The ITI TXM corpora: Tissue expressions and protein-protein interactions

Beatrice Alex; Claire Grover; Barry Haddow; Mijail Kabadjov; Ewan Klein; Michael Matthews; Stuart Roebuck; Richard Tobin; Xinglong Wang

The ITI TXM corpora: Tissue expressions and protein-protein interactions

Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjov, Ewan Klein, Michael Matthews, Stuart Roebuck, Richard Tobin, Xinglong Wang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

We report on two large corpora of semantically annotated full-text biomedical research papers created in order to develop information extraction (IE) tools for the TXM project. Both corpora have been annotated with a range of entities (CellLine, Complex, Developmental-Stage, Disease, DrugCompound, ExperimentalMethod, Fragment, Fusion, GOMOP, Gene, Modification, mRNAcDNA, Mutant, Protein, Tissue), normalisations of selected entities to the NCBI Taxonomy, RefSeq, EntrezGene, ChEBI and MeSH and enriched relations (protein-protein interactions, tissue expressions and fragment- or mutant-protein relations). While one corpus targets protein-protein interactions (PPIs), the focus of other is on tissue expressions (TEs). This paper describes the selected markables and the annotation process of the ITI TXM corpora, and provides a detailed breakdown of the inter-annotator agreement (IAA).

Original language	English
Title of host publication	LREC 2008 Workshop
Subtitle of host publication	Building and evaluating resources for biomedical text mining
Number of pages	8
Publication status	Published - May 2008

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Alex Grover 2008 The ITI TXM Corpora Tissue Expressions and Protein Protein Interactions

http://www.nactem.ac.uk/workshops/lrec08_ws/abstracts.htm

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@inproceedings{a479114af13e47c18cbfc7668eb8abb8,

title = "The ITI TXM corpora: Tissue expressions and protein-protein interactions",

abstract = "We report on two large corpora of semantically annotated full-text biomedical research papers created in order to develop information extraction (IE) tools for the TXM project. Both corpora have been annotated with a range of entities (CellLine, Complex, Developmental-Stage, Disease, DrugCompound, ExperimentalMethod, Fragment, Fusion, GOMOP, Gene, Modification, mRNAcDNA, Mutant, Protein, Tissue), normalisations of selected entities to the NCBI Taxonomy, RefSeq, EntrezGene, ChEBI and MeSH and enriched relations (protein-protein interactions, tissue expressions and fragment- or mutant-protein relations). While one corpus targets protein-protein interactions (PPIs), the focus of other is on tissue expressions (TEs). This paper describes the selected markables and the annotation process of the ITI TXM corpora, and provides a detailed breakdown of the inter-annotator agreement (IAA).",

author = "Beatrice Alex and Claire Grover and Barry Haddow and Mijail Kabadjov and Ewan Klein and Michael Matthews and Stuart Roebuck and Richard Tobin and Xinglong Wang",

year = "2008",

month = may,

language = "English",

booktitle = "LREC 2008 Workshop",

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TY - GEN

T1 - The ITI TXM corpora

T2 - Tissue expressions and protein-protein interactions

AU - Alex, Beatrice

AU - Grover, Claire

AU - Haddow, Barry

AU - Kabadjov, Mijail

AU - Klein, Ewan

AU - Matthews, Michael

AU - Roebuck, Stuart

AU - Tobin, Richard

AU - Wang, Xinglong

PY - 2008/5

Y1 - 2008/5

N2 - We report on two large corpora of semantically annotated full-text biomedical research papers created in order to develop information extraction (IE) tools for the TXM project. Both corpora have been annotated with a range of entities (CellLine, Complex, Developmental-Stage, Disease, DrugCompound, ExperimentalMethod, Fragment, Fusion, GOMOP, Gene, Modification, mRNAcDNA, Mutant, Protein, Tissue), normalisations of selected entities to the NCBI Taxonomy, RefSeq, EntrezGene, ChEBI and MeSH and enriched relations (protein-protein interactions, tissue expressions and fragment- or mutant-protein relations). While one corpus targets protein-protein interactions (PPIs), the focus of other is on tissue expressions (TEs). This paper describes the selected markables and the annotation process of the ITI TXM corpora, and provides a detailed breakdown of the inter-annotator agreement (IAA).

AB - We report on two large corpora of semantically annotated full-text biomedical research papers created in order to develop information extraction (IE) tools for the TXM project. Both corpora have been annotated with a range of entities (CellLine, Complex, Developmental-Stage, Disease, DrugCompound, ExperimentalMethod, Fragment, Fusion, GOMOP, Gene, Modification, mRNAcDNA, Mutant, Protein, Tissue), normalisations of selected entities to the NCBI Taxonomy, RefSeq, EntrezGene, ChEBI and MeSH and enriched relations (protein-protein interactions, tissue expressions and fragment- or mutant-protein relations). While one corpus targets protein-protein interactions (PPIs), the focus of other is on tissue expressions (TEs). This paper describes the selected markables and the annotation process of the ITI TXM corpora, and provides a detailed breakdown of the inter-annotator agreement (IAA).

M3 - Conference contribution

BT - LREC 2008 Workshop

ER -

The ITI TXM corpora: Tissue expressions and protein-protein interactions

Abstract

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