In the latest effort to make myself obsolete by the end of this year, we are looking for a software developer to help us better make our data available to both humans and machines. The main responsibilities of this position will be the further development of the UniProt web site and the UniProt RDF distribution.
In order to bulk-load RDF data into Oracle (Spatial) 11g, the data needs to be converted to N-Triples first. If the data set is large, this step can add quite a bit of overhead, which is why I decided to benchmark and compare several options.
The UniProt RDF distribution is over 5GB large. To help people retrieve the data more efficiently, we now mirror the data and provide a Metalink file that describes all the file locations.
We’ve been looking for a decent ontology editor for a while now. The problem is that most editors are either to technical or too cumbersome to use for entering a lot of data. But it looks like we have finally found something suitable!
Brief review of Data and Reality by William Kent. This book was written in 1978, but is still remarkably relevant in many ways.
From a recent review article in Nature Genetics:
[...] current ad hoc IR systems are not able to retrieve our example sentence when they are given the query ‘yeast cell cycle’. Instead, this could be achieved by realizing that ‘yeast’ is a synonym for S. cerevisiae, that ‘cell cycle’ is a Gene Ontology term, that the word ‘Cdc28′ refers to an S. cerevisiae protein and finally, by looking up the Gene Ontology terms that relate to Cdc28 to connect it to the yeast cell cycle. Although this will not be easy, we see this form of query expansion as the next logical step for ad hoc IR.