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20 Νοε 2013 (πριν από 3 χρόνια και 8 μήνες)

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Bio
-
ontologies

SIG

in conjunction with ISMB 2010

9
-
10 July

Boston, USA

http://www.bio
-
ontologies.org.uk


General Info


94 participants


mainly from USA and
moslty

Stanford University.



Online proceedings will be published


the
authors who are interested must prepare a
camera
-
ready according to special requirements,
if they want they paper to be in a referred
edition.



All PPT presentations are available on the SIG
website.


Interesting Presentations


The
Bioportal



facilities

http://bioportal.bioontology.org/



ISA Software Suit


annotation of experimental data (assays),
annotation according to
ontologies

http://isatab.sourceforge.net/



Knowledge Blog

http://ontologies.knowledgeblog.org



Journal of Biomedical Semantics

http://www.jbiomedsem.com



Other conferences OBML, ICBO,

SMBM

Interesting Presentations


Ciccarese

& Clark


Metadata is kept separately from the data and can be used to find crossing
points with other documents



Ghazvinian

et
al.

How
Orthogonal are the OBO Foundry
Ontologies
?


Numbers


53
ontologies

in total


93% overlap


13
ontologies

reuse terms


only 3
ontologies

are fully orthogonal


Reasons

terms representing the same entity with same name

terms representing related but different entities with the same name

terms represent different entities with the same name




OpenTox

related Issues


Definition of
ontologies

[
Rzhetsky
, A.]:


Tool for structuring,
organising
, mathematical theory


Walking shoes


Esperanto


common language



Referencing
ontologies


MIREOT
-

Minimum information to reference an
external ontology
terms

http://obi
-
ontology.org/page/MIREOT



Upload to
Bioportal



info@bioportal.org




OpenTox

related Issues


Available
ontologies


E
-
Lico

project

http://www.e
-
lico.eu/?q=node/155


eProPlan

(e
-
Lico

Protégé
-
based Planning) & Data Mining Work Flow Ontology


Data Mining Ontology for Workflow Optimization (DMOP) through Meta
-
Mining


OntoDM
: An Ontology of Data Mining
-

2008

http://portal.acm.org/citation.cfm?id=1490755


Exposé


DDI
-

An Ontology for Drug Discovery Investigations

http://users.aber.ac.uk/ddq/ddi/wiki/index.php?title=Main_Page



Web Protégé = Collaborative Protégé

Different partners can use one of those for editing the same ontology



Soon compatibility between Protégé 3 and 4 is expected

Important Contacts


Dr. Larisa N.
Soldatova



SIG co
-
organiser

RC UK Fellow, Computer Science Department,

The University of Wales,
Aberystwyth
, UK

lss@aber.ac.uk




Prof. Ross King


with previous experience in predictive toxicology

Group Coordinator

Computational Biology Group

Department of Computer Science

Aberystwyth

University

rdk@aber.ac.uk



Julia
Kozlovsky

(AstraZeneca)


Pistoia Alliance (open standards)
-

http://www.pistoiaalliance.org/


Innovative Medicines Initiative
-

http://imi.europa.eu/



James Malone

http://www.ebi.ac.uk/~malone/



bioontologies@gmail.com

a mailing list where one could ask related questions