Evidence map›Paper›PMID 24961236›Full record

ArticleDatabase : the journal of biological databases and curation2014

BioC implementations in Go, Perl, Python and Ruby.

Wanli Liu, Rezarta Islamaj Doğan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W John Wilbur, Donald C Comeau

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. BioC viewer: a web-based tool for displaying and merging annotations in BioC.Database : the journal of biological databases and curation · 2016
    Article
  6. Article
  7. BioC interoperability track overview.Database : the journal of biological databases and curation · 2014
    Review
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Wanli LiuNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
Rezarta Islamaj DoğanNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
Dongseop KwonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
Hernani MarquesNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
Fabio RinaldiNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
W John WilburNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland.
Donald C ComeauNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA, Department of Computer Engineering, Myongji University, Yongin, Republic of Korea and Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland comeau@ncbi.nlm.nih.gov.

Funding

Natural Language Processing Techniques To Enhance Information Access.ZIALM000090 · NLM · NATIONAL LIBRARY OF MEDICINE · PI WILBUR, WILLY · 2009 to 2015
$3.4M
Intramural NIH HHS
6 · The paper itself

Abstract

As part of a communitywide effort for evaluating text mining and information extraction systems applied to the biomedical domain, BioC is focused on the goal of interoperability, currently a major barrier to wide-scale adoption of text mining tools. BioC is a simple XML format, specified by DTD, for exchanging data for biomedical natural language processing. With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. We extend BioC to Perl, Python, Go and Ruby. We used SWIG to extend the C++ implementation for Perl and one Python implementation. A second Python implementation and the Ruby implementation use native data structures and libraries. BioC is also implemented in the Google language Go. BioC modules are functional in all of these languages, which can facilitate text mining tasks. BioC implementations are freely available through the BioC site: http://bioc.sourceforge.net. Database URL: http://bioc.sourceforge.net/

Indexed as

Programming LanguagesAlgorithmsDatabases as TopicData MiningUser-Computer Interface

Identifiers

PMID24961236
PMCPMC4067548

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.