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CSHALS 2009

CSHALS 2009

Discussion, observations, and comments from the 2009 Conference on Semantics in Healthcare and Life Sciences. CSHALS is an official conference of the International Society for Computational Biology (ISCB).
Blog
Vijay Bulusu
file cabinet approach not suitable for the volume of information we deal with in Pharma R&D
Eric Neumann
from letters to texting...
Eric Neumann
Practical Knowledge Engineering for Pharma R&D - Ted Slater
Helena Deus
Ted Slater
Mark Wilkinson sees ontologies, workflows, and queries as equivalent things.
Ted Slater
Mark Wilkinson is asking for and making decisions on data that don't even exist at query time. This is a very cool take on web services discovery.
Ted Slater
Mark Wilkinson exposes just parts of his ontologies (e.g., single OWL classes) as web services, rather than focusing on SPARQL endpoints. This allows much finer control over what he's doing than you could otherwise get.
Ted Slater
Mark Wilkinson advocates publishing small, independent, single OWL classes, and claims that this is cheap, scalable, and flexible in comparison to developing huge ontologies.
Wilkinson uses OWL defined classes - defined by the properties - Joanne Luciano
Jonas Almeida
SPARQL-DL: http://clarkparsia.com/weblog... , anyone has a better link I can study this?
Eric Neumann
SPARQL => Service ... would be also cool to do Service => SPARQL
what is service => SPARQL if not the standard SPARQL protocol? - Lee Feigenbaum
Service to SPARQL is fixing all existing complicated web-services into SPARQL forms - Eric Neumann
Isn't that SPARQL => service? :) - Lee Feigenbaum
Jonas Almeida
Mark just posed, and answered, a complex database query with no database. There's something you don't see every day. - Ted Slater
Eric Neumann
Implicit service analytics ala SPARQL interface
Eric Neumann
Advanced Technologies Presentation: "Cardioshare" - Mark Wilkinson
Eric Neumann
'Ontologies should represent current possible forms of reality' ... then to be tested and removed if false.
Lee Feigenbaum
I like to distinguish between ontologies that model information and ontologies that model "the real world" - in my experience, the former is very useful for driving UIs, data collection, linking data, etc. and the latter is very useful for taxonomies and enabling semantic search, navigation, etc.
Of course, it often makes sense to use the 2 in conjunction - Lee Feigenbaum
Vijay Bulusu
Ontologies should represent reality?...Not always.
Eric Neumann
Discussion: small vs large ontologies... different uses?
First volley: Only as big as they need to be to solve the particular problem for which they're developed. - Ted Slater
Ted Slater
One great thing about working with semantic technologies is the wealth of tools available for free. There is much to be done, certainly, but there is much that has been done already and there are ample opportunities to contribute.
Jonas Almeida
Eric Neumann
Eric Neumann
Good idea using crowd-sourcing around Ontology annotations...
Ted Slater
Open Biomedical Annotator: A web service that converts a piece of free text (e.g., a journal abstract of 200 to 300 words), into a set of recognized and related ontology concepts and terms. - http://bioontology.org/tools...
Ted Slater
CBioC: collaborative curation of biological facts from literature. - http://cbioc.eas.asu.edu/
Helena Deus
Eric Neumann
Ontologies in Annotations: which way? there seem to be many ways to apply...
Helena Deus
Until BioPortal there was a lack of one stop shops of bioontologies :)
Lee Feigenbaum
Is there any work going on in the pharma/LS communities using the knoodl platform for collaborative ontology development?
Ted Slater
Nigam Shah is telling us about ontology services at the National Center for Biomedical Ontology. - http://bioontology.org/
Excellent point about 'just enough semantics' and 'it's all about annotated data' - William Hayes
Lee Feigenbaum
"It's about the annotated data". ...well, sometimes.
Helena Deus
It is for this sort of work that ontology development DOES make sense :-)
With the caveat that Tim B-L gave us yesterday: it's likely that we can't predict the all the benefits we'll enjoy if we represent our information ontologically, but those benefits could be huge. - Ted Slater
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