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[protege-discussion] NCBO Webinar: Using ontologies to do integrative systems biology - Dec. 5 at 10:00am PST

Trish Whetzel plwhetzel at
Fri Nov 30 10:12:54 PST 2012

The next NCBO Webinar will be presented by Chris Evelo from Maastricht
University on "Using ontologies to do integrative systems biology" at
10:00am PST, Wednesday, Dec. 5.  Below is information on how to join the
online meeting via WebEx and accompanying teleconference. For the full
schedule of the NCBO Webinar presentations see:

To really get ahead with complex health problems like cancer and diabetes
we need to become better at combining different types of studies, including
large scale genomics and genetics studies and we need to learn to better
combine such studies with existing biological knowledge. Typically this
leads to questions like “I did this study with high-fat low fat diet
comparison in mice and looked at the transcriptomics results in liver, fat
and muscle. Has anyone else perform a study like this and published the
data, maybe for proteomics? Can I find that in one of these open data
repositories?”. Or, “I did that, can I find which biological pathways are
affected most and whether any of the proteins in that pathway is a known
target for an existing drug?”.  Or even “I did that study, could I find
another study that yielded the same kind of biological results even if it
was from a different research field with a completely different result?”.
To answer these kind of questions we need to describe studies and study
results, structure knowledge allow mapping of “equal” things with different
identifier schemes and essentially do a lot of mapping to and between
ontologies. More and more of this is getting real. I will discuss how
ISA-tab inspired our study capture tool in which we use templates to get
consistent ontology choices. How we use identifier mapping to allow
analyses and visualisation of different kinds of data of "domain" annotated
knowledge. And finally, how we use all kinds of mappings to extend
knowledge captured in pathways with other information in databases. In that
way I will hop, step and jump through ISA-tab, the phenotype database,
WikiPathways and Open PHACTS using ontologies and mappings as a jumping

Chris Evelo is the head of the department of Bioinformatics at Maastricht
University. He is involved in a number of initiatives relevant to this
topic. The phenotypic database initiative that uses ISA-tab based
approaches to describe studies, samples and assays and links to data
processing pipelines and actual data at different stages of processing for
many technologies (see WikiPathways and its accompanying tools
to structure existing knowledge in biological pathways and make it
available for usage in analytical tools and Open PHACTS which builds a
large Open Pharmacological Knowledge space based on semantic web technology
for drug discovery.

To start or join the online meeting
Go to
Meeting Number: 925 343 903
Meeting Password: ncbo

Audio conference information
To receive a call back, provide your phone number when you join the
meeting, or call the number below and enter the access code.
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers:

Access code:925 343 903

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

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