Friday, July 22, 2011

ICBO2011 Preparations, part two

Via the email lists for the Clinical Data Interchange Consortium (CDISC) Terminology team, and for the Electronic Health Records for Clinical Research (EHR4CR) one of the Innovative Medicines Initiative (IMI) project, I have see some recent discussions on cross-terminology mapping challenges. Challenges  due to the fact that terminologies and coding nomenclatures, such as SNOMED CT, LOINC, CDISC SDTM CT:s, and MedDRA, all have been developed for different purposes, with disparate approaches and structures.

Together with attendances from NCI, NCBO, FDA, Mayo, SAS, Stanford and other organizations, I and a few colleagues, will attend the International Conference on Biomedical Ontology (ICBO) next week . See my previous blogpost with some more background. 


Photo (Flickr): Automania

Apples and Oranges
In preparations for the workshop the first day, Representing Adverse Events, I did find this paper highly interesting as it compare and contrast SNOMED CT and MedDRA, and also describes the challenges in mapping between them: Heterogeneous but “standard” coding systems for adverse events: Issues in achieving interoperability between apples and oranges.



OBO Foundry based ontologies as "catalyst"
I hope the adverse event workshop, and the whole ICBO event, will be an opportunity for me to learn more about the Open Biology and Biomedical Ontologies (OBO) Foundry approach, and to discuss the challenges and opportunities in a “common language with which to energize cross-disciplinary research1)


I hope to better understand “how legacy terminologies, such as SNOMED CT, and the data coded with their aid can be successfully used for information-driven clinical and translational research2). My understanding is that the approach to be discussed at this event is the use of OBO Foundry based high-level reference ontologies, such as the Ontology for General Medical Science (OGMS), as a kind of catalyst instead of direct terminology-to-terminology mappings.


Yet another "standard", or ...
At the same time I did find this cartoon, circulating on Twitter this week, quite amusing. So, I think it will be a hot and interesting week in Buffalo, NY..
xkcd: Standards
Here's a brief introduction to the use case I and a colleague will present at the adverse event workshop:
"A use case will be presented describing how a query from a regulatory authority is handled as part of the regular ongoing pharmacovigilance in pharmaceutical research and development. It will illustrate how databases and literature are being reviewed manually, exemplify how different databases are structured and highlight some of issues in the coding of data. With this use case, we hope to provide a background to our interest in an ontologically based approach to enable a more automatic way to access, structure and analyze patient safety related data."
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