Literature DB >> 26609498

Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources.

Rajarshi Guha1, Dac-Trung Nguyen1, Noel Southall1, Ajit Jadhav1.   

Abstract

Over the last 20 years, there has been an explosion in the amount and type of biological and chemical data that has been made publicly available in a variety of online databases. While this means that vast amounts of information can be found online, there is no guarantee that it can be found easily (or at all). A scientist searching for a specific piece of information is faced with a daunting task - many databases have overlapping content, use their own identifiers and, in some cases, have arcane and unintuitive user interfaces. In this overview, a variety of well known data sources for chemical and biological information are highlighted, focusing on those most useful for chemical biology research. The issue of using multiple data sources together and the associated problems such as identifier disambiguation are highlighted. A brief discussion is then provided on Tripod, a recently developed platform that supports the integration of arbitrary data sources, providing users a simple interface to search across a federated collection of resources.

Entities:  

Year:  2012        PMID: 26609498      PMCID: PMC4655879          DOI: 10.1002/9780470559277.ch110262

Source DB:  PubMed          Journal:  Curr Protoc Chem Biol        ISSN: 2160-4762


  44 in total

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2.  ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

Authors:  Alexander Lachmann; Huilei Xu; Jayanth Krishnan; Seth I Berger; Amin R Mazloom; Avi Ma'ayan
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3.  Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research.

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Journal:  J Chem Inf Model       Date:  2010-07-26       Impact factor: 4.956

4.  Development of human protein reference database as an initial platform for approaching systems biology in humans.

Authors:  Suraj Peri; J Daniel Navarro; Ramars Amanchy; Troels Z Kristiansen; Chandra Kiran Jonnalagadda; Vineeth Surendranath; Vidya Niranjan; Babylakshmi Muthusamy; T K B Gandhi; Mads Gronborg; Nieves Ibarrola; Nandan Deshpande; K Shanker; H N Shivashankar; B P Rashmi; M A Ramya; Zhixing Zhao; K N Chandrika; N Padma; H C Harsha; A J Yatish; M P Kavitha; Minal Menezes; Dipanwita Roy Choudhury; Shubha Suresh; Neelanjana Ghosh; R Saravana; Sreenath Chandran; Subhalakshmi Krishna; Mary Joy; Sanjeev K Anand; V Madavan; Ansamma Joseph; Guang W Wong; William P Schiemann; Stefan N Constantinescu; Lily Huang; Roya Khosravi-Far; Hanno Steen; Muneesh Tewari; Saghi Ghaffari; Gerard C Blobe; Chi V Dang; Joe G N Garcia; Jonathan Pevsner; Ole N Jensen; Peter Roepstorff; Krishna S Deshpande; Arul M Chinnaiyan; Ada Hamosh; Aravinda Chakravarti; Akhilesh Pandey
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

5.  hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds.

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Journal:  Database (Oxford)       Date:  2011-05-17       Impact factor: 3.451

6.  Linked open drug data for pharmaceutical research and development.

Authors:  Matthias Samwald; Anja Jentzsch; Christopher Bouton; Claus Stie Kallesøe; Egon Willighagen; Janos Hajagos; M Scott Marshall; Eric Prud'hommeaux; Oktie Hassenzadeh; Elgar Pichler; Susie Stephens
Journal:  J Cheminform       Date:  2011-05-16       Impact factor: 5.514

7.  Disease Ontology: a backbone for disease semantic integration.

Authors:  Lynn Marie Schriml; Cesar Arze; Suvarna Nadendla; Yu-Wei Wayne Chang; Mark Mazaitis; Victor Felix; Gang Feng; Warren Alden Kibbe
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8.  DrugBank: a comprehensive resource for in silico drug discovery and exploration.

Authors:  David S Wishart; Craig Knox; An Chi Guo; Savita Shrivastava; Murtaza Hassanali; Paul Stothard; Zhan Chang; Jennifer Woolsey
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

9.  A side effect resource to capture phenotypic effects of drugs.

Authors:  Michael Kuhn; Monica Campillos; Ivica Letunic; Lars Juhl Jensen; Peer Bork
Journal:  Mol Syst Biol       Date:  2010-01-19       Impact factor: 11.429

10.  PDTD: a web-accessible protein database for drug target identification.

Authors:  Zhenting Gao; Honglin Li; Hailei Zhang; Xiaofeng Liu; Ling Kang; Xiaomin Luo; Weiliang Zhu; Kaixian Chen; Xicheng Wang; Hualiang Jiang
Journal:  BMC Bioinformatics       Date:  2008-02-19       Impact factor: 3.169

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  1 in total

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Authors:  Matthew H Ung; Frederick S Varn; Chao Cheng
Journal:  Expert Opin Drug Discov       Date:  2016-10-11       Impact factor: 6.098

  1 in total

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