@article {19721,
	title = {InterPro in 2011: new developments in the family and domain prediction database.},
	journal = {Nucleic Acids Res},
	volume = {40},
	year = {2012},
	month = {2012 Jan},
	pages = {D306-12},
	abstract = {<p>InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.</p>},
	keywords = {Databases, Protein, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, software, Terminology as Topic, User-Computer Interface},
	issn = {1362-4962},
	doi = {10.1093/nar/gkr948},
	author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf and Attwood, Teresa K and Bateman, Alex and Bernard, Thomas and Binns, David and Bork, Peer and Burge, Sarah and de Castro, Edouard and Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D and Fraser, Matthew and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn, Antony F and Rivoire, Catherine and Sangrador-Vegas, Amaia and Jeremy D Selengut and Sigrist, Christian J A and Scheremetjew, Maxim and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D and Wu, Cathy H and Yeats, Corin and Yong, Siew-Yit}
}
@article {17487,
	title = {Visual Exploration across Biomedical Databases},
	journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
	volume = {8},
	year = {2011},
	month = {2011/04//March},
	pages = {536 - 550},
	abstract = {Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration. A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases. Databases are modeled as an entity-relation graph containing nodes (database records) and links (relationships between records). Users specify a keyword search string to retrieve an initial set of nodes, and then explore intra- and interdatabase links. Results are visualized with user-defined semantic substrates to take advantage of the rich set of attributes usually present in biomedical data. Comments from domain experts indicate that this visualization method is potentially advantageous for biomedical knowledge exploration.},
	keywords = {Bioinformatics, Biomedical computing, biomedical databases, cross-database exploration, Data exploration and discovery, Data visualization, database management systems, Databases, Factual, DNA, graph theory, Information Storage and Retrieval, information visualization., Keyword search, medical computing, natural language processing, Proteins, semantic networks, semantics, sequences, text mining, User-Computer Interface, user-defined semantics, visual databases},
	isbn = {1545-5963},
	doi = {10.1109/TCBB.2010.1},
	author = {Lieberman,M.D. and Taheri, S. and Guo,Huimin and Mirrashed,F. and Yahav,I. and Aris,A. and Shneiderman, Ben}
}
@article {17250,
	title = {Interactive Entity Resolution in Relational Data: A Visual Analytic Tool and Its Evaluation},
	journal = {IEEE Transactions on Visualization and Computer Graphics},
	volume = {14},
	year = {2008},
	month = {2008/10//Sept},
	pages = {999 - 1014},
	abstract = {Databases often contain uncertain and imprecise references to real-world entities. Entity resolution, the process of reconciling multiple references to underlying real-world entities, is an important data cleaning process required before accurate visualization or analysis of the data is possible. In many cases, in addition to noisy data describing entities, there is data describing the relationships among the entities. This relational data is important during the entity resolution process; it is useful both for the algorithms which determine likely database references to be resolved and for visual analytic tools which support the entity resolution process. In this paper, we introduce a novel user interface, D-Dupe, for interactive entity resolution in relational data. D-Dupe effectively combines relational entity resolution algorithms with a novel network visualization that enables users to make use of an entity{\textquoteright}s relational context for making resolution decisions. Since resolution decisions often are interdependent, D-Dupe facilitates understanding this complex process through animations which highlight combined inferences and a history mechanism which allows users to inspect chains of resolution decisions. An empirical study with 12 users confirmed the benefits of the relational context visualization on the performance of entity resolution tasks in relational data in terms of time as well as users{\textquoteright} confidence and satisfaction.},
	keywords = {algorithms, Computer Graphics, D-Dupe, data visualisation, database management systems, Databases, Factual, graphical user interface, Graphical user interfaces, human-centered computing, Image Interpretation, Computer-Assisted, Information Storage and Retrieval, Information Visualization, interactive entity resolution, relational context visualization, Relational databases, relational entity resolution algorithm, User interfaces, user-centered design, User-Computer Interface, visual analytic tool},
	isbn = {1077-2626},
	doi = {10.1109/TVCG.2008.55},
	author = {Kang,Hyunmo and Getoor, Lise and Shneiderman, Ben and Bilgic,M. and Licamele,L.}
}
@article {16983,
	title = {Balancing Systematic and Flexible Exploration of Social Networks},
	journal = {IEEE Transactions on Visualization and Computer Graphics},
	volume = {12},
	year = {2006},
	month = {2006/10//Sept},
	pages = {693 - 700},
	abstract = {Social network analysis (SNA) has emerged as a powerful method for understanding the importance of relationships in networks. However, interactive exploration of networks is currently challenging because: (1) it is difficult to find patterns and comprehend the structure of networks with many nodes and links, and (2) current systems are often a medley of statistical methods and overwhelming visual output which leaves many analysts uncertain about how to explore in an orderly manner. This results in exploration that is largely opportunistic. Our contributions are techniques to help structural analysts understand social networks more effectively. We present SocialAction, a system that uses attribute ranking and coordinated views to help users systematically examine numerous SNA measures. Users can (1) flexibly iterate through visualizations of measures to gain an overview, filter nodes, and find outliers, (2) aggregate networks using link structure, find cohesive subgroups, and focus on communities of interest, and (3) untangle networks by viewing different link types separately, or find patterns across different link types using a matrix overview. For each operation, a stable node layout is maintained in the network visualization so users can make comparisons. SocialAction offers analysts a strategy beyond opportunism, as it provides systematic, yet flexible, techniques for exploring social networks},
	keywords = {Aggregates, algorithms, attribute ranking, Cluster Analysis, Computer Graphics, Computer simulation, Coordinate measuring machines, coordinated views, Data analysis, data visualisation, Data visualization, exploratory data analysis, Filters, Gain measurement, graph theory, Graphical user interfaces, Information Storage and Retrieval, interactive graph visualization, matrix algebra, matrix overview, Models, Biological, Navigation, network visualization, Pattern analysis, Population Dynamics, Social Behavior, social network analysis, Social network services, social networks, social sciences computing, Social Support, SocialAction, software, statistical analysis, statistical methods, User-Computer Interface},
	isbn = {1077-2626},
	doi = {10.1109/TVCG.2006.122},
	author = {Perer,A. and Shneiderman, Ben}
}
@article {17849,
	title = {The virtual microscope},
	journal = {IEEE Transactions on Information Technology in Biomedicine},
	volume = {7},
	year = {2003},
	month = {2003/12//},
	pages = {230 - 248},
	abstract = {We present the design and implementation of the virtual microscope, a software system employing a client/server architecture to provide a realistic emulation of a high power light microscope. The system provides a form of completely digital telepathology, allowing simultaneous access to archived digital slide images by multiple clients. The main problem the system targets is storing and processing the extremely large quantities of data required to represent a collection of slides. The virtual microscope client software runs on the end user{\textquoteright}s PC or workstation, while database software for storing, retrieving and processing the microscope image data runs on a parallel computer or on a set of workstations at one or more potentially remote sites. We have designed and implemented two versions of the data server software. One implementation is a customization of a database system framework that is optimized for a tightly coupled parallel machine with attached local disks. The second implementation is component-based, and has been designed to accommodate access to and processing of data in a distributed, heterogeneous environment. We also have developed caching client software, implemented in Java, to achieve good response time and portability across different computer platforms. The performance results presented show that the Virtual Microscope systems scales well, so that many clients can be adequately serviced by an appropriately configured data server.},
	keywords = {biomedical optical imaging, client software, client/server architecture, Computer architecture, Computer Graphics, computer platforms, Computer simulation, Concurrent computing, configured data server, data server software, database management systems, database software, Database systems, digital slide images, digital telepathology, diseases, emulation, Environment, Equipment Design, Equipment Failure Analysis, high power light microscope, Image databases, Image Enhancement, Image Interpretation, Computer-Assisted, Image retrieval, Information retrieval, Information Storage and Retrieval, java, local disks, microscope image data, Microscopy, multiple clients, optical microscopy, PACS, software, Software design, software system, Software systems, Systems Integration, Telepathology, User-Computer Interface, virtual microscope design, Virtual reality, Workstations},
	isbn = {1089-7771},
	doi = {10.1109/TITB.2004.823952},
	author = {Catalyurek,U. and Beynon,M. D and Chang,Chialin and Kurc, T. and Sussman, Alan and Saltz, J.}
}
