The Semantic Web is (quote) "a new form of Web content that is meaningful to computers". It will "unleash a revolution of new possibilities" using a magical "new" artificially intelligent technology called ontology. So says a much-cited article in Scientific American published back in May 2001. Most people who have read this article, fall into two camps: "believers" and "non-believers". Let me tell you a short story about a religious war between these two groups...
After a long hiatus SciView is back with a new interview with Dr Roderic Page from the University of Glasgow. Dr Page is the current Editor in Chief of Syatematic Biology and developer of TreeView(X), the beloved phylogenetic tree visualization software. He was also the editor of the Current Protocols in Bioinformatics.
As usual here is the link.
Enjoy.
The Journal of Biomedical Informatics (JBI), will soon be publishing their special issue on Semantic Biomedical Mashups (can you fit any more buzzwords into a Call For Papers?!). Ben Good and friends have submitted a paper on their Entity Describer which extends connotea using some Semantic Web goodness. They'd appreciate your comments on their submitted manuscript over at i9606. As Ben says, their pre-publication turns out to be an interesting experiment "figuring out how blogging might fit into the academic publishing landscape". If this interests you, get commenting now!
I've put together a web site called http://bioguid.info which, rather grandly, is an attempt to bootstrap the biodiversity Semantic Web by providing resolvable URIs for biological objects, such as publications, taxonomic names, nucleotide sequences, and specimens. These URIs (or "GUIDs") can be resolved by a web browser to display HTML, but under the hood are resolved to RDF (which you can see by viewing the source of the web page you get for a URI).
Steven Salzberg has an opinion piece in Genome Biology that talks about Wikis for managing genome annotation and the problem of bit rot in gene annotation (would that be annotation rot?).
I wrote a quick post about it. This harkens to the other gene wiki discussions on nodalpoint as well as some of the things Ian Holmes and his group are thinking about on the GbrowseAJAX mailing list.
Happy Christmas from the myGrid team, who are pleased to announce the release of version 1.5.0 of the Open Source Taverna bioinformatics workflow toolkit [1]. This is now available for download on the Sourceforge site and includes some substantial changes to version 1.4.
All I want for Christmas is a book about the semantic web, written by people who are actually building and using it, rather than “visionaries” who don't have to. Maybe this year I'll be lucky...
This amusing picture-parody of the semantic web is worth a thousand words, was conceived of by Mark Butler for a presentation [1] and drawn by Rachel Murphy of Rude Girl Designs.
The Fifth International Semantic Web Conference (ISWC 2006) is currently underway in Athens, Georgia, USA (near Atlanta) which is famous for, errrm, being the birthplace of (Hey Ya!) The Outkast. Anyway, three bioinformatics related papers and workshops caught my eye this year and might be of interest to the wider community.
The discussion on impact factors got me wondering - is there a public, free access citation database for articles in Medline / Pubmed? I know of Scopus, ISI WOS (but theyre not free, and their content is proprietary) and Google Scholar (only give 'cited by', when I want 'this article cites x and y')?
How would one build such a database, if its not accessible? I know that ISI actually scans articles (not doable by myself) - I don't know how Scopus got their index, though.
Such a database would help tremendously on some bibliomics work I'm doing. Is it technically feasible to get references for all Medline articles (at least, those past 1996?). Where would you get the information - scrape/spider&index publishers website, if this information is even freely accessible (without a subscription?) and then match against a local Medline database (which I already have)? If anyone can help, it'd be appreciated :)
