Samuel's Project Blog

Since I'm originally a windows user and still using it sometimes, I'm keeping an eye on the status of git on windows.

Seems like there's more to do, but some things are happening: MSysGit Seems to be the currently best solution, while GitSharp looks promising. For MSysGit there's a guide on getting started with Git and GitHub on Windows.

Realized I would need to go through a git tutorial containing the basics.

I liked this one. Very concise, and has sections for the typical roles you might have as a git user. I liked this one too. A good complement to the other.

After som hard work by Egon (finally resulting in this commit), which includes (in addition to the plugin file structure created with the Bioclipse SDK) an eclipse product file which means Bioclipse can now be started with the (empty) drprolog plugin enabled, and available in the JavaScript console inside Bioclipse.

I ran into troubles trying to check out a specific branch from github.

I asked about it at #git on FreeNode IRC channel. I'll summarize how to do it:

First run:
git clone git://github.com/...[path to your project]...git

Then go:
git branch -a
...to see what branches you have.

So, one week has passed, or almost one, since my official (degree-)project start this monday.

Will start off with a short presentation of what I'm doing (or going to). My suggested project title is "Integration of DR-PROLOG for semantic reasoning in Bioclipse".

Reading up on Life Science databases et.c... which continues to generate "abbreviations" that are useful to know well.

Databases

• DBPedia - RDF version of Wikipedia
• LODD - Linking Open Drug Data (contains an overview of the included databases)
• PubChem

Formats et.c.

• InChI - IUPAC International Chemical Identifier

Will now start the work of creating a Bioclipse manager for the integration of DR-PROLOG into Bioclipse.

Egon pointed me to a blog post about a feature they've made in order to make it easier for us who are new to Bioclipse development to get started. Nice, det tackar vi för!

I now got up and running Bioclipse (2.2) on Eclipse 3.5 :)

I had problems first when just copying the old worspace (Bioclipse 2.0 for Eclipse 3.4), but it was just because I had forgot to upgrade the Bioclipse code base. So I did it, with the command:

 git pull

Then i had to refresh all the projects in Eclipse, one by one, (select projects and click F5, one at a time).

A collegue of Mats Gustafsson mentioned about Blipkit today. Seems worth checking up.

The thought struck me for a second that it could be even more interesting to integrate, than DR-PROLOG, since it is biomedically oriented. Maybe not, but worth thinking of I guess.

EDIT: Checked up with Egon, who pointed out that it doesn't seem to have a good interface for integration to Java, which would complicate things. Seems like a good point.

Reading the paper on the Bio2RDF database.

It contains something that I need, an overview of different techniques, databases and formats that are common in the semantic web community, but of which I know to few still.

Some useful abbreviations just learned (some I knew somewhat, but was not sure):

Formats / Languages

• RDF - Resource Description Framework
• OWL - Web Ontology Language
• LSID - Life Sciences ID
• Dublin core

Databases

• Bio2RDF
• KEGG - Kyoto Encyclopedia of Genes and Genomes