SWAT4LS2009 – Linking Open Drug Data to Cheminformatics abd Proteochemometrics

November 20, 2009 1 Comment

Structure of ascorbic acid also called vitamin C
Image via Wikipedia

(Notes frm the presentation as it happens)

Knowledge is not uni or bivariate, but we think of it as such: this leads to information loss.

Naming things: showing example of a trivial name, an IUPAC systematic name and an InChI and points out that these have different information content.

Points out scaling problem: drug discovery is multivariate and happens in a space of approx 1016 molecules (all molecules that are feasible and thought to be drug-like). Information loss occurs as you traverse this space backwards and forwards.

Now talks about molecular information in RDF: http://rdf.openmolecules.net for the provision of derefernceable URIs for molecules….and plugging the Chemistry Development Kit (CDK) as a means for cnverting between multiple representations of a molecule. Now moves on to Bioclipse as an integrating tool that allows chemical data transformations and the tracking of vwhy these transformations occur (version-controllable scripts to drive Bioclipse).

RDF extension to bioclipse: local RDF storage, read/write RDF, run SPARQL queries and extract RDF from XHTTML/RDFa.

Now shows an example of the expression of the CDK data model using ontologies but no details. Brief mention of his recent descriptor ontology.

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SWAT4LS2009 – Matthias Loebe: TIM A semantic web application for the specification of metadata items in clinical research

November 20, 2009 1 Comment

(Again, these are live notes as bullet points.)

Problems with the Specification of Clinical Trials

  • Development of trial protocol
  • Preparation of study centres
  • Registration of patients etc…..
  • Case report Forms capture data at different time points (lab results, therapy outcomes, treatment history etc..) relevant for answering clinical questions
  • Misconceptions and misinterpretations of data occur frequently either through underspecification or lack of metadata

Benefits of Detailing and Reusing Items

  • Efficiency
  • Data Quality
  • Metaanalysis

Requirements for an Item Data Model

  • Expressiveness – Items consist of subitems
  • Adaptable system of rules – validity and consistency checking
  • Supporting context
  • Providing views – facests. Different information requirements for different types ofusers.
  • Exploiting conceptual relations
  • Mapping to terminologies

Architecture of Trial Item Manager

  • Application behaviour is ontology driven…
  • working data stored as rdf in separate model
  • multiple rdf models (combined, raw, inferred)

Showing the specification of various trial items in rdf…..and examples of the ontology driving the app…

Advantage of th Semantic Approach

  • open linked data, referencability
  • extensible rules
  • user guidence using semantics but invisible to user
  • rapid response to change
  • import external item sets
  • personalisation on a per-user/user type basis
  • navigation
  • semantic search

Caveats:

  • Open world reasoning sometimes gives unexpected results…..;-)
  • No unique name assumption
  • Performance
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What’s Eating Scientific Data? – Google Tech Talk on the Chemical Semantic Web

July 9, 2009 Leave a comment

google

Jim and I recently visited Google, where we were invited to give a tech talk about our research and the work that the PMR group in Cambridge is doing. It’s now online and you can watch it on YouTube here:

We are discussing the semantic toolstack as applied to chemistry and show how CML, RDF and ontologies can be used to bring chemical data into the 21st century. Jim also talks extensively about Lensfield – our system for the generation, management and publication of semantically rich linkeed data. A big thank you also to David Konerding for hosting us during the day and for the great discussions!

(If the video doesn’t show up in your feedreader, please click through to the the webpage.)

Looking forward to your comments!

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