Datasets:
jnlpba

Tasks:

Token Classification

Sub-tasks: named-entity-recognition

Languages: English

Multilinguality: monolingual

Size Categories: 10K<n<100K

Language Creators: expert-generated

Annotations Creators: expert-generated

Source Datasets: extended|other-genia-v3.02

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train · 18.5k rows

id stringlengths 1 5	tokens sequence	ner_tags sequence
1	[ "IL-2", "gene", "expression", "and", "NF-kappa", "B", "activation", "through", "CD28", "requires", "reactive", "oxygen", "production", "by", "5-lipoxygenase", "." ]	[ 1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0 ]
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3	[ "In", "primary", "T", "lymphocytes", "we", "show", "that", "CD28", "ligation", "leads", "to", "the", "rapid", "intracellular", "formation", "of", "reactive", "oxygen", "intermediates", "(", "ROIs", ")", "which", "are", "required", "for", "CD28", "-mediated", "activation", "of", "the", "NF-kappa", "B", "/", "CD28-responsive", "complex", "and", "IL-2", "expression", "." ]	[ 0, 7, 8, 8, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 9, 10, 0, 9, 10, 0, 9, 0, 0 ]
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5	[ "Our", "data", "suggest", "that", "lipoxygenase", "metabolites", "activate", "ROI", "formation", "which", "then", "induce", "IL-2", "expression", "via", "NF-kappa", "B", "activation", "." ]	[ 0, 0, 0, 0, 9, 10, 0, 0, 0, 0, 0, 0, 9, 0, 0, 9, 10, 0, 0 ]
6	[ "These", "findings", "should", "be", "useful", "for", "therapeutic", "strategies", "and", "the", "development", "of", "immunosuppressants", "targeting", "the", "CD28", "costimulatory", "pathway", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 0 ]
7	[ "The", "peri-kappa", "B", "site", "mediates", "human", "immunodeficiency", "virus", "type", "2", "enhancer", "activation", "in", "monocytes", "but", "not", "in", "T", "cells", "." ]	[ 0, 1, 2, 2, 0, 1, 2, 2, 2, 2, 2, 0, 0, 7, 0, 0, 0, 7, 8, 0 ]
8	[ "Human", "immunodeficiency", "virus", "type", "2", "(", "HIV-2", ")", ",", "like", "HIV-1", ",", "causes", "AIDS", "and", "is", "associated", "with", "AIDS", "cases", "primarily", "in", "West", "Africa", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
9	[ "HIV-1", "and", "HIV-2", "display", "significant", "differences", "in", "nucleic", "acid", "sequence", "and", "in", "the", "natural", "history", "of", "clinical", "disease", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
10	[ "Consistent", "with", "these", "differences", ",", "we", "have", "previously", "demonstrated", "that", "the", "enhancer/promoter", "region", "of", "HIV-2", "functions", "quite", "differently", "from", "that", "of", "HIV-1", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
11	[ "Whereas", "activation", "of", "the", "HIV-1", "enhancer", "following", "T-cell", "stimulation", "is", "mediated", "largely", "through", "binding", "of", "the", "transcription", "factor", "NF-kappa", "B", "to", "two", "adjacent", "kappa", "B", "sites", "in", "the", "HIV-1", "long", "terminal", "repeat", ",", "activation", "of", "the", "HIV-2", "enhancer", "in", "monocytes", "and", "T", "cells", "is", "dependent", "on", "four", "cis-acting", "elements", ":", "a", "single", "kappa", "B", "site", ",", "two", "purine-rich", "binding", "sites", ",", "PuB1", "and", "PuB2", ",", "and", "a", "pets", "site", "." ]	[ 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 9, 10, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 2, 2, 0, 0, 0, 0, 1, 2, 0, 7, 0, 7, 8, 0, 0, 0, 0, 1, 2, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 2, 0, 1, 0, 1, 0, 0, 0, 1, 2, 0 ]
12	[ "We", "have", "now", "identified", "a", "novel", "cis-acting", "element", "within", "the", "HIV-2", "enhancer", ",", "immediately", "upstream", "of", "the", "kappa", "B", "site", ",", "designated", "peri-kappa", "B", "." ]	[ 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 1, 2, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 1, 2, 0 ]
13	[ "This", "site", "is", "conserved", "among", "isolates", "of", "HIV-2", "and", "the", "closely", "related", "simian", "immunodeficiency", "virus", ",", "and", "transfection", "assays", "show", "this", "site", "to", "mediate", "HIV-2", "enhancer", "activation", "following", "stimulation", "of", "monocytic", "but", "not", "T-cell", "lines", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 5, 0, 0, 5, 6, 0 ]
14	[ "This", "is", "the", "first", "description", "of", "an", "HIV-2", "enhancer", "element", "which", "displays", "such", "monocyte", "specificity", ",", "and", "no", "comparable", "enhancer", "element", "has", "been", "clearly", "defined", "for", "HIV-1", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0 ]
15	[ "While", "a", "nuclear", "factor", "(", "s", ")", "from", "both", "peripheral", "blood", "monocytes", "and", "T", "cells", "binds", "the", "peri-kappa", "B", "site", ",", "electrophoretic", "mobility", "shift", "assays", "suggest", "that", "either", "a", "different", "protein", "binds", "to", "this", "site", "in", "monocytes", "versus", "T", "cells", "or", "that", "the", "protein", "recognizing", "this", "enhancer", "element", "undergoes", "differential", "modification", "in", "monocytes", "and", "T", "cells", ",", "thus", "supporting", "the", "transfection", "data", "." ]	[ 0, 0, 9, 10, 0, 0, 0, 0, 0, 7, 8, 8, 0, 7, 8, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 7, 8, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 7, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0 ]
16	[ "Further", ",", "while", "specific", "constitutive", "binding", "to", "the", "peri-kappa", "B", "site", "is", "seen", "in", "monocytes", ",", "stimulation", "with", "phorbol", "esters", "induces", "additional", ",", "specific", "binding", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
17	[ "Understanding", "the", "monocyte-specific", "function", "of", "the", "peri-kappa", "B", "factor", "may", "ultimately", "provide", "insight", "into", "the", "different", "role", "monocytes", "and", "T", "cells", "play", "in", "HIV", "pathogenesis", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 7, 8, 0, 0, 0, 0, 0 ]
18	[ "E1A", "gene", "expression", "induces", "susceptibility", "to", "killing", "by", "NK", "cells", "following", "immortalization", "but", "not", "adenovirus", "infection", "of", "human", "cells", "." ]	[ 1, 2, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0 ]
19	[ "Adenovirus", "(", "Ad", ")", "infection", "and", "E1A", "transfection", "were", "used", "to", "model", "changes", "in", "susceptibility", "to", "NK", "cell", "killing", "caused", "by", "transient", "vs", "stable", "E1A", "expression", "in", "human", "cells", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 7, 8, 0 ]
20	[ "Only", "stably", "transfected", "target", "cells", "exhibited", "cytolytic", "susceptibility", ",", "despite", "expression", "of", "equivalent", "levels", "of", "E1A", "proteins", "in", "Ad-infected", "targets", "." ]	[ 0, 0, 5, 6, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 5, 6, 0 ]
21	[ "The", "inability", "of", "E1A", "gene", "products", "to", "induce", "cytolytic", "susceptibility", "during", "infection", "was", "not", "explained", "by", "an", "inhibitory", "effect", "of", "viral", "infection", "on", "otherwise", "susceptible", "target", "cells", "or", "by", "viral", "gene", "effects", "on", "class", "I", "MHC", "antigen", "expression", "on", "target", "cells", "." ]	[ 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 1, 2, 0, 0, 9, 10, 10, 10, 0, 0, 7, 8, 0 ]
22	[ "This", "differential", "effect", "of", "E1A", "expression", "on", "the", "cytolytic", "phenotypes", "of", "infected", "and", "stably", "transfected", "human", "cells", "suggests", "that", "human", "NK", "cells", "provide", "an", "effective", "immunologic", "barrier", "against", "the", "in", "vivo", "survival", "and", "neoplastic", "progression", "of", "E1A-immortalized", "cells", "that", "may", "emerge", "from", "the", "reservoir", "of", "persistently", "infected", "cells", "in", "the", "human", "host", "." ]	[ 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 7, 8, 0, 0, 7, 8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 6, 0, 0, 0, 0, 0, 0, 0, 7, 8, 8, 0, 0, 0, 0, 0 ]
23	[ "Distinct", "signaling", "properties", "identify", "functionally", "different", "CD4", "epitopes", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 10, 0 ]
24	[ "The", "CD4", "coreceptor", "interacts", "with", "non-polymorphic", "regions", "of", "major", "histocompatibility", "complex", "class", "II", "molecules", "on", "antigen-presenting", "cells", "and", "contributes", "to", "T", "cell", "activation", "." ]	[ 0, 9, 10, 0, 0, 9, 10, 0, 9, 10, 10, 10, 10, 10, 0, 7, 8, 0, 0, 0, 0, 0, 0, 0 ]
25	[ "We", "have", "investigated", "the", "effect", "of", "CD4", "triggering", "on", "T", "cell", "activating", "signals", "in", "a", "lymphoma", "model", "using", "monoclonal", "antibodies", "(", "mAb", ")", "which", "recognize", "different", "CD4", "epitopes", "." ]	[ 0, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 10, 0, 9, 0, 0, 0, 0, 9, 10, 0 ]
26	[ "We", "demonstrate", "that", "CD4", "triggering", "delivers", "signals", "capable", "of", "activating", "the", "NF-AT", "transcription", "factor", "which", "is", "required", "for", "interleukin-2", "gene", "expression", "." ]	[ 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 9, 0, 0, 0 ]
27	[ "Whereas", "different", "anti-CD4", "mAb", "or", "HIV-1", "gp120", "could", "all", "trigger", "activation", "of", "the", "protein", "tyrosine", "kinases", "p56lck", "and", "p59fyn", "and", "phosphorylation", "of", "the", "Shc", "adaptor", "protein", ",", "which", "mediates", "signals", "to", "Ras", ",", "they", "differed", "significantly", "in", "their", "ability", "to", "activate", "NF-AT", "." ]	[ 0, 0, 9, 10, 0, 9, 10, 0, 0, 0, 0, 0, 0, 9, 10, 10, 9, 0, 9, 0, 0, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0 ]
28	[ "Lack", "of", "full", "activation", "of", "NF-AT", "could", "be", "correlated", "to", "a", "dramatically", "reduced", "capacity", "to", "induce", "calcium", "flux", "and", "could", "be", "complemented", "with", "a", "calcium", "ionophore", "." ]	[ 0, 0, 0, 0, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
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30	[ "Ligand-dependent", "repression", "of", "the", "erythroid", "transcription", "factor", "GATA-1", "by", "the", "estrogen", "receptor", "." ]	[ 0, 0, 0, 0, 9, 10, 10, 9, 0, 0, 9, 10, 0 ]
31	[ "High-dose", "estrogen", "administration", "induces", "anemia", "in", "mammals", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0 ]
32	[ "In", "chickens", ",", "estrogens", "stimulate", "outgrowth", "of", "bone", "marrow-derived", "erythroid", "progenitor", "cells", "and", "delay", "their", "maturation", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 7, 8, 8, 8, 8, 0, 0, 0, 0, 0 ]
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35	[ "To", "address", "potential", "mechanisms", "by", "which", "estrogens", "suppress", "erythropoiesis", ",", "we", "have", "examined", "their", "effects", "on", "GATA-1", ",", "an", "erythroid", "transcription", "factor", "that", "participates", "in", "the", "regulation", "of", "the", "majority", "of", "erythroid", "cell-specific", "genes", "and", "is", "necessary", "for", "full", "maturation", "of", "erythrocytes", "." ]	[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9, 0, 0, 9, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 0, 0, 0, 0, 7, 0 ]
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38	[ "GATA-1", "and", "ER", "bind", "to", "each", "other", "in", "vitro", "in", "the", "absence", "of", "DNA", "." ]	[ 9, 0, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
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42	[ "(", "ABSTRACT", "TRUNCATED", "AT", "250", "WORDS", ")" ]	[ 0, 0, 0, 0, 0, 0, 0 ]
43	[ "Mouse", "interleukin-2", "receptor", "alpha", "gene", "expression", "." ]	[ 1, 2, 2, 2, 2, 0, 0 ]
44	[ "Interleukin-1", "and", "interleukin-2", "control", "transcription", "via", "distinct", "cis-acting", "elements", "." ]	[ 9, 0, 9, 0, 0, 0, 0, 1, 2, 0 ]
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47	[ "The", "transcriptional", "response", "of", "the", "IL-2R", "alpha", "gene", "to", "stimulation", "by", "IL-1", "+", "IL-2", "is", "biphasic", "." ]	[ 0, 0, 0, 0, 0, 1, 2, 2, 0, 0, 0, 9, 0, 9, 0, 0, 0 ]
48	[ "IL-1", "induces", "a", "rapid", ",", "protein", "synthesis-independent", "appearance", "of", "IL-2R", "alpha", "mRNA", "that", "is", "blocked", "by", "inhibitors", "of", "NF-kappa", "B", "activation", "." ]	[ 9, 0, 0, 0, 0, 0, 0, 0, 0, 3, 4, 4, 0, 0, 0, 0, 0, 0, 9, 10, 0, 0 ]
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53	[ "IL-2", "responsiveness", "requires", "three", "distinct", "elements", "within", "the", "enhancer", "." ]	[ 9, 0, 0, 0, 0, 1, 0, 0, 1, 0 ]
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55	[ "Hematopoietic", "lineage", "commitment", ":", "role", "of", "transcription", "factors", "." ]	[ 7, 8, 0, 0, 0, 0, 9, 10, 0 ]
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Dataset Card for JNLPBA

Dataset Summary

The data came from the GENIA version 3.02 corpus (Kim et al., 2003). This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus.

Supported Tasks and Leaderboards

NER

Languages

English

Dataset Structure

Data Instances

{ 'id': '1', 'tokens': ['IL-2', 'gene', 'expression', 'and', 'NF-kappa', 'B', 'activation', 'through', 'CD28', 'requires', 'reactive', 'oxygen', 'production', 'by', '5-lipoxygenase', '.'], 'ner_tags': [1, 2, 0, 0, 9, 10, 0, 0, 9, 0, 0, 0, 0, 0, 9, 0], }

Data Fields

id: Sentence identifier.
tokens: Array of tokens composing a sentence.
ner_tags: Array of tags, where 0 indicates no bio-entity mentioned, 1 signals the first token of a bio-entity and 2 the subsequent bio-entity tokens.

Data Splits

Train samples: 37094 Validation samples: 7714

Dataset Creation

Curation Rationale

[Needs More Information]

Source Data

Initial Data Collection and Normalization

[Needs More Information]

Who are the source language producers?

[Needs More Information]

Annotations

Annotation process

[Needs More Information]

Who are the annotators?

[Needs More Information]

Personal and Sensitive Information

[Needs More Information]

Considerations for Using the Data

Social Impact of Dataset

[Needs More Information]

Discussion of Biases

[Needs More Information]

Other Known Limitations

[Needs More Information]

Additional Information

Dataset Curators

[Needs More Information]

Licensing Information

[Needs More Information]

Citation Information

@inproceedings{collier-kim-2004-introduction, title = "Introduction to the Bio-entity Recognition Task at {JNLPBA}", author = "Collier, Nigel and Kim, Jin-Dong", booktitle = "Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications ({NLPBA}/{B}io{NLP})", month = aug # " 28th and 29th", year = "2004", address = "Geneva, Switzerland", publisher = "COLING", url = "https://aclanthology.org/W04-1213", pages = "73--78", }