Whatizit protocols

View Whatizit computational protocol

Whatizit statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Chemical entity recognition chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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 in pipelines

 (2)
2009
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 […]

2009
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 […]


To access a full list of citations, you will need to upgrade to our premium service.

Whatizit in publications

 (31)
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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

Whatizit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Whatizit