Up at 5AM: The 5AM Solutions Blog

Highlights from the Conference on Semantics in Healthcare and Life Sciences (CSHALS)

Posted on Wed, Mar 05, 2014 @ 10:04 AM

This was the fourth time I've attended the Conference on Semantics in Healthcare and Life Sciences (CSHALS), and every time I come back with new ideas. This conference has a much greater emphasis on implementation than in the past. Considering that this conference has been going for seven years, that means a very clear evolution from its more speculative origins. Organized by the International Society for Computational Biology (ISCB), it's perhaps the best blend I've seen of people from industry and academia centered around applying semantic technologies and strategies to biomedical research.

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Tags: Data Science, semantics, SPARQL, CSHALS

6 Points Along the Ontology Spectrum

Posted on Tue, Dec 03, 2013 @ 06:00 AM

This is the first post in our data modeling series. Today we give a broad perspective for different ways to represent knowledge and data. Some of our posts have talked about ontologies, controlled vocabularies, data models, and other kinds of knowledge representation. All of these share some commonalities, and exist along the Ontology (or sometimes Semantic) Spectrum.

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Tags: biobanking, semantics, ontology

4 Reasons Why Semantics Help Make Biobanks Better

Posted on Tue, Oct 01, 2013 @ 06:00 AM

The Semantic Web provides a means to link information on the web to each other and to things in real life in an interoperable way. Internationalized Resource Identifiers, of which URLs are a type, are used to identify nearly everything, and linked data makes it possible to visit those URLs to get more information about the things they represent. This has some very useful applications, especially in biobanking. Semantics was literally made for biomedical research, and here are four ways in which that relationship can help make biobanks better information resources:

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Tags: biobanking, biobanking software, semantics, PROV-O

Two Secret Ingredients for Effective Patient Consent Management

Posted on Tue, Sep 24, 2013 @ 06:00 AM

Clinical trials require collection and management of patient Informed Consent Forms (ICF). This includes outlining parameters for which de-identified information, clinical/analytical data, and specimen collected (during and post clinical trial) would be used. 

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Tags: biobanking, consent, biobanking software, semantics, annotation

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