BioBuilder as a database development and functional annotation platform for proteins
J. Daniel Navarro,J. Daniel Navarro,Naveen Talreja,Suraj Peri,Suraj Peri,B. M. Vrushabendra,B. P. Rashmi,N. Padma,Vineeth Surendranath,Chandra Kiran Jonnalagadda,P. S. Kousthub,Nandan P. Deshpande,Kalyan Shanker,Akhilesh Pandey +13 more
TL;DR: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases.
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Abstract: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org
, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.
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Citations
Human Protein Reference Database—2009 update
T. S. Keshava Prasad,Renu Goel,Kumaran Kandasamy,Kumaran Kandasamy,Shivakumar Keerthikumar,Sameer Kumar,Suresh Mathivanan,Deepthi Telikicherla,Rajesh Raju,Beema Shafreen,Abhilash K. Venugopal,Lavanya Balakrishnan,Arivusudar Marimuthu,Sutopa Banerjee,Devi S. Somanathan,Aimy Sebastian,Sandhya G. Rani,Somak Ray,C. J. Harrys Kishore,Sashi Kanth,Mukhtar Ahmed,Manoj Kumar Kashyap,Manoj Kumar Kashyap,Riaz Mohmood,Y. L. Ramachandra,Venkatarangaiah Krishna,B. Abdul Rahiman,Subburaman Mohan,Prathibha Ranganathan,Subhashri Ramabadran,Raghothama Chaerkady,Akhilesh Pandey +31 more
TL;DR: A number of new features in HPRD are added, including PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest, and a protein distributed annotation system—Human Proteinpedia.
Human protein reference database—2006 update
Gopa R. Mishra,M.K. Suresh,K. Kumaran,N. Kannabiran,Shubha Suresh,P. Bala,K. Shivakumar,N. Anuradha,Raghunath Reddy,T. Madhan Raghavan,Shalini Menon,G. Hanumanthu,Malvika Gupta,Sapna Upendran,Shweta Gupta,Madhu Mahesh,Bincy Jacob,Pinky Mathew,P. Chatterjee,K. S. Arun,Salil Sharma,K N Chandrika,Nandan P. Deshpande,Kshitish Palvankar,R. Raghavnath,R. Krishnakanth,Hiren Karathia,B. Rekha,Rashmi Nayak,G. Vishnupriya,H. G. Mohan Kumar,M. Nagini,G. S. Sameer Kumar,Rojan Jose,P. Deepthi,Subburaman Mohan,Tejal K. Gandhi,H. C. Harsha,Krishna S. Deshpande,Malabika Sarker,T. S. Keshava Prasad,Akhilesh Pandey +41 more
TL;DR: This work has introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer, developed by us that allows integration of genomic and proteomic information.
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis
TL;DR: A composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia is provided to provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases.
Novel proteomic approaches for tissue analysis.
Michael A. Tangrea,Benjamin S Wallis,John W. Gillespie,Gallya Gannot,Michael R. Emmert-Buck,Rodrigo F. Chuaqui +5 more
TL;DR: An overview of the current proteomic tools used in the analysis of tissues, beginning with conventional methods such as western blot analysis and 2D polyacrylamide gel electrophoresis and the most current high-throughput techniques being used today are reviewed.
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Future-proofing synthetic biology: educating the next generation
Jennifer Hallinan,Anil Wipat,Richard I. Kitney,Simon Woods,K. Taylor,Angel Goñi-Moreno +5 more
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TL;DR: The authors identify some of the key areas required for the education of new synthetic biologists to equip them with both adequate background and sufficient flexibility to tackle these challenges and therefore to future-proof synthetic biology.
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TL;DR: The Human Protein Reference Database (HPRD) as mentioned in this paper is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease, including protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization.
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