Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer

Lee, Bernett T. K.; Song, Chun Meng; Yeo, Boon Huat; Chung, Cheuk Wang; Chan, Ying Leong; Lim, Teng Ting; Chua, Yen Bing; Loh, Marie; Ang, Boon Keong; Vijayakumar, Praveen; Liew, Lailing; Lim, Jiahao; Lim, Yun Ping; Wong, Chee-Hong; Chuon, Danny; Rajagopal, G.; Hill, Jeffrey

doi:10.1177/117727190600100005

Cited by 3 publications

(4 citation statements)

References 24 publications

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“…There are several other more specific databases in different diseases, such as the US Environmental Protection Agency Biomarker Database ( https://cfpub.epa.gov/ncea/risk/recordisplay.cfm? deid=85844 ) for children’s healthcare ( 17 ), Tuberculosis Biomarker Database ( https://www.finddx.org/publication/tuberculosis-biomarker-database-2/ ) for tuberculosis ( 18 ), Infectious Disease Biomarker Database ( http://biomarker.cdc.go.kr ) for infectious diseases ( 19 ), Gastric Cancer (Biomarkers) Knowledgebase ( http://biomarkers.bii.a-star.edu.sg/background/gastricCancerBiomarkersKb.php ) for gastric cancer ( 20 ) and Liver Cancer bioMarker Reference Into Function (LiverCancerMarkerRIF) ( http://btm.tmu.edu.tw/LiverCancerMarkerRIF/ ) for liver cancer ( 21 ), which have provided a large amount of useful information for both researchers and clinicians. However, no such biomarker database in CRC has been reported for public usage.…”

Section: Introductionmentioning

confidence: 99%

CBD: a biomarker database for colorectal cancer

et al. 2018

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Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD.Database URL: http://sysbio.suda.edu.cn/CBD/

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Section: Introductionmentioning

confidence: 99%

CBD: a biomarker database for colorectal cancer

et al. 2018

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“…cfm?deid=85844) [16], the Tuberculosis Biomarker Database specifically for tuberculosis (https://www.finddx.org/ publication/tuberculosis-biomarker-database-2/) [17], and the Infectious Disease Biomarker Database dedicated to infectious diseases (http://biomarker.cdc.go.kr) [18]. Furthermore, for oncology-centric research, there is the Gastric Cancer (Biomarkers) Knowledgebase for gastric cancer (http://biomarkers.bii.a-star.edu.sg/background/ gastricCancerBiomarkersKb.php) [19], and the Liver Cancer Biomarker Reference Into Function (LiverCancer-MarkerRIF) tailored for liver cancer (http://btm.tmu.edu. tw/LiverCancerMarkerRIF/) [20].…”

Section: Discussionmentioning

confidence: 99%

“…Databases with more specific pathophysiological focuses include the US Environmental Protection Agency Biomarker Database catering to children's healthcare ( https://cfpub.epa.gov/ncea/risk/recordisplay.cfm?deid=85844 ) [ 16 ], the Tuberculosis Biomarker Database specifically for tuberculosis ( https://www.finddx.org/publication/tuberculosis-biomarker-database-2/ ) [ 17 ], and the Infectious Disease Biomarker Database dedicated to infectious diseases ( http://biomarker.cdc.go.kr ) [ 18 ]. Furthermore, for oncology‐centric research, there is the Gastric Cancer (Biomarkers) Knowledgebase for gastric cancer ( http://biomarkers.bii.a-star.edu.sg/background/gastricCancerBiomarkersKb.php ) [ 19 ], and the Liver Cancer Biomarker Reference Into Function (LiverCancerMarkerRIF) tailored for liver cancer ( http://btm.tmu.edu.tw/LiverCancerMarkerRIF/ ) [ 20 ]. An eye biomarker database released by us provided a standardized platform for ocular biomarkers, and a driving force for future ophthalmic precision medicine [ 21 ].…”

Section: Discussionmentioning

confidence: 99%

CBD2: A functional biomarker database for colorectal cancer

Zhang,

Li,

et al. 2023

iMeta

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The rapidly evolving landscape of biomarkers for colorectal cancer (CRC) necessitates an integrative, updated repository. In response, we constructed the Colorectal Cancer Biomarker Database (CBD), which collected and displayed the curated biomedicine information for 870 CRC biomarkers in the previous study. Building on CBD, we have now developed CBD2, which includes information on 1569 newly reported biomarkers derived from different biological sources (DNA, RNA, protein, and others) and clinical applications (diagnosis, treatment, and prognosis). CBD2 also incorporates information on nonbiomarkers that have been identified as unsuitable for use as biomarkers in CRC. A key new feature of CBD2 is its network analysis function, by which users can investigate the visible and topological network between biomarkers and identify their relevant pathways. CBD2 also allows users to query a series of chemicals, drug combinations, or multiple targets, to enable multidrug, multitarget, multipathway analyses, toward facilitating the design of polypharmacological treatments for CRC. CBD2 is freely available at http://www.eyeseeworld.com/cbd.

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“…Despite intensified interest and research, however, the rate of development of novel biomarkers has been falling ( 6 ), suggesting that a resource that leverages existing data is overdue. At present the databases containing information about biomarkers are focused predominantly on cancer: early detection research network ( 7 ), gastric cancer knowledgebase ( 8 ), integrated cancer biomarker information system ( 9 ) and database for cancer, asthma and autism for children's study ( 10 ). Even here, although 15–20% of cancers are linked to infectious diseases and chronic infection causes cancer ( 11 ), no systematic effort has been described for integrating information from the cancer biomarker and the infectious disease domains.…”

Section: Introductionmentioning

confidence: 99%

IDBD: Infectious Disease Biomarker Database

Yang

Ryu

Cho

et al. 2007

Nucleic Acids Research

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Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

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Gastric Cancer (Biomarkers) Knowledgebase (GCBKB): A Curated and Fully Integrated Knowledgebase of Putative Biomarkers Related to Gastric Cancer

Cited by 3 publications

References 24 publications

CBD: a biomarker database for colorectal cancer

CBD: a biomarker database for colorectal cancer

CBD2: A functional biomarker database for colorectal cancer

IDBD: Infectious Disease Biomarker Database

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