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10651	MTX2	1A-R_gene_document_retrieval::10651	10651	The gene is a protein-coding gene located on chromosome 2q31.1. It belongs to the following gene groups: Metaxins. Functionally, The protein encoded by this gene is highly similar to the metaxin 2 protein from mouse, which has been shown to interact with the mitochondrial membrane protein metaxin 1. Because of this sim...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10653	SPINT2	1A-R_gene_document_retrieval::10653	10653	The gene is a protein-coding gene located on chromosome 19q13.2. Functionally, This gene encodes a transmembrane protein with two extracellular Kunitz domains that inhibits a variety of serine proteases. The protein inhibits HGF activator which prevents the formation of active hepatocyte growth factor. This gene is a p...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10659	CELF2	1A-R_gene_document_retrieval::10659	10659	The gene is a protein-coding gene located on chromosome 10p14. It belongs to the following gene groups: RNA binding motif containing. Functionally, Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa betwe...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10664	CTCF	1A-R_gene_document_retrieval::10664	10664	The gene is a protein-coding gene located on chromosome 16q22.1. It belongs to the following gene groups: Zinc fingers C2H2-type and Cilia and flagella associated. Functionally, This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10667	FARS2	1A-R_gene_document_retrieval::10667	10667	The gene is a protein-coding gene located on chromosome 6p25.1. It belongs to the following gene groups: Aminoacyl tRNA synthetases, Class II. Functionally, This gene encodes a protein that transfers phenylalanine to its cognate tRNA. This protein localizes to the mitochondrion and plays a role in mitochondrial protein...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10677	AVIL	1A-R_gene_document_retrieval::10677	10677	The gene is a protein-coding gene located on chromosome 12q14.1. It belongs to the following gene groups: Gelsolin/villins. Functionally, The protein encoded by this gene is a member of the gelsolin/villin family of actin regulatory proteins. This protein has structural similarity to villin. It binds actin and may play...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10682	EBP	1A-R_gene_document_retrieval::10682	10682	The gene is a protein-coding gene located on chromosome Xp11.23. Functionally, The protein encoded by this gene is an integral membrane protein of the endoplasmic reticulum. It is a high affinity binding protein for the antiischemic phenylalkylamine Ca2+ antagonist [3H]emopamil and the photoaffinity label [3H]azidopami...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10686	CLDN16	1A-R_gene_document_retrieval::10686	10686	The gene is a protein-coding gene located on chromosome 3q28. It belongs to the following gene groups: Claudins. Functionally, Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	1071	CETP	1A-R_gene_document_retrieval::1071	1071	The gene is a protein-coding gene located on chromosome 16q13. It belongs to the following gene groups: BPI fold containing. Functionally, The protein encoded by this gene is found in plasma, where it is involved in the transfer of cholesteryl ester from high density lipoprotein (HDL) to other lipoproteins. Defects in ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10714	POLD3	1A-R_gene_document_retrieval::10714	10714	The gene is a protein-coding gene located on chromosome 11q13.4. It belongs to the following gene groups: DNA polymerases and Protein phosphatase 1 regulatory subunits. Functionally, This gene encodes the 66-kDa subunit of DNA polymerase delta. DNA polymerase delta possesses both polymerase and 3' to 5' exonuclease act...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10716	TBR1	1A-R_gene_document_retrieval::10716	10716	The gene is a protein-coding gene located on chromosome 2q24.2. It belongs to the following gene groups: T-box transcription factors. Functionally, This gene is a member of a conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation ...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10730	YME1L1	1A-R_gene_document_retrieval::10730	10730	The gene is a protein-coding gene located on chromosome 10p12.1. It belongs to the following gene groups: AAA ATPases. Functionally, The protein encoded by this gene is the human ortholog of yeast mitochondrial AAA metalloprotease, Yme1p. It is localized in the mitochondria and can functionally complement a yme1 disrup...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10735	STAG2	1A-R_gene_document_retrieval::10735	10735	The gene is a protein-coding gene located on chromosome Xq25. It belongs to the following gene groups: Cohesin complex, Armadillo like helical domain containing, and STAG family cohesin complex components. Functionally, The protein encoded by this gene is a subunit of the cohesin complex, which regulates the separation...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10736	SIX2	1A-R_gene_document_retrieval::10736	10736	The gene is a protein-coding gene located on chromosome 2p21. It belongs to the following gene groups: SINE class homeoboxes. Functionally, This gene is a member of the vertebrate gene family which encode proteins homologous to the Drosophila 'sine oculis' homeobox protein. The encoded protein is a transcription factor...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10755	GIPC1	1A-R_gene_document_retrieval::10755	10755	The gene is a protein-coding gene located on chromosome 19p13.12. It belongs to the following gene groups: PDZ domain containing. Functionally, GIPC1 is a scaffolding protein that regulates cell surface receptor expression and trafficking (Lee et al., 2008 [PubMed 18775991]).[supplied by OMIM, Apr 2009]	train
1A-R_gene_document_retrieval	1	Concept Grounding	1080	CFTR	1A-R_gene_document_retrieval::1080	1080	The gene is a protein-coding gene located on chromosome 7q31.2. It belongs to the following gene groups: Chloride channels, ATP-gated CFTR and ATP binding cassette subfamily C. Functionally, This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. The encoded protein functions as a chloride...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10801	SEPTIN9	1A-R_gene_document_retrieval::10801	10801	The gene is a protein-coding gene located on chromosome 17q25.3. It belongs to the following gene groups: Septins. Functionally, This gene is a member of the septin family involved in cytokinesis and cell cycle control. This gene is a candidate for the ovarian tumor suppressor gene. Mutations in this gene cause heredit...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10804	GJB6	1A-R_gene_document_retrieval::10804	10804	The gene is a protein-coding gene located on chromosome 13q12.11. It belongs to the following gene groups: Gap junction proteins. Functionally, Gap junctions allow the transport of ions and metabolites between the cytoplasm of adjacent cells. They are formed by two hemichannels, made up of six connexin proteins assembl...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10815	CPLX1	1A-R_gene_document_retrieval::10815	10815	The gene is a protein-coding gene located on chromosome 4p16.3. It belongs to the following gene groups: Complexins. Functionally, Proteins encoded by the complexin/synaphin gene family are cytosolic proteins that function in synaptic vesicle exocytosis. These proteins bind syntaxin, part of the SNAP receptor. The prot...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10841	FTCD	1A-R_gene_document_retrieval::10841	10841	The gene is a protein-coding gene located on chromosome 21q22.3. Functionally, The protein encoded by this gene is a bifunctional enzyme that channels 1-carbon units from formiminoglutamate, a metabolite of the histidine degradation pathway, to the folate pool. Mutations in this gene are associated with glutamate formi...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10848	PPP1R13L	1A-R_gene_document_retrieval::10848	10848	The gene is a protein-coding gene located on chromosome 19q13.32. It belongs to the following gene groups: Ankyrin repeat domain containing. Functionally, IASPP is one of the most evolutionarily conserved inhibitors of p53 (TP53; MIM 191170), whereas ASPP1 (MIM 606455) and ASPP2 (MIM 602143) are activators of p53.[supp...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10861	SLC26A1	1A-R_gene_document_retrieval::10861	10861	The gene is a protein-coding gene located on chromosome 4p16.3. It belongs to the following gene groups: Solute carrier family 26. Functionally, This gene is a member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length amon...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10878	CFHR3	1A-R_gene_document_retrieval::10878	10878	The gene is a protein-coding gene located on chromosome 1q31.3. It belongs to the following gene groups: Sushi domain containing and Complement system regulators and receptors. Functionally, The protein encoded by this gene is a secreted protein, which belongs to the complement factor H-related protein family. It binds...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10907	TXNL4A	1A-R_gene_document_retrieval::10907	10907	The gene is a protein-coding gene located on chromosome 18q23. It belongs to the following gene groups: U5 small nuclear ribonucleoprotein. Functionally, The protein encoded by this gene is a member of the U5 small ribonucleoprotein particle (snRNP), and is involved in pre-mRNA splicing. This protein contains a thiored...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10913	EDAR	1A-R_gene_document_retrieval::10913	10913	The gene is a protein-coding gene located on chromosome 2q13. It belongs to the following gene groups: Tumor necrosis factor receptor superfamily. Functionally, This gene encodes a member of the tumor necrosis factor receptor family. The encoded transmembrane protein is a receptor for the soluble ligand ectodysplasin A...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10939	AFG3L2	1A-R_gene_document_retrieval::10939	10939	The gene is a protein-coding gene located on chromosome 18p11.21. It belongs to the following gene groups: AAA ATPases. Functionally, This gene encodes a protein localized in mitochondria and closely related to paraplegin. The paraplegin gene is responsible for an autosomal recessive form of hereditary spastic parapleg...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10982	MAPRE2	1A-R_gene_document_retrieval::10982	10982	The gene is a protein-coding gene located on chromosome 18q12.1-q12.2. It belongs to the following gene groups: Microtubule associated protein RP/EB family. Functionally, The protein encoded by this gene shares significant homology to the adenomatous polyposis coli (APC) protein-binding EB1 gene family. This protein is...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10991	SLC38A3	1A-R_gene_document_retrieval::10991	10991	The gene is a protein-coding gene located on chromosome 3p21.31. It belongs to the following gene groups: Solute carrier family 38. Functionally, Enables L-amino acid transmembrane transporter activity. Involved in carboxylic acid transport. Located in plasma membrane. Implicated in developmental and epileptic encephal...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10992	SF3B2	1A-R_gene_document_retrieval::10992	10992	The gene is a protein-coding gene located on chromosome 11q13.1. It belongs to the following gene groups: Armadillo like helical domain containing and SF3b complex. Functionally, This gene encodes subunit 2 of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA uni...	train
1A-R_gene_document_retrieval	1	Concept Grounding	10999	SLC27A4	1A-R_gene_document_retrieval::10999	10999	The gene is a protein-coding gene located on chromosome 9q34.11. It belongs to the following gene groups: Acyl-CoA synthetase family and Solute carrier family 27. Functionally, This gene encodes a member of a family of fatty acid transport proteins, which are involved in translocation of long-chain fatty acids cross th...	train

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OntologyBench

OntologyBench is a tiered benchmark for structured biomedical knowledge retrieval. This dataset exposes the paper's model-independent positive training pairs and held-out test pairs as one Hugging Face DatasetDict with train and test splits.

Dataset structure

Each row contains:

task_name: canonical OntologyBench task name.
query_id: source query identifier.
query: biomedical query text.
target_id: task-scoped target identifier used for split assignment.
raw_target_id: source document identifier.
target: positive target text.
split: train or test.

All rows are positive query-target pairs; negatives are not materialized. Retrieval training code should construct in-batch or mined negatives as appropriate.

Split construction

Task-scoped target identifiers are sorted, shuffled with seed 42, and assigned 80% to train and 20% to test. All positive pairs for a target stay in one split. Duplicate normalized query-target text pairs are removed within each split. The split is target-disjoint within each task but transductive across tasks because the same biomedical entity may occur in different task namespaces.

Loading

from datasets import load_dataset

dataset = load_dataset("/OntologyBench")
print(dataset)
print(dataset["train"].features)

Source and limitations

The benchmark was derived from public biomedical resources including HPO, Mondo, HGNC, and NCBI Gene. The task artifacts are intended for biomedical retrieval research, not clinical diagnosis or patient-care decisions. Ontology-aware reference systems use a different information regime from text-only retrievers and should not be treated as directly comparable learned systems.

See the accompanying paper and software repository for full construction details, metrics, provenance limitations, and validation warnings.

License

The released task data are available under CC BY 4.0. Upstream biomedical resources retain their own attribution and licensing requirements.

Citation

@inproceedings{zhang2026ontologybench,
  title     = {{OntologyBench}: Can Dense Retrieval Satisfy Structured Biomedical Constraints?},
  author    = {Zhang, Xiao Yu Cindy and Wasserman, Wyeth W. and Zhu, Jian},
  booktitle = {Proceedings of the 2026 Conference on Empirical Methods in Natural Language Processing},
  month     = oct,
  year      = {2026},
  address   = {Budapest, Hungary},
  publisher = {Association for Computational Linguistics},
  note      = {To appear}
}

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