Literature DB >> 22789588

MyMiner: a web application for computer-assisted biocuration and text annotation.

David Salgado1, Martin Krallinger, Marc Depaule, Elodie Drula, Ashish V Tendulkar, Florian Leitner, Alfonso Valencia, Christophe Marcelle.   

Abstract

MOTIVATION: The exponential growth of scientific literature has resulted in a massive amount of unstructured natural language data that cannot be directly handled by means of bioinformatics tools. Such tools generally require structured data, often generated through a cumbersome process of manual literature curation. Herein, we present MyMiner, a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems. MyMiner allows easy classification and labelling of textual data according to user-specified classes as well as predefined biological entities. The usefulness and efficiency of this application have been tested for a range of real-life annotation scenarios of various research topics. AVAILABILITY: http://myminer.armi.monash.edu.au.

Mesh:

Year:  2012        PMID: 22789588     DOI: 10.1093/bioinformatics/bts435

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  17 in total

1.  Beyond accuracy: creating interoperable and scalable text-mining web services.

Authors:  Chih-Hsuan Wei; Robert Leaman; Zhiyong Lu
Journal:  Bioinformatics       Date:  2016-02-16       Impact factor: 6.937

Review 2.  Community challenges in biomedical text mining over 10 years: success, failure and the future.

Authors:  Chung-Chi Huang; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-05-01       Impact factor: 11.622

3.  An extensive review of tools for manual annotation of documents.

Authors:  Mariana Neves; Jurica Ševa
Journal:  Brief Bioinform       Date:  2021-01-18       Impact factor: 11.622

4.  Mutationmapper: a tool to aid the mapping of protein mutation data.

Authors:  Shabana Vohra; Philip C Biggin
Journal:  PLoS One       Date:  2013-08-09       Impact factor: 3.240

5.  Evaluating the impact of pre-annotation on annotation speed and potential bias: natural language processing gold standard development for clinical named entity recognition in clinical trial announcements.

Authors:  Todd Lingren; Louise Deleger; Katalin Molnar; Haijun Zhai; Jareen Meinzen-Derr; Megan Kaiser; Laura Stoutenborough; Qi Li; Imre Solti
Journal:  J Am Med Inform Assoc       Date:  2013-09-03       Impact factor: 4.497

6.  The CHEMDNER corpus of chemicals and drugs and its annotation principles.

Authors:  Martin Krallinger; Obdulia Rabal; Florian Leitner; Miguel Vazquez; David Salgado; Zhiyong Lu; Robert Leaman; Yanan Lu; Donghong Ji; Daniel M Lowe; Roger A Sayle; Riza Theresa Batista-Navarro; Rafal Rak; Torsten Huber; Tim Rocktäschel; Sérgio Matos; David Campos; Buzhou Tang; Hua Xu; Tsendsuren Munkhdalai; Keun Ho Ryu; S V Ramanan; Senthil Nathan; Slavko Žitnik; Marko Bajec; Lutz Weber; Matthias Irmer; Saber A Akhondi; Jan A Kors; Shuo Xu; Xin An; Utpal Kumar Sikdar; Asif Ekbal; Masaharu Yoshioka; Thaer M Dieb; Miji Choi; Karin Verspoor; Madian Khabsa; C Lee Giles; Hongfang Liu; Komandur Elayavilli Ravikumar; Andre Lamurias; Francisco M Couto; Hong-Jie Dai; Richard Tzong-Han Tsai; Caglar Ata; Tolga Can; Anabel Usié; Rui Alves; Isabel Segura-Bedmar; Paloma Martínez; Julen Oyarzabal; Alfonso Valencia
Journal:  J Cheminform       Date:  2015-01-19       Impact factor: 5.514

7.  Egas: a collaborative and interactive document curation platform.

Authors:  David Campos; Jóni Lourenço; Sérgio Matos; José Luís Oliveira
Journal:  Database (Oxford)       Date:  2014-06-11       Impact factor: 3.451

8.  PubTator: a web-based text mining tool for assisting biocuration.

Authors:  Chih-Hsuan Wei; Hung-Yu Kao; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2013-05-22       Impact factor: 16.971

9.  Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.

Authors:  Mariana Neves; Alexander Damaschun; Nancy Mah; Fritz Lekschas; Stefanie Seltmann; Harald Stachelscheid; Jean-Fred Fontaine; Andreas Kurtz; Ulf Leser
Journal:  Database (Oxford)       Date:  2013-04-18       Impact factor: 3.451

10.  MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.

Authors:  Pankaj Kumar; Anna Halama; Shahina Hayat; Anja M Billing; Manish Gupta; Noha A Yousri; Gregory M Smith; Karsten Suhre
Journal:  Biomed Res Int       Date:  2015-08-25       Impact factor: 3.411

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