?

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