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Protocols

Whatizit specifications

Information


Unique identifier OMICS_01200
Name Whatizit
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Dietrich Rebholz-Schuhmann

Publication for Whatizit

Whatizit citations

 (44)
call_split

Usage of cell nomenclature in biomedical literature

2017
BMC Bioinformatics
PMCID: 5763300
PMID: 29322912
DOI: 10.1186/s12859-017-1978-0
call_split See protocol

[…] We used the Whatizit [] entity recognition pipeline to annotate cell type and cell line names in the Open Access full text articles by using our dictionaries on cell types and cell lines. Whatizit employs taggers […]

library_books

Semantic annotation in biomedicine: the current landscape

2017
J Biomed Semantics
PMCID: 5610427
PMID: 28938912
DOI: 10.1186/s13326-017-0153-x

[…] mbiguation with appropriate concepts, BeCAS makes use of Gimli, an open source tool that implements Conditional Random Fields (CRF) for named entity recognition in biomedical texts [] (see section). Whatizit is a freely available Web service for annotation of biomedical texts with concepts from several ontologies and structured vocabularies []. Like previously described tools, it is also develope […]

library_books

Text Mining in Biomedical Domain with Emphasis on Document Clustering

2017
Healthc Inform Res
PMCID: 5572517
PMID: 28875048
DOI: 10.4258/hir.2017.23.3.141

[…] xt mining in the field of biomarkers. (1) MeinfoText [] is a tool that provides knowledge about associations between gene methylation and cancer through the mining of large amounts of literature. (2) Whatizit [] is a tool that identifies terms from a web source, such as PubMed abstracts, and then links them to the corresponding entries in bioinformatics databases. […]

library_books

SciLite: a platform for displaying text mined annotations as a means to link research articles with biological data

2017
Wellcome Open Res
PMCID: 5527546
PMID: 28948232
DOI: 10.21956/wellcomeopenres.10999.r18949

[…] ; ; ; ). There are a number of text-mining based tools that have been developed to facilitate automated extraction of various article types and biological concepts, such as Textpresso ( ), iHOP ( ), Whatizit ( ), EAGLi ( ; ) EVEX ( ), PubTator ( ) and Argo ( ). Among these tools, Textpresso has been significantly adapted by data providers and the curation community to triage articles for curation […]

library_books

Literature evidence in open targets a target validation platform

2017
J Biomed Semantics
PMCID: 5461726
PMID: 28587637
DOI: 10.1186/s13326-017-0131-3

[…] We used the Europe PMC text-mining pipeline, which is based on Whatizit [], to annotate target and disease names in text with the two dictionaries described above. Although we reduce a very high level of ambiguity by applying the dictionary refinement process bef […]

library_books

Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition

2016
J Biomed Semantics
PMCID: 5018193
PMID: 27613112
DOI: 10.1186/s13326-016-0096-7

[…] ms from Biological Process (F-measure 0.42) and Molecular Function (F-measure 0.14) were much more difficult to recognize in text. Campos et al. present a framework called Neji and compare it against Whatizit on the CRAFT corpus []; they find similar best performance (Cellular Component 0.70, Biological Process/Molecular Function 0.35). Other work explored the impact of case sensitivity and inform […]

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Whatizit institution(s)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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