Literature DB >> 31838514

An extensive review of tools for manual annotation of documents.

Mariana Neves1, Jurica Ševa1.   

Abstract

MOTIVATION: Annotation tools are applied to build training and test corpora, which are essential for the development and evaluation of new natural language processing algorithms. Further, annotation tools are also used to extract new information for a particular use case. However, owing to the high number of existing annotation tools, finding the one that best fits particular needs is a demanding task that requires searching the scientific literature followed by installing and trying various tools.
METHODS: We searched for annotation tools and selected a subset of them according to five requirements with which they should comply, such as being Web-based or supporting the definition of a schema. We installed the selected tools (when necessary), carried out hands-on experiments and evaluated them using 26 criteria that covered functional and technical aspects. We defined each criterion on three levels of matches and a score for the final evaluation of the tools.
RESULTS: We evaluated 78 tools and selected the following 15 for a detailed evaluation: BioQRator, brat, Catma, Djangology, ezTag, FLAT, LightTag, MAT, MyMiner, PDFAnno, prodigy, tagtog, TextAE, WAT-SL and WebAnno. Full compliance with our 26 criteria ranged from only 9 up to 20 criteria, which demonstrated that some tools are comprehensive and mature enough to be used on most annotation projects. The highest score of 0.81 was obtained by WebAnno (of a maximum value of 1.0).
© The Author(s) 2019. Published by Oxford University Press. All rights reserved.

Entities:  

Keywords:  annotation tools; corpus construction; manual annotation

Year:  2021        PMID: 31838514      PMCID: PMC7820865          DOI: 10.1093/bib/bbz130

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  35 in total

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

Authors:  David Salgado; Martin Krallinger; Marc Depaule; Elodie Drula; Ashish V Tendulkar; Florian Leitner; Alfonso Valencia; Christophe Marcelle
Journal:  Bioinformatics       Date:  2012-07-12       Impact factor: 6.937

2.  The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions.

Authors:  María Herrero-Zazo; Isabel Segura-Bedmar; Paloma Martínez; Thierry Declerck
Journal:  J Biomed Inform       Date:  2013-07-29       Impact factor: 6.317

3.  Coreferential Relations in Basque: The Annotation Process.

Authors:  Klara Ceberio; Itziar Aduriz; Arantza Díaz de Ilarraza; Ines Garcia-Azkoaga
Journal:  J Psycholinguist Res       Date:  2018-04

4.  Automatic semantic classification of scientific literature according to the hallmarks of cancer.

Authors:  Simon Baker; Ilona Silins; Yufan Guo; Imran Ali; Johan Högberg; Ulla Stenius; Anna Korhonen
Journal:  Bioinformatics       Date:  2015-10-09       Impact factor: 6.937

5.  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

6.  Deep learning of mutation-gene-drug relations from the literature.

Authors:  Kyubum Lee; Byounggun Kim; Yonghwa Choi; Sunkyu Kim; Wonho Shin; Sunwon Lee; Sungjoon Park; Seongsoon Kim; Aik Choon Tan; Jaewoo Kang
Journal:  BMC Bioinformatics       Date:  2018-01-25       Impact factor: 3.169

7.  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

8.  Event extraction across multiple levels of biological organization.

Authors:  Sampo Pyysalo; Tomoko Ohta; Makoto Miwa; Han-Cheol Cho; Jun'ichi Tsujii; Sophia Ananiadou
Journal:  Bioinformatics       Date:  2012-09-15       Impact factor: 6.937

9.  Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings.

Authors:  Anne-Dominique Pham; Aurélie Névéol; Thomas Lavergne; Daisuke Yasunaga; Olivier Clément; Guy Meyer; Rémy Morello; Anita Burgun
Journal:  BMC Bioinformatics       Date:  2014-08-07       Impact factor: 3.169

10.  Automating Quality Measures for Heart Failure Using Natural Language Processing: A Descriptive Study in the Department of Veterans Affairs.

Authors:  Jennifer Hornung Garvin; Youngjun Kim; Glenn Temple Gobbel; Michael E Matheny; Andrew Redd; Bruce E Bray; Paul Heidenreich; Dan Bolton; Julia Heavirland; Natalie Kelly; Ruth Reeves; Megha Kalsy; Mary Kane Goldstein; Stephane M Meystre
Journal:  JMIR Med Inform       Date:  2018-01-15
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  4 in total

1.  TeamTat: a collaborative text annotation tool.

Authors:  Rezarta Islamaj; Dongseop Kwon; Sun Kim; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

2.  TAX-Corpus: Taxonomy based Annotations for Colonoscopy Evaluation.

Authors:  Shorabuddin Syed; Adam Jackson Angel; Hafsa Bareen Syeda; Carole Franc Jennings; Joseph VanScoy; Mahanazuddin Syed; Melody Greer; Sudeepa Bhattacharyya; Shaymaa Al-Shukri; Meredith Zozus; Fred Prior; Benjamin Tharian
Journal:  Biomed Eng Syst Technol Int Jt Conf BIOSTEC Revis Sel Pap       Date:  2022-02

3.  A computational ecosystem to support eHealth Knowledge Discovery technologies in Spanish.

Authors:  Alejandro Piad-Morffis; Yoan Gutiérrez; Yudivian Almeida-Cruz; Rafael Muñoz
Journal:  J Biomed Inform       Date:  2020-07-24       Impact factor: 6.317

4.  MedTAG: a portable and customizable annotation tool for biomedical documents.

Authors:  Fabio Giachelle; Ornella Irrera; Gianmaria Silvello
Journal:  BMC Med Inform Decis Mak       Date:  2021-12-18       Impact factor: 2.796

  4 in total

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