On this blog you are able to follow my degree project(master thesis in Bioinformatics) which have the title Pharmaceutical knowledge retrieval through reasoning of ChEMBL RDF.
My supervisor is Egon Willighagen, http://chem-bla-ics.blogspot.com/.


måndag 8 februari 2010

A whole new world...

I've seen a completely new world when looking into the functions of Bio2RDF. I see great linking between knowledge. To be able to collect information from one knowledge base and link to another obtaining more information and always extending knowledge is great!

In my work in running queries against ChEMBL to collect active (later on also inactive) compounds I find this linking valuable. For example drugbank holds lots of great information about the compound. Not only physical information but also id's such as chebi id that will make a linking to chebi possible.

Kegg is an other kb that could be useful, Kegg:ligand, Kegg:drug and Kegg:compound. Uniprot could provide article info, chebi compound info, PDB could give target protein data, etc.

I believe that users should be able to decide what kind of information they want/need. This aim could be solved when interacting with Bioclipse. My aim is to use substructure mining on the drugs but of course other aims should be possible(the use of other Bioclipse plug-ins than Moss).

Perhaps a table representation is a nice way to display the data. And if lots of information about a drug is wanted perhaps info page is the way to display it.

DBpedia is another valuable source way to get resources: names, descriptions, inchi's, smiles, images etc. One mayor disadvantage is that unknown compound will not be found.

And now I got a link chem2bio2rdf from my supervisor. It has collected all chemical URI's in one place, I will immediately look into it and run queries!

2 kommentarer:

  1. Annzi, you should make URL links as much as possible. That makes the blog more useful to others, and when you link to other blogs, your blog will show up on their radars.

  2. Thanks for the one-liners describing the different databases and in which way they are useful in relation to each other!

    I find them highly useful as I try to learn to know what these DBs are as well but feel I'm approaching a slight "stack overflow" with all new names (dbs + formats + tools + ontologies + etc etc) :-o.