Datasets:

bigbio
/

genia_term_corpus

id stringlengths 1 6	document_id stringlengths 8 8	passages list	entities list	events list	coreferences list	relations list
0	95369245	[ { "id": "1", "type": "title", "text": [ "IL-2 gene expression and NF-kappa B activation through CD28 requires reactive oxygen production by 5-lipoxygenase." ], "offsets": [ [ 0, 114 ] ] }, { "id": "2", "type": "abstract", "text": [ "Act...	[ { "id": "3", "type": "other_name", "text": [ "IL-2 gene expression" ], "offsets": [ [ 0, 20 ] ], "normalized": [] }, { "id": "4", "type": "DNA_domain_or_region", "text": [ "IL-2 gene" ], "offsets": [ [ 0, ...	[]	[]	[]
43	95333264	[ { "id": "44", "type": "title", "text": [ "The peri-kappa B site mediates human immunodeficiency virus type 2 enhancer activation in monocytes but not in T cells." ], "offsets": [ [ 0, 119 ] ] }, { "id": "45", "type": "abstract", "text": [ ...	[ { "id": "46", "type": "DNA_domain_or_region", "text": [ "peri-kappa B site" ], "offsets": [ [ 4, 21 ] ], "normalized": [] }, { "id": "47", "type": "other_name", "text": [ "human immunodeficiency virus type 2 enhancer activation" ...	[]	[]	[]
118	95343554	[ { "id": "119", "type": "title", "text": [ "E1A gene expression induces susceptibility to killing by NK cells following immortalization but not adenovirus infection of human cells." ], "offsets": [ [ 0, 136 ] ] }, { "id": "120", "type": "abstract"...	[ { "id": "121", "type": "other_name", "text": [ "E1A gene expression" ], "offsets": [ [ 0, 19 ] ], "normalized": [] }, { "id": "122", "type": "DNA_domain_or_region", "text": [ "E1A gene" ], "offsets": [ [ 0, ...	[]	[]	[]
154	95347379	[ { "id": "155", "type": "title", "text": [ "Distinct signaling properties identify functionally different CD4 epitopes." ], "offsets": [ [ 0, 75 ] ] }, { "id": "156", "type": "abstract", "text": [ "The CD4 coreceptor interacts with non-p...	[ { "id": "157", "type": "protein_family_or_group", "text": [ "CD4 epitopes" ], "offsets": [ [ 62, 74 ] ], "normalized": [] }, { "id": "158", "type": "protein_molecule", "text": [ "CD4 coreceptor" ], "offsets": [ [ ...	[]	[]	[]
196	95280913	[ { "id": "197", "type": "title", "text": [ "Ligand-dependent repression of the erythroid transcription factor GATA-1 by the estrogen receptor." ], "offsets": [ [ 0, 98 ] ] }, { "id": "198", "type": "abstract", "text": [ "High-dose estrog...	[ { "id": "199", "type": "other_name", "text": [ "Ligand-dependent repression" ], "offsets": [ [ 0, 27 ] ], "normalized": [] }, { "id": "200", "type": "protein_family_or_group", "text": [ "erythroid transcription factor" ], "o...	[]	[]	[]
257	95256242	[ { "id": "258", "type": "title", "text": [ "Mouse interleukin-2 receptor alpha gene expression. Interleukin-1 and interleukin-2 control transcription via distinct cis-acting elements." ], "offsets": [ [ 0, 139 ] ] }, { "id": "259", "type": "abstra...	[ { "id": "260", "type": "other_name", "text": [ "Mouse interleukin-2 receptor alpha gene expression" ], "offsets": [ [ 0, 50 ] ], "normalized": [] }, { "id": "261", "type": "DNA_domain_or_region", "text": [ "Mouse interleukin-2 recep...	[]	[]	[]
318	95338146	[ { "id": "319", "type": "title", "text": [ "Hematopoietic lineage commitment: role of transcription factors." ], "offsets": [ [ 0, 64 ] ] }, { "id": "320", "type": "abstract", "text": [ "This review focuses on the roles of transcription ...	[ { "id": "321", "type": "other_name", "text": [ "Hematopoietic lineage commitment" ], "offsets": [ [ 0, 32 ] ], "normalized": [] }, { "id": "322", "type": "cell_type", "text": [ "Hematopoietic lineage" ], "offsets": [ [...	[]	[]	[]
342	95266275	[ { "id": "343", "type": "title", "text": [ "Epstein-Barr virus replicative gene transcription during de novo infection of human thymocytes: simultaneous early expression of BZLF-1 and its repressor RAZ." ], "offsets": [ [ 0, 158 ] ] }, { "id": "344", ...	[ { "id": "345", "type": "other_name", "text": [ "Epstein-Barr virus replicative gene transcription" ], "offsets": [ [ 0, 49 ] ], "normalized": [] }, { "id": "346", "type": "virus", "text": [ "Epstein-Barr virus" ], "offsets":...	[]	[]	[]
399	95236292	[ { "id": "400", "type": "title", "text": [ "Identification and purification of human Stat proteins activated in response to interleukin-2." ], "offsets": [ [ 0, 94 ] ] }, { "id": "401", "type": "abstract", "text": [ "A key cytokine induc...	[ { "id": "402", "type": "protein_family_or_group", "text": [ "human Stat proteins" ], "offsets": [ [ 35, 54 ] ], "normalized": [] }, { "id": "403", "type": "protein_molecule", "text": [ "interleukin-2" ], "offsets": [ [...	[]	[]	[]
427	95197524	[ { "id": "428", "type": "title", "text": [ "E2F-1 and a cyclin-like DNA repair enzyme, uracil-DNA glycosylase, provide evidence for an autoregulatory mechanism for transcription." ], "offsets": [ [ 0, 134 ] ] }, { "id": "429", "type": "abstract", ...	[ { "id": "430", "type": "protein_molecule", "text": [ "E2F-1" ], "offsets": [ [ 0, 5 ] ], "normalized": [] }, { "id": "431", "type": "protein_family_or_group", "text": [ "cyclin-like DNA repair enzyme" ], "offsets": [ [...	[]	[]	[]
479	95370702	[ { "id": "480", "type": "title", "text": [ "Cellular and molecular mechanisms of IFN-gamma production induced by IL-2 and IL-12 in a human NK cell line." ], "offsets": [ [ 0, 108 ] ] }, { "id": "481", "type": "abstract", "text": [ "Inter...	[ { "id": "482", "type": "(AND other_name other_name)", "text": [ "Cellular and molecular mechanisms" ], "offsets": [ [ 0, 33 ] ], "normalized": [] }, { "id": "483", "type": "", "text": [ "Cellular" ], "offsets": [ [ ...	[]	[]	[]
583	95349600	[ { "id": "584", "type": "title", "text": [ "A functional T-cell receptor signaling pathway is required for p95vav activity." ], "offsets": [ [ 0, 79 ] ] }, { "id": "585", "type": "abstract", "text": [ "Stimulation of the T-cell antigen r...	[ { "id": "586", "type": "other_name", "text": [ "functional T-cell receptor signaling pathway" ], "offsets": [ [ 2, 46 ] ], "normalized": [] }, { "id": "587", "type": "protein_family_or_group", "text": [ "T-cell receptor" ], ...	[]	[]	[]
669	95329717	[ { "id": "670", "type": "title", "text": [ "Positive and negative regulation of granulocyte-macrophage colony-stimulating factor promoter activity by AML1-related transcription factor, PEBP2." ], "offsets": [ [ 0, 147 ] ] }, { "id": "671", "type":...	[ { "id": "672", "type": "(AND other_name other_name)", "text": [ "Positive and negative regulation" ], "offsets": [ [ 0, 32 ] ], "normalized": [] }, { "id": "673", "type": "", "text": [ "Positive" ], "offsets": [ [ ...	[]	[]	[]
756	96075792	[ { "id": "757", "type": "title", "text": [ "IFN-gamma priming of monocytes enhances LPS-induced TNF production by augmenting both transcription and MRNA stability." ], "offsets": [ [ 0, 119 ] ] }, { "id": "758", "type": "abstract", "text": [ ...	[ { "id": "759", "type": "protein_molecule", "text": [ "IFN-gamma" ], "offsets": [ [ 0, 9 ] ], "normalized": [] }, { "id": "760", "type": "cell_type", "text": [ "monocytes" ], "offsets": [ [ 21, 30 ...	[]	[]	[]
828	95280917	[ { "id": "829", "type": "title", "text": [ "A Myc-associated zinc finger protein binding site is one of four important functional regions in the CD4 promoter." ], "offsets": [ [ 0, 114 ] ] }, { "id": "830", "type": "abstract", "text": [ ...	[ { "id": "831", "type": "DNA_domain_or_region", "text": [ "Myc-associated zinc finger protein binding site" ], "offsets": [ [ 2, 49 ] ], "normalized": [] }, { "id": "832", "type": "protein_family_or_group", "text": [ "Myc-associated ...	[]	[]	[]
866	95263486	[ { "id": "867", "type": "title", "text": [ "Erythropoietin stimulates transcription of the TAL1/SCL gene and phosphorylation of its protein products." ], "offsets": [ [ 0, 105 ] ] }, { "id": "868", "type": "abstract", "text": [ "Activati...	[ { "id": "869", "type": "protein_molecule", "text": [ "Erythropoietin" ], "offsets": [ [ 0, 14 ] ], "normalized": [] }, { "id": "870", "type": "DNA_domain_or_region", "text": [ "TAL1/SCL gene" ], "offsets": [ [ ...	[]	[]	[]
925	95397944	[ { "id": "926", "type": "title", "text": [ "Nonradioactive quantification of glucocorticoid receptor expression during differentiation of human monocytic cells (U937)." ], "offsets": [ [ 0, 123 ] ] }, { "id": "927", "type": "abstract", "text":...	[ { "id": "928", "type": "other_name", "text": [ "Nonradioactive quantification" ], "offsets": [ [ 0, 29 ] ], "normalized": [] }, { "id": "929", "type": "other_name", "text": [ "glucocorticoid receptor expression" ], "offsets"...	[]	[]	[]
957	95266282	[ { "id": "958", "type": "title", "text": [ "Induction of Sp1 phosphorylation and NF-kappa B-independent HIV promoter domain activity in T lymphocytes stimulated by okadaic acid." ], "offsets": [ [ 0, 133 ] ] }, { "id": "959", "type": "abstract", ...	[ { "id": "960", "type": "other_name", "text": [ "Sp1 phosphorylation" ], "offsets": [ [ 13, 32 ] ], "normalized": [] }, { "id": "961", "type": "protein_molecule", "text": [ "Sp1" ], "offsets": [ [ 13, 16...	[]	[]	[]
1035	95236293	[ { "id": "1036", "type": "title", "text": [ "The role of shared receptor motifs and common Stat proteins in the generation of cytokine pleiotropy and redundancy by IL-2, IL-4, IL-7, IL-13, and IL-15." ], "offsets": [ [ 0, 154 ] ] }, { "id": "1037", ...	[ { "id": "1038", "type": "protein_substructure", "text": [ "shared receptor motifs" ], "offsets": [ [ 12, 34 ] ], "normalized": [] }, { "id": "1039", "type": "protein_family_or_group", "text": [ "common Stat proteins" ], "off...	[]	[]	[]
1080	95184007	[ { "id": "1081", "type": "title", "text": [ "Control of I kappa B-alpha proteolysis by site-specific, signal-induced phosphorylation." ], "offsets": [ [ 0, 88 ] ] }, { "id": "1082", "type": "abstract", "text": [ "I kappa B-alpha inhibits...	[ { "id": "1083", "type": "other_name", "text": [ "I kappa B-alpha proteolysis" ], "offsets": [ [ 11, 38 ] ], "normalized": [] }, { "id": "1084", "type": "protein_molecule", "text": [ "I kappa B-alpha" ], "offsets": [ [ ...	[]	[]	[]
1109	95388524	[ { "id": "1110", "type": "title", "text": [ "Regulation of transcription of the human erythropoietin receptor gene by proteins binding to GATA-1 and Sp1 motifs." ], "offsets": [ [ 0, 115 ] ] }, { "id": "1111", "type": "abstract", "text": [ ...	[ { "id": "1112", "type": "other_name", "text": [ "transcription" ], "offsets": [ [ 14, 27 ] ], "normalized": [] }, { "id": "1113", "type": "DNA_domain_or_region", "text": [ "human erythropoietin receptor gene" ], "offsets": [...	[]	[]	[]
1192	95365382	[ { "id": "1193", "type": "title", "text": [ "Overexpression of DR-nm23, a protein encoded by a member of the nm23 gene family, inhibits granulocyte differentiation and induces apoptosis in 32Dc13 myeloid cells." ], "offsets": [ [ 0, 165 ] ] }, { "id":...	[ { "id": "1195", "type": "protein_molecule", "text": [ "DR-nm23" ], "offsets": [ [ 18, 25 ] ], "normalized": [] }, { "id": "1196", "type": "DNA_family_or_group", "text": [ "nm23 gene family" ], "offsets": [ [ 64...	[]	[]	[]
1243	96032864	[ { "id": "1244", "type": "title", "text": [ "An interferon-gamma activation sequence mediates the transcriptional regulation of the IgG Fc receptor type IC gene by interferon-gamma." ], "offsets": [ [ 0, 136 ] ] }, { "id": "1245", "type": "abstrac...	[ { "id": "1246", "type": "DNA_domain_or_region", "text": [ "interferon-gamma activation sequence" ], "offsets": [ [ 3, 39 ] ], "normalized": [] }, { "id": "1247", "type": "other_name", "text": [ "transcriptional regulation" ], ...	[]	[]	[]
1310	95327953	[ { "id": "1311", "type": "title", "text": [ "Constitutively activated Jak-STAT pathway in T cells transformed with HTLV-I." ], "offsets": [ [ 0, 77 ] ] }, { "id": "1312", "type": "abstract", "text": [ "Human T cell lymphotropic virus I (...	[ { "id": "1313", "type": "other_name", "text": [ "Jak-STAT pathway" ], "offsets": [ [ 25, 41 ] ], "normalized": [] }, { "id": "1314", "type": "protein_family_or_group", "text": [ "Jak" ], "offsets": [ [ 25, ...	[]	[]	[]
1355	95340873	[ { "id": "1356", "type": "title", "text": [ "Nitric oxide decreases cytokine-induced endothelial activation. Nitric oxide selectively reduces endothelial expression of adhesion molecules and proinflammatory cytokines." ], "offsets": [ [ 0, 172 ] ] }, { ...	[ { "id": "1358", "type": "inorganic", "text": [ "Nitric oxide" ], "offsets": [ [ 0, 12 ] ], "normalized": [] }, { "id": "1359", "type": "other_name", "text": [ "cytokine-induced endothelial activation" ], "offsets": [ [...	[]	[]	[]
1422	95280909	[ { "id": "1423", "type": "title", "text": [ "MIP1 alpha nuclear protein (MNP), a novel transcription factor expressed in hematopoietic cells that is crucial for transcription of the human MIP-1 alpha gene." ], "offsets": [ [ 0, 160 ] ] }, { "id": "142...	[ { "id": "1425", "type": "protein_molecule", "text": [ "MIP1 alpha nuclear protein" ], "offsets": [ [ 0, 26 ] ], "normalized": [] }, { "id": "1426", "type": "protein_molecule", "text": [ "MNP" ], "offsets": [ [ ...	[]	[]	[]
1486	96055286	[ { "id": "1487", "type": "title", "text": [ "The effect of Toremifene on the expression of some genes in human mononuclear cells." ], "offsets": [ [ 0, 84 ] ] }, { "id": "1488", "type": "abstract", "text": [ "Toremifene exerts multiple a...	[ { "id": "1489", "type": "other_organic_compound", "text": [ "Toremifene" ], "offsets": [ [ 14, 24 ] ], "normalized": [] }, { "id": "1490", "type": "cell_type", "text": [ "human mononuclear cells" ], "offsets": [ [ ...	[]	[]	[]

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Dataset Card for GENIA Term Corpus

The identification of linguistic expressions referring to entities of interest in molecular biology such as proteins, genes and cells is a fundamental task in biomolecular text mining. The GENIA technical term annotation covers the identification of physical biological entities as well as other important terms. The corpus annotation covers the full 1,999 abstracts of the primary GENIA corpus.

Citation Information

@inproceedings{10.5555/1289189.1289260,
author = {Ohta, Tomoko and Tateisi, Yuka and Kim, Jin-Dong},
title = {The GENIA Corpus: An Annotated Research Abstract Corpus in Molecular Biology Domain},
year = {2002},
publisher = {Morgan Kaufmann Publishers Inc.},
address = {San Francisco, CA, USA},
booktitle = {Proceedings of the Second International Conference on Human Language Technology Research},
pages = {82–86},
numpages = {5},
location = {San Diego, California},
series = {HLT '02}
}

@article{Kim2003GENIAC,
  title={GENIA corpus - a semantically annotated corpus for bio-textmining},
  author={Jin-Dong Kim and Tomoko Ohta and Yuka Tateisi and Junichi Tsujii},
  journal={Bioinformatics},
  year={2003},
  volume={19 Suppl 1},
  pages={
          i180-2
        }
}

@inproceedings{10.5555/1567594.1567610,
author = {Kim, Jin-Dong and Ohta, Tomoko and Tsuruoka, Yoshimasa and Tateisi, Yuka and Collier, Nigel},
title = {Introduction to the Bio-Entity Recognition Task at JNLPBA},
year = {2004},
publisher = {Association for Computational Linguistics},
address = {USA},
booktitle = {Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and Its
Applications},
pages = {70–75},
numpages = {6},
location = {Geneva, Switzerland},
series = {JNLPBA '04}
}

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