August Publication Corner
Welcome to the LINKS Publication Corner, where you will find the latest peer-reviewed articles referencing or describing caBIG® technology and principles. These articles, written and reviewed by your peers, showcase the reality of what is possible when using the caBIG® infrastructure and services. While some articles require a membership, others are freely available for reading, so please enjoy.
Crowley RS, Castine M, Mitchell K, Chavan G, McSherry T, Feldman M.. caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue speciments in support of translational research. J AM Med Inform Assoc. 2010;17(3):253-264.
Researchers at the University of Pittsburgh, University of Pennsylvania, Thomas Jefferson University, and Washington University St. Louis are using the Cancer Tissue Information Extraction System (caTIES) to support collaborative tissue banking and text mining. This publication describes how caTIES supports multi-site tissue banking needs by providing researchers with the ability to query, browse and annotate tissue data without network restrictions. Find out how caTIES is advancing research by providing researchers with a federation of research data sources derived from clinical systems, a regulatory and security model to support multi-center collaborative research, and an easy-to-navigate user interface where researchers can mine text documents for related terms, concepts, and relationships. Read the full article here.
Floratos A, Smith K, Watkinson J, Califano A. geWorkbench: an open platform for integrative genomics. Bioinformatics. 2010.
The genomics Workbench (geWorkbench), is providing researchers with unprecedented access to data from a wide variety of genomics domains (gene expression, sequence, protein structure and systems biology). This publication describes the more than 70 distinct plug-in modules currently in use through geWorkbench. Discover how geWorkbench is offering researchers both classical analysis capabilities and state of the art algorithms, while leveraging standards-based technologies that provide seamless access to remote data, annotation and computational servers. Read the full article here.
Thomas DG, Pappu RV, Baker NA. Nanoparticle ontology for cancer nanotechnology research. J Biomed Inform. 2010 Mar 6. [Epub ahead of print.]
Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. This publication describes specific ontologies that provide a unifying knowledge framework for annotating the data and facilitating data sharing. Explore the design and development of the NanoParticle Ontology (NPO), which provides researchers with collective knowledge on the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Read the full article here.
Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Med Genomics. 2010;3(1):11.
CNAReporter offers a user-friendly way to visualize and analyze the genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment. With the CNAReporter, users can visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. Read the full article here.
