I was asked to give a brief talk in a Seminar (Semantic Web in Biomedicine), on computational tools that make the task of using all the great ontologies (like MIRIAM, SBO, ChEBI, UniProt, KEGG) that we have come to love easier.
In the presentation I introduce several of the Web Services at the EBI, libAnnotationSBML and SAINT.
7. Systems Biology Ontology
Quantitative
Roles of Precise List of
parameters
reaction classification simulation Entity Interaction
used in
participants of rate laws frameworks
biochemistry
Macromolecule Reaction
Substrate Hill coefficient Hill function Discrete
Non-covalent
Control
complex
Biochemical
Simple chemical
process
First order
Michaelis
Catalyst reversible math Continuous
constant
action kinetics
Empty set Combination
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16. EBI Web Service
Java Clients exist for all services
Documentation is sparse, however
method calls are intuitive
WSDL files work fine with .NET
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18. LibAnnotationSBML
Java – Library for Reading / Writing
Annotations for SBML files using
ChEBI
SBO
MIRIAM
KEGG
UniProt
All wrapped into one unified API
http://sbml.org/Community/Programs/libAnnotationSBML
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20. LibAnnotationSBML
Several Examples using
LibAnnotationSBML exist today:
SbmlReactionBalancer: determines whether
the reactions specified within an SBML file
are elementally balanced (retrieves formulae
of reaction participants)
AnnotationWizard / AutoCompleter provides
OntologyTerms for a given name
http://sbml.org/Community/Programs/libAnnotationSBML
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21. SAINT
http://saint-annotate.sourceforge.net/
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45. Credit where Credit is due
the libAnnotationSBML UML slide
comes from Neil’s slideshare:
http://www.slideshare.net/neilswainston/liban
notationsbml
Most of the SAINT slides come from
Allyson’s slideshare:
http://shrinkster.com/1cqb
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