TY  - GEN
TI  - Web-based Named Entity Recognition and Data Integration to Accelerate Molecular Biology Research
KW  - Datenintegration 
KW  -  Text Mining 
KW  -  Dokumentenerweiterung 
KW  -  Web ServicesData integration 
KW  -  text mining 
KW  -  knowledge summaries 
KW  -  document enrichment 
KW  -  web services
Y1  - 2008///
ID  - heidok8970
AV  - public
A1  - Pafilis, Evangelos
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/8970/
N2  - Finding information about a biological entity is a step tightly bound to molecular biology research. Despite ongoing efforts, this task is both tedious and time consuming, and tends to become Sisyphean as the number of entities increases. Our aim is to assist researchers by providing them with summary information about biological entities while they are browsing the web, as well as with simplified programmatic access to biological data. To materialise this aim we employ emerging web technologies offering novel web-browsing experiences and new ways of software communication Reflect is a tool that couples biological named entity recognition with informative summaries, and can be applied to any web page, during web browsing. Invoked either via its browser extensions or via its web page, Reflect highlights gene, protein and chemical molecule names in a web page, and, dynamically, attaches to them summary information. The latter provides an overview of what is known about the entity, such as a description, the domain composition, the 3D structure and links to more detailed resources. The annotation process occurs via easy-to-use interfaces. The fast performance allows for Reflect to be an interactive companion for scientific readers/researchers, while they are surfing the internet.  OnTheFly is a web-based application that not only extends Reflect functionality to Microsoft Word, Microsoft Excel, PDF and plain text format files, but also supports the extraction of networks of known and predicted interactions about the entities recognised in a document.  A combination of Reflect and OnTheFly offers a data annotation solution for documents used by life science researchers throughout their work.  EasySRS is a set of remote methods that expose the functionality of the Sequence Retrieval System (SRS), a data integration platform used in providing access to life science information including genetic, protein, expression and pathway data. EasySRS supports simultaneous queries to all of the integrated resources. Accessed from a single point, via the web, and based on a simple, common query format, EasySRS facilitates the task of biological data collection and annotation. EasySRS has been employed to enrich the entries of a Plant Defence Mechanism database.  UniprotProfiler is a prototype application that employs EasySRS to generate graphs of knowledge based on database record cross-references. These graphs are converted into 3D diagrams of interconnected data. The 3D diagram generation occurs via Systems Biology visualisation tools that employ intuitive graphs to replace long result lists and facilitate hypothesis generation and knowledge discovery.
ER  -