DO NOT REPLY TO THIS EMAIL, BUT PLEASE POST YOUR BUG· RELATED COMMENTS THROUGH THE WEB INTERFACE AVAILABLE AT <http://issues.apache.org/bugzilla/show_bug.cgi?id=35741>. ANY REPLY MADE TO THIS MESSAGE WILL NOT BE COLLECTED AND· INSERTED IN THE BUG DATABASE.
http://issues.apache.org/bugzilla/show_bug.cgi?id=35741 Summary: [Link] iHOP - Information Hyperlinked over Proteins Product: Cocoon 2 Version: Current SVN 2.1 Platform: Other URL: http://www.pdg.cnb.uam.es/UniPub/iHOP/ OS/Version: All Status: NEW Severity: enhancement Priority: P2 Component: Documentation AssignedTo: [email protected] ReportedBy: [EMAIL PROTECTED] Version used: Cocoon 2.17 --- Summary iHOP (Information Hyperlinked over Proteins) is a public information system for the biomedical sciences, providing the network of gene synonyms as a mean of navigating the scientific literature. By employing genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed (National Library of Medicine) can be converted into one navigable resource. This way the information in more than twelve million abstracts in PubMed can be converted into one small world that brings all advantages of the internet to scientific literature research. The current network provided in iHOP contains two million sentences and 30000 different genes from human, mouse, fly, worm, fish, plants and yeast. Hoffmann, R., Valencia, A. A Gene Network for Navigating the Literature. Nature Genetics 36, 664 (2004) --- Additional Technical information Underlying data In a process previous to the web application, genes and proteins and MeSH terms (biomedical thesaurus) are identified in about 12 million biomedical abstracts from PubMed. Of a total number of 200000 genes, about 30000 genes were identified in 2 million abstracts. Starting from this index, 1 XML document was created for each abstract, 1 for each gene and 2 different xml documents for each of the gene in the literature. Thus the total number of different XML documents is around 2.3 million. These documents essentially contain the original text divided into individual sentences with gene synonyms, MeSH terms, and verbs tagged. Gene documents also contain general information, such as database references, synonyms, and a list of homologous genes, which in the web application are used to provide links to external resources. Web application The web application currently consists of the data in 2.3 million XML-documents, 33 XSP scripts and 37 different transformation style sheets for all the different views on the gene and abstract data. Dynamic effects are achieved through the HTML and JavaScript layer on the client side to minimize server load and to avoid complex front-end database queries. This way, extremely fast response times are obtained and multiple concurrent usage of the system is possible. --- * How can we verify this site is actually built with Cocoon? Calling an inexistent page, e.g. "http://www.pdg.cnb.uam.es/UniPub/iHOP/nil/anything";, will lead to the Cocoon error message. Credit is given to the Cocoon project on the first page of iHOP. * How much time did it take to build the site from design to publication? 16 month * How many people were involved in the project? Just me. * How much traffic does the site handle? Around 10000 different IPs per day. * What made you choose Cocoon to build the site? The book "Java and XML by Brett McLaughlin. The perfect separation between lots of fairly stable data in XML and it's everchanging HTML representation. * What other information do you want to disclose (e.g. how does it work, how did you build it, what parts of Cocoon did you use)? See technical information. * Contact Robert Hoffmann Memorial Sloan-Kettering Cancer Center, MSKCC [EMAIL PROTECTED], http://www.cbio.mskcc.org/~hoffmann/ -- Configure bugmail: http://issues.apache.org/bugzilla/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.
