published by jesseerdmann on Fri, 02/25/2011 - 13:02
Sudeshna Das Mass. General Hospital, Harvard Medical School Cambridge, US
Previous efforts
MGED
OBI
EFO Experiment Factor Ontology
Investigation/Study/Assay format (ISA-Tab)
Tried to find a common way of expressing studies in terms of design, data acquisition (OBI), data processing (OBI), data analysis and data interpretation (OBI).
published by jesseerdmann on Fri, 02/25/2011 - 11:31
Dexter Pratt Selventa Cambridge, US
This talk was about an extension of the BEL talk. It represents a longer term look at being able to reason over resources written in BEL and produce reasonable hypotheses about the data and track the users analysis steps and changes to the hypotheses.
Genstruct Technology Platform
extract meaning from large volume of data using causal relations in a transparent manner
The HYP, consolidation of graph of relationships to a causal graph
published by jesseerdmann on Fri, 02/25/2011 - 11:16
John F. Madden Duke University, Durham, US
voiD: vocabulary of interlinked datasets (http://vocab.deri.ie/void)
Includes provenance, etc.
published by jesseerdmann on Fri, 02/25/2011 - 10:14
published by jesseerdmann on Fri, 02/25/2011 - 09:35
Nigam H. Shah Stanford School of Medicine California, USA
Using either the website at bioportal.bioontology.org or the API at rest.bioontology.org allow for the search of many ontologies and assorted resources. Unfortunately gene lists don't appear to be listed as part of the annotations on the resources. May still be useful.
YouTube introductory video
The Unreasonable Effectiveness of Data
published by jesseerdmann on Fri, 02/25/2011 - 09:08
Mike Miller Assistant Research Professor, U. Washington Founder/Chief Scientist, Cloudant Inc. Boston, USA
CloudAnt is a company primarily concerned with handling large data physics experiments using NoSQL (Not Only SQL in their parlance).
Five types of NoSQL databases:
published by jesseerdmann on Fri, 02/25/2011 - 08:35
Dr. Yolanda Gil Associate Director for Research, Intelligent Systems Division, USC/ISI Research Professor of Computer Science Information Sciences Institute University of Southern California, Los Angeles, USA
A lot of the ideas presented here are also goals of the Galaxy team, but they tend to eschew Semantics. Perhaps there is work that can be done/funded here?
published by jesseerdmann on Thu, 02/24/2011 - 16:55
Dr. Charles Mead National Cancer Institute Center for Biomedical Informatics and Information Technology (CBIIT) Rockville, USA
caGrid: focus on lowering barrier to entry based a multi-factored evaluation with regards to the group and level of interoperability for the tool to be shared. Several SemWeb proponents are working on the interfaces for 2.0 and they are intending on providing better interfaces to the semantics on the services provided on the grid.
published by jesseerdmann on Thu, 02/24/2011 - 15:37
James Balhoff National Evolutionary Synthesis Center Durham, US (NESCent)
Extremely detailed ability to describe phenotypes, probably too much for us. May be worth looking into anyway for our limited phenotype use.
OBO-Edit & Phenote -> Phenex
OBD: Ontology-Based Database
published by jesseerdmann on Thu, 02/24/2011 - 14:35
Eric Neumann Clinical Semantics Bedford, US
A presentation on moving from using a reference genome to assembling a unique genome specifically for clinical usage and in support of the development of Personalized Medicine. In addition, the collaboration of Clinical Semantics, BBN and PCAB are interested in tying clinical records to whatever information is available including genomic assemblies and discovered SNPs, etc.
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