My FOAF network #5: SPARQL-ing my network

FOAF rulez: it’s RDF. With RDF comes SPARQL. SPARQL needs a query engine, however. And there comes OpenRDF which created Sesame. I have to catch the train in about 15 minutes, so will not elaborate too much, but here are some Sesame 2.0.1 work:

1 minute read

My FOAF network #4: Tabulating my publications

Richard informed me (via Planet RDF) about N3 support in Tabulator. N3 is a more compressed version of RDF/XML, which I have been using so far, but both are RDF. Now, I don’t plan to use N3 for my FOAF experimenting, but two things caught my eye in the nice blog item.

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Sugammadex: the molecular condom

Two things I like blogging: 1. the turn-over of information; 2. the informal nature. There are more. The turn-over is optimized by commonly: 1. short blog items; 2. easily allows scanning tons of headlines; 3. often full of links if you want to know the details.

less than 1 minute read

My FOAF network #3: My publications

As promised, I’ll write a bit about using Bibliographic Ontology Specification (BIBO) over as bibliontology.com. I have written a basic XSLT to create a HTML GUI (open the RDF source in e.g. Firefox). Really basic: it only converts articles, and even assumes some conventions I found in examples in the BIBO wiki. I have not spotted a BIBO validator yet, so guessing a bit. The BibTeX mapping examples are under discussion, but provide some insight to those who are used to using that (JabRef users, for example).

3 minute read

The Chemical Object Identifier; or, the freedom to identify chemicals

IUPAC chemical names, SMILES and InChIs are too long. InChIKeys are not unique enough because of safety reasons (you have a 1 in 10 billion chance of blowing up your building; well, odds are actually much, much lower than getting hit by Osama or friends, let alone a car). Wikipedia URIs do not cover enough chemical space.

4 minute read

My FOAF network #2: XSLT for a HTML GUI

Because the ACS meeting where Henry will present something about FOAF in chemistry, is nearing very fast now (here’s the first blog it this series), it becomes urgent to beef up the Blue Obelisk FOAF network, now consisting of 7 members. All do now show up in the FOAFExplorer:

2 minute read

Metabolomics Ontologies: SKOS-ified the ArMet specification

The MetWare project is going to make use of ontology technologies to control the content of the database, and a first step is to convert our MetWare database design into something using a formal ontology language. I have played with OWL in the past (see for example its use in Bioclipse), but was not overly happy with it in all situations.

1 minute read