nodalpoint.org

If you are interested in running a Drupal site with PubMed content you should check the screencast below. It explains how it can be done with existing Drupal modules. I'm working with a student from the University of Szeged on a PubMed module for Drupal. So in the future this should become a bit more straightforward ;)

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.

I've been trying to come up with a nice way to mashup and process RSS feeds, mostly for the reason to be able to track articles from Journals that publish content that interests me. The best solution seems to be the workflows that can be constructed at Yahoo Pipes.

Spotted this article a while back: Everything about HubMed. A nice overview of HubMed's features such as RSS feeds, the biologging site (depreciated in favour of HubMed tags ?), link-outs, touch-graph etc.

I'm sitting in on the BioDASH demo, Eric Neumann is giving a broad strokes introduction to the semantic web, resources need metadata, basically if we can share and aggregate data and everything will be wonderful.

Now he's talking about semantic lenses, this I think is Haystack specific, he's talking about FOAF now. The slide he's using is the same one that was used in the bio-ontologies, for links see the comments here.

Yeast hub

This is the talk I was genuinely interested in seeing, it is supposedly all about semantic web...

- Time is right for using the semantic web...

So the introduction is fairly general, the web is full of heterogeneous data and access methods, we need metadata and we need a standard format to put our metadata in which in this case is RDF.

The speaker is now talking about the proliferation of all the different BioXML standards, for example MAGE-ML, SBML, etc. The problem in pathway databases is particularly bad with many formats describing the same thing. So according to the speaker we should unify on RDF/XML. Then we get all the so-called "stuff for free" e.g. inference, integration etc.

Via hublog: "NCBI's PubMed is to offer RSS feeds for searches. Only took them 2½ years."

Update: Pubmed RSS is now live. After doing a Pubmed search, click on the drop down menu for "send to" and RSS is now one of the options. The feature allows you to specify a name for the feed and number of items to include, see here for an example of the result. Pubmed is using RSS version 2.0 and dumping the content of the HTML citation display directly into the description tag. For most users this won't matter as the display in most aggregators, like bloglines for example (see the bioinformatics folder), will be the same as the regular Pubmed site. However using RSS 1.0 with available modules would have enabled more metadata to be added to the feeds, see for example the semantically rich feeds produced by Connotea. Which is great if you're a Semantic Web fan, which we all are right ?

Interestingly it looks like RSS export is going to be part of the Eutils web services (see the feed url). Now if RSS 1.0 export was available from all the NCBI databases then we would have instant RDF data.

I'll leave commenting on issues such as the correct identifiers to use in the Pubmed RSS (lsids ?) and whether or not the RSS 2.0 feeds are valid, use best practices (entity encoding the HTML in the description elements) etc. for later as I'm busy with ISMB related activities.