nodalpoint.org - 2006: Year of the OWL? - Comments

Re: 2006: Year of the OWL?

ejain — Thu, 16 Feb 2006 15:53:59 -0500

I'm not sure it would still be feasable (or even desirable) to create and maintain a comprehensive and up to date directory that would suit all people. More interesting would be a standard for describing projects in a machine readable manner, perhaps something like FOAF or DOAP. These files could be hosted and maintained by the projects themselves, and could be crawled and indexed by anyone.

There are two issues here:

Greg — Fri, 20 Jan 2006 02:58:46 -0500

There are two issues here: discovery and query. Not only is it necessary to open up those relational databases hiding in the 'deep web' but we also need to find them.

Providing a metadata description of your database in RDF, using a controlled vocabulary (ontology if you like) is one step towards finding all this hidden data. The use case I see here is that when a group publishes in the NAR databases, a link to an RDF description of that databases must be submitted. These descriptions could then be aggregated much like RSS or FOAF.

While this is far from an optimal solution, see BioMoby for something more ambitious, it does serve the purpose of raising awareness of semantic web technologies and metadata.

As for querying, REST (or maybe SOAP) interfaces are likely to be the easiest way to unlocking biological data stored in relational databases (short of downloading a mysql dump). What would be better is if each databases provided a SPARQL query interface. SPARQL query interfaces for biological databases will be on my wish list for 2008...

Deep Web

agbiotec — Thu, 12 Jan 2006 11:44:00 -0500

To see how usefull this would be, I am directing you to an article in ComputerWorld journal, related to the "Deep Web" :

ComputerWorld, Dec 19th issue

And as it is mentioned in this article:

The deep Web, also called the invisible Web, refers to the mass of information that can be accessed via the World Wide Web but can't be indexed by traditional search engines -- often because it's locked up in databases and served up as dynamic pages in response to specific queries or searches.

I thing this is pretty much the case with Bio-data, also mentioned @my Hopes & Fears for 2006, labs that create data and put them in a custom mySQL database that hide behind an HTML interface...

Semantic Webheads

Greg — Wed, 11 Jan 2006 22:05:37 -0500

Semantic Webheads would probably argue that the world would be a better place if these classifications of databases and web servers were expressed using the Web Ontology Language (OWL) or its poor cousin RDF...

Semantic Webheads, the horror :) however I would include myself in that category. I have a project page on the wiki to build schemas/vocabularies/ontologies for the description of biological resources (DOBR), for example a biological database. DOBR is vapourware at the moment, awaiting more motivation on my part. A simple metadata description of a biological database would be helpful for discovering what kind of data is available. It might also be helpful in bootstrapping awareness of the semantic web in the biology community.

A use case might be that when a new database is published an RDF file describing the database (data sources, maintainers, construction method etc.) must be linked on the site. It would be simple enough to crawl these descriptions to build a comprehensive database of all available databases...

2006: Year of the OWL?

Duncan — Wed, 11 Jan 2006 13:05:25 -0500

Two related articles in the December 2005 issue of Plos Computational Biology describe the state of the art in biomedical ontologies and where they might be going in 2006.