11111011011 Pedro Lopes pedrolopes@ua.pt
‣ WAVe
‣ GEN2PHEN
• Research
• WAVe
• Development
• Leicester internship
• Publications ‣ RECOMB2010 + JBI2010 + ITAB2010 + SPGH2010 + HM (?)
‣ http://bioinformatics.ua.pt/WAVe
‣ From relational databases to semantic web knowledge • 2 prototype apps
‣ EU-ADR • Web Platform Preview ‣ XSD + Workflow
2010
2010
{ coeus } + { diseasecard } + { wave } + { writing }
guidelines
‣ Semantic Web Application Framework • Streamlined application deployment ‣ Web server + database + configuration file = SW app • Federation ‣ Distributed knowledge network
‣ Research & Development • Monthly release cycle • Alpha release expected for June ‣ DiseaseCard seed
coeus
1955 COEUS CONNECTORS CSV
JS
SQL
WS
XML
3S DB Package: COEUS Data, Connectors Result: Knowledge Seed [only data] - Seed ready for usage
coeus
1985 3S DB SEED
COEUS API REST + SOAP
SPARQL
WEB APP
Package: COEUS API Result: Knowledge Seed + Web App - App online + Seed "on garden"
coeus
2015 SEED
SEED SEED
SEED
SEED SEED
COEUS FEDERATION COEUS API REST + SOAP
SPARQL Package: COEUS Federation Result: Federated Knowledge Garden - Distributed Knowledge Network
coeus
KNOWLEDGE GARDGEN
coeus
Concept
Seed
Host coeus:isResourceOf Description
Version coeus:host
coeus:hasModule
coeus:hasResource
coeus:isModuleOf
coeus:extends
Shortname
Public (boolean)
rdfs:versionInfo coeus:public Seed
rdfs:label
Version rdfs:versionInfo Resource
rdfs:description Description coeus:hasModule
Description
coeus:method
coeus:isIncludedIn Entity
Name rdfs:label
Module
Bridge Method
Name
Description coeus:loadsFrom
Item property
coeus:loadsFor
Shortname
coeus:property coeus:query
XML
coeus:hasBridge
Concept
coeus:loadsFrom Concept
coeus:isConceptOf rdfs:description
dc:title Item
coeus:isConceptOf coeus:isAssociatedTo
SQL Token
Description
coeus:replace SQL
dc:title
rdfs:label
coeus:hasConcept
Predicate
coeus:property Name
Concept
XML Token
coeus:loadsFor
coeus:hasConcept
coeus:isConnnectedTo
SQL Query
coeus:query coeus:username Description
rdfs:description Shortname
coeus:password
rdfs:label coeus:loadsFrom Shortname Name coeus:enabled coeus:loadsFor
Username
coeus:column
Password
Item coeus:isAssociatedTo
Column Name
Enabled (Boolean)
CSV
coeus
XPath Query
coeus:replace
coeus:isBridgedTo coeus:hasEntity Enabled (Boolean)
coeus:isConnnectedTo
Predicate
Enabled (Boolean) Extension
coeus:enabled
coeus:isEntityOf
Address
coeus:method
Access Method
coeus:enabled
dc:source Bridge Plugin (Boolean) coeus:extension
Module rdfs:label
dc:source
rdfs:description Shortname
dc:title coeus:plugin rdfs:label
coeus:isModuleOf rdfs:description
Entity
Name
dc:title
Name
rdfs:label
coeus:includes
rdfs:description
coeus:property
Predicate
coeus:column coeus:line coeus:replace coeus:delimiter
Column Number
Line Delimiter
CSV Token
‣ DiseaseCard4 • Requirements analysis completed • New UI ‣ New interaction paradigm
‣ Bridging the gap between the genotype to the phenotype ‣ Development • COEUS-based • First prototype/seed/proof-of-concept
diseasecard
‣ Status • v1.2.1 online • Human Mutation publication waiting confirmation...
‣ Development • There is always something to update.. • Monthly release cycle ‣ Next: v1.2.2 this week
wave
‣ Publications • COEUS ‣ SWAT4LS2011
‣ Thesis • Define structure ‣ ASAP
‣ Software Engineering Journal
• Writing begins after COEUS
‣ Whatever opens up...
• Starting around October...
• EU-ADR
writing
omments, questions, suggestions, critics, advice, feedbac