?
Complex network architecture
Layered network architecture
Layered network architecture
specimenknuckle
genomeknuckle
literatureknuckle
taxonomyknuckle
Layered network architecture
specimenknuckle
genomeknuckle
literatureknuckle
taxonomyknuckle
Layered network architecture
specimenknuckle
genomeknuckle
literatureknuckle
taxonomyknuckle
StrainInfo.net bioportal scope
Data warehousing
Stein LD (2003), Integrating biological databases, Nat Rev Genet 4(5):337-45.
Knuckles-and-nodes approach
Stein LD (2003), Integrating biological databases, Nat Rev Genet 4(5):337-45.
Semantic web technologies• Globally Unique Identifiers (GUID)
Digital Object Identifiers (DOI)
Life Science Identifiers (LSID)
http://www.doi.org
http://lsid.sourceforge.net
• Ontologies
domain-specific vocabularies (entity-relationships)
RDF triples, XML Schema
Gene Ontology (GO-terms), CABRI, ABCD
Semantic web technologies• Web Services
“A web service is a software system designed to support interoperable machine-to-machine interaction over a network. It has an interface described in a machine-processable format (specifically WSDL)”
HTTP binding
FTP binding
SOAP binding
• Workflow Management Systems
Taverna Workbench (MyGrid Project)
BioMoby
Pegasys
The End
www.StrainInfo.net
WEB
online since February 1st, 2007
Accumulative learning
Intrusion detection
Error in NCIMB 8233T
RIA 1038 RIA 1040
Error in DSM 40066T
CBS 498.68 CBS 500.68
12.5% of the type strainswould have been affected by the inconsistencies present in the originating data sources, without the implementation of an error detection/correction strategy
“GARBAGE IN GARBAGE OUT”
PRINCIPLE
Intrusion detection
Intrusion detection
Integrating information sources
Integrating information sources
Navigate the information space
?
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird partyinformationinformation
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird partyinformationinformation
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird partyinformationinformation
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird party
informationinformation
AJ011504
AJ011504
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird party
informationinformation
Pseudomonas sp.
BKME-9
Mohn W.W. et al.
Navigating information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird party
informationinformation
AJ011504
Pseudomonas sp.
BKME-9
Mohn W.W. et al.
Navigate the information space
Navigate the information space
ATCC 700689CCUG 50779CIP 106708DSM 17554LMG 20220
Pseudomonas abietaniphila(type strain)
Navigate the information space
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird party
informationinformation
AJ011504
Pseudomonas sp.
BKME-9
Mohn W.W. et al.
ATCC 700689CCUG 50779CIP 106708DSM 17554LMG 20220
Pseudomonas abietaniphila(type strain)
Pseudomonas abietaniphila(type strain)
Navigate the information space
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird party
informationinformation
AJ011504
Pseudomonas sp.
BKME-9
Mohn W.W. et al.
ATCC 700689CCUG 50779CIP 106708DSM 17554LMG 20220
Pseudomonas abietaniphila(type strain)
Pseudomonas abietaniphila(type strain)
AJ011504
Navigate the information space
specimenspecimen
sequencessequences literatureliterature
taxonomytaxonomythird partythird party
informationinformation
Pseudomonas abietaniphila(type strain)
Glueing it all together
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