Evidence map›Paper›PMID 25168057›Full record

ArticleDatabase : the journal of biological databases and curation2014

LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations.

Hong-Jie Dai, Johnny Chi-Yang Wu, Wei-San Lin, Aaron James F Reyes, Mira Anne C Dela Rosa, Shabbir Syed-Abdul, Richard Tzong-Han Tsai, Wen-Lian Hsu

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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 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. CBD: a biomarker database for colorectal cancer.Database : the journal of biological databases and curation · 2018
    Article
  7. Article
  8. Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy.Database : the journal of biological databases and curation · 2017
    Article
  9. MET network in PubMed: a text-mined network visualization and curation system.Database : the journal of biological databases and curation · 2016
    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

8 authors.

Hong-Jie DaiGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China hjdai@tmu.edu.tw.
Johnny Chi-Yang WuGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.
Wei-San LinGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.
Aaron James F ReyesGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.
Mira Anne C Dela RosaGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.
Shabbir Syed-AbdulGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.
Richard Tzong-Han TsaiGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.
Wen-Lian HsuGraduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Xin Street, Taipei, Taiwan 110, Republic of China, Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China, Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, Taiwan 115, Republic of China and Department of Computer Science and Information Engineering, National Central University, 300, Jhongda Road, Jhongli City, Taoyuan County, Taiwan 320, Republic of China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Biomarkers are biomolecules in the human body that can indicate disease states and abnormal biological processes. Biomarkers are often used during clinical trials to identify patients with cancers. Although biomedical research related to biomarkers has increased over the years and substantial effort has been expended to obtain results in these studies, the specific results obtained often contain ambiguities, and the results might contradict each other. Therefore, the information gathered from these studies must be appropriately integrated and organized to facilitate experimentation on biomarkers. In this study, we used liver cancer as the target and developed a text-mining-based curation system named LiverCancerMarkerRIF, which allows users to retrieve biomarker-related narrations and curators to curate supporting evidence on liver cancer biomarkers directly while browsing PubMed. In contrast to most of the other curation tools that require curators to navigate away from PubMed and accommodate distinct user interfaces or Web sites to complete the curation process, our system provides a user-friendly method for accessing text-mining-aided information and a concise interface to assist curators while they remain at the PubMed Web site. Biomedical text-mining techniques are applied to automatically recognize biomedical concepts such as genes, microRNA, diseases and investigative technologies, which can be used to evaluate the potential of a certain gene as a biomarker. Through the participation in the BioCreative IV user-interactive task, we examined the feasibility of using this novel type of augmented browsing-based curation method, and collaborated with curators to curate biomarker evidential sentences related to liver cancer. The positive feedback received from curators indicates that the proposed method can be effectively used for curation. A publicly available online database containing all the aforementioned information has been constructed at http://btm.tmu.edu.tw/livercancermarkerrif in an attempt to facilitate biomarker-related studies. DATABASE URL: http://btm.tmu.edu.tw/LiverCancerMarkerRIF/

Indexed as

Biomarkers, TumorLiver NeoplasmsComputational BiologyDatabase Management SystemsData CurationData MiningHumansInternetUser-Computer InterfaceBiomarkers, Tumor

Identifiers

PMID25168057
PMCPMC4147259

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.