Whatizit protocols

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Whatizit specifications


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


  • person_outline Dietrich Rebholz-Schuhmann <>

Publication for Whatizit

Whatizit in pipelines

PMCID: 2723093
PMID: 19635172
DOI: 10.1186/1471-2105-10-233

[…] may be of little practical significance, but it does necessitate the use of weaker scoring criteria than are generally applied to the evaluation of gpi extraction methods. consequently we excluded whatizit from most of the comparative evaluations undertaken for this paper, although we do separately assess its performance on our chosen gpi corpora., it is also worth noting that, as the whatizit […]

PMCID: 2723093
PMID: 19635172
DOI: 10.1186/1471-2105-10-233

[…] that very high levels of recall (around 90%) would be achievable using a system that combined all three of them, suggesting that hybrid systems may prove highly effective. (indeed, this is what whatizit already does in the context of mapping names to uniprot identifiers.), thirdly, our baseline approach using perl regular expressions was deliberately simple. given that it performed […]

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Whatizit in publications

PMCID: 5763300
PMID: 29322912
DOI: 10.1186/s12859-017-1978-0

[…] final cell type dictionary consists of 3838 term referring to 2180 distinct cell types while the cell line dictionary consists of 76,747 terms belonging to 38,605 distinct cell lines., 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 […]

PMCID: 5572517
PMID: 28875048
DOI: 10.4258/hir.2017.23.3.141

[…] 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., web mining, a part text mining […]

PMCID: 5461726
PMID: 28587637
DOI: 10.1186/s13326-017-0131-3

[…] a total of 104,434 and 29,846 terms respectively. these dictionaries are available from ftp://ftp.ebi.ac.uk/pub/databases/pmc/otar/., 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 […]

PMCID: 5018193
PMID: 27613112
DOI: 10.1186/s13326-016-0096-7

[…] 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 […]

PMCID: 4834204
PMID: 27087307
DOI: 10.1093/database/baw049

[…] the development of chemical ner systems for scientific literature, by providing a large-scale standard corpus (). typical approaches applied to chemical ner in representative systems such as whatizit (), oscar3/4 (, ), chemspot () and tmchem () included dictionary lookup (), machine learning-based models (, , ) and hybrid methods that combined a dictionary with a machine learning-based […]

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

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