Evidence map›Paper›PMID 25052701›Full record

ArticleDatabase : the journal of biological databases and curation2014

Assisting manual literature curation for protein-protein interactions using BioQRator.

Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W John Wilbur

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 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. BioKC: a collaborative platform for curation and annotation of molecular interactions.Database : the journal of biological databases and curation · 2024
    Article
  2. Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023
    Review
  3. Review
  4. Article
  5. Article
  6. Constructing knowledge graphs and their biomedical applications.Computational and structural biotechnology journal · 2020
    Review
  7. Article
  8. Article
  9. Article
  10. BioC viewer: a web-based tool for displaying and merging annotations in BioC.Database : the journal of biological databases and curation · 2016
    Article
  11. neXtA5: accelerating annotation of articles via automated approaches in neXtProt.Database : the journal of biological databases and curation · 2016
    Article
  12. Mining clinical attributes of genomic variants through assisted literature curation in Egas.Database : the journal of biological databases and curation · 2016
    Article
  13. Text Mining for Protein Docking.PLoS computational biology · 2015
    Article
  14. Article
  15. 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

5 authors.

Dongseop KwonDepartment of Computer Engineering, Myongji University, Yongin 449-728, South Korea, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Department of Biomedical Informatics, Asan Medical Center, Seoul 138-736, South Korea and Institute for Research in Immunology and Cancer, Université de Montréal, Montréal QC H3C 3J7, Canada dongseop@mju.ac.kr.
Sun KimDepartment of Computer Engineering, Myongji University, Yongin 449-728, South Korea, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Department of Biomedical Informatics, Asan Medical Center, Seoul 138-736, South Korea and Institute for Research in Immunology and Cancer, Université de Montréal, Montréal QC H3C 3J7, Canada sun.kim@nih.gov.
Soo-Yong ShinDepartment of Computer Engineering, Myongji University, Yongin 449-728, South Korea, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Department of Biomedical Informatics, Asan Medical Center, Seoul 138-736, South Korea and Institute for Research in Immunology and Cancer, Université de Montréal, Montréal QC H3C 3J7, Canada.
Andrew Chatr-aryamontriDepartment of Computer Engineering, Myongji University, Yongin 449-728, South Korea, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Department of Biomedical Informatics, Asan Medical Center, Seoul 138-736, South Korea and Institute for Research in Immunology and Cancer, Université de Montréal, Montréal QC H3C 3J7, Canada.
W John WilburDepartment of Computer Engineering, Myongji University, Yongin 449-728, South Korea, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Department of Biomedical Informatics, Asan Medical Center, Seoul 138-736, South Korea and Institute for Research in Immunology and Cancer, Université de Montréal, Montréal QC H3C 3J7, Canada.

Funding

Natural Language Processing Techniques To Enhance Information Access.ZIALM000090 · NLM · NATIONAL LIBRARY OF MEDICINE · PI WILBUR, WILLY · 2009 to 2015
$3.4M
General and Semi-supervised Machine Learning Applied to BioinformaticsZIALM000089 · NLM · NATIONAL LIBRARY OF MEDICINE · PI WILBUR, WILLY · 2009 to 2015
$3.2M
Free Text Gene Name RecognitionZIALM000093 · NLM · NATIONAL LIBRARY OF MEDICINE · PI WILBUR, WILLY · 2009 to 2015
$1.6M
A Document Processing SystemZIALM000022 · NLM · NATIONAL LIBRARY OF MEDICINE · PI WILBUR, WILLY · 2009 to 2015
$1.3M
Intramural NIH HHS
6 · The paper itself

Abstract

The time-consuming nature of manual curation and the rapid growth of biomedical literature severely limit the number of articles that database curators can scrutinize and annotate. Hence, semi-automatic tools can be a valid support to increase annotation throughput. Although a handful of curation assistant tools are already available, to date, little has been done to formally evaluate their benefit to biocuration. Moreover, most curation tools are designed for specific problems. Thus, it is not easy to apply an annotation tool for multiple tasks. BioQRator is a publicly available web-based tool for annotating biomedical literature. It was designed to support general tasks, i.e. any task annotating entities and relationships. In the BioCreative IV edition, BioQRator was tailored for protein- protein interaction (PPI) annotation by migrating information from PIE the search. The results obtained from six curators showed that the precision on the top 10 documents doubled with PIE the search compared with PubMed search results. It was also observed that the annotation time for a full PPI annotation task decreased for a beginner-intermediate level annotator. This finding is encouraging because text-mining techniques were not directly involved in the full annotation task and BioQRator can be easily integrated with any text-mining resources. Database URL: http://www.bioqrator.org/.

Indexed as

InternetSoftwareData CurationData MiningHumansProtein Interaction Mapping

Identifiers

PMID25052701
PMCPMC4105708

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.