Mark’s new CCO/RDF hosting functionality (see also my post two days ago) requires RDF/XML format, so I updated my code to convert the Chempedia Substances data into RDF/XML instead of N3 (I have asked Rich to put a new download link online). This is the Groovy code I used:
Oscar uses a Maximum Entropy Markov Model (MEMM) based on n-grams. Peter Corbett has written this up (doi:10.1186/1471-2105-9-S11-S4). So, it basically is statistics once more. If you really want a proper bioinformatics education, so do your PhD at a (proteo)chemometrics department.
The two earlier posts in this series showed screenshots of results of Oscar, but the title also promised results by Lezan’s ChemicalTagger. Sam helped with getting the HTML pages online via the Cambridge Hudson installation. Where Oscar find named entities (chemical compounds, processes, etc), ChemicalTagger finds roles, like solvent, acid, base, catalyst. Roles are properties of chemical compounds in certain situations.
Say, you have your own dictionary of chemical compounds. For example, like your company’s list of yet-unpublished internal research codes. Still, you want to index your local listserv to make it easier for your employees to search for particular chemistry you are working on and perhaps related to something done at other company sites. This is what Oscar is for.
One goal of my three month project is to take Oscar4 to the community. We want to get it used more, and we need a larger development community. Oscar4 and the related technologies do a good, sometimes excellent, job, but have to be maintained, just like any other piece of code. To make using it easier, we are developing new APIs, as well as two user-oriented applications: a Taverna 2 plugin , and command line utilities.
Last month I reported a few things I missed in CiteULike. One of them was support for CiTO (see doi:10.1186/2041-1480-1-S1-S6), a great Citation Typing Ontology.
Besides getting Oscar used by ChEBI (hopefully via Taverna ), my main task in my three month Oscar project is to refactor things to make it more modular, and remove some features no longer needed (e.g. an automatically created workspace environment). Clearly, I need to define a lot of new unit tests to ensure my assumptions on how to code works are valid.
One of the goals of my project in Cambridge is to make Oscar available as Taverna plugin (source code, Hudson build). I have progressed somewhat, but still struggling with getting the update site working.
As Peter announced in his blog, and I tweeted earlier, I have started as postdoctoral research associate in Peter’s group at the University of Cambridge, to work the next three months on Oscar, a chemical text mining tool. My tasks will focus on programmatical plumbing instead of method development, and I am aiming at integration with CDK-Taverna (see doi:10.1186/1471-2105-11-159, and which is currently being ported to Taverna 2.2 by Andreas).
AJCann posted a blog today about what he doesn’t like about Mendeley. Abhishek replied that he does not like people complain about one tool, instead of pointing out a good alternative. Mendeley has two alternatives, Zotero and CiteULike (there is also Connotea, but got behind in evolution).