Upload
imelda-porter
View
29
Download
0
Embed Size (px)
DESCRIPTION
Acknowledgements. The ‘Virtual Tech Team’. Erik van M ulligen Marco Roos Scott Marshall Maarten Hekkelmans Martijn Schuemie Ivo Fokkema Marc van Driel Barend Mons. Marc Weeber Christine Chicester Daniel Kinzler Ravi Kalaputapu. Nigam Shah Andrew Gibson Gerard Meijssen - PowerPoint PPT Presentation
Citation preview
• Erik van Mulligen• Marco Roos• Scott Marshall• Maarten Hekkelmans• Martijn Schuemie• Ivo Fokkema• Marc van Driel• Barend Mons
• Nigam Shah• Andrew Gibson• Gerard Meijssen• Yaron Koren
• Marc Weeber• Christine Chicester• Daniel Kinzler• Ravi Kalaputapu
Acknowledgements
•Antoine van Kampen• Ruben Kok• Gert Jan van Ommen• Johan den Dunnen• Bill Melton
The ‘Virtual Tech Team’
• Albert Mons•Jan Velterop•Jacintha van Beemen•Geoffrey Bilder•Mark Musen• Carole Goble• Frank van Harmelen
Financial support Logistics and advise
Token Object
Concept
‘cancer’
‘cancer’Malignant NeoplasmsKrebskrankheitEtcC0-265
Unique ID
Concepts (with Unique Concept Identifiers – CIDs)
Digital Objects (with Digital Object Identifiers – DOIswhich are a form of Uniform Resource Name – URN)
Uniform Resource Locators – URLs
URLs not incorporating unique object or concept identifiers
Triples incorporating concept identifiers
(CIDs)
URLs incorporating object identifiers (DOIs URNs)
Objects can be digital or tangible, but this context is only about digital objects
Concepts can be conceptual or tangible, but never digital – they can be represented digitally or not
Unique concept identifiers are particularly important when they are represented digitally
Uniform Resource Identifier – URI – is an umbrella term for URNs and URLs
Concept 1 Concept 2Concept 3
Barend Mons ‘published’ This article (DOI)
CAPN3_000265 ‘has pathogenicity’ LGMD2A
Dystrophin (Homo Sapiens) ‘interacts with’ SNT3
Calpain-3 (Homo Sapiens) ‘has GO annotation’ ProteosomeEndopeptidaseactivity
Information silos
MRSIndex, virtual concepts
Daily feed
Triple Store
<ID1><edge><ID2>
Triple construction(unsupervised)
UniprotPubMed
NextprotCALIPHO
InWeb WikiPro SERMO BioBanksLOVD
GEO GWA
Tools, RDF, OWL, OBO, Protege
CommunityAnnotation(a posteriori)
CommunityAnnotation(a posteriori)
Direct feedBlogs, etc.
CommunityAnnotation(a priori)
Peregrine
Concept MappingQuery (expanded)
Harmonized data
<rdf:Description rdf:about="http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059"><cwa:typeRelation rdf:resource="http://www.nbic.nl/cwa#cooccurrence"/><cwa:strength>0.0625</cwa:strength><cwa:has_query>Limb girdle</cwa:has_query><cwa:discovered_by rdf:resource="http://www.nbic.nl/cwa#TripleMiner"/><cwa:timestamp>1240641052059</cwa:timestamp><cwa:annotation rdf:resource="http://www.uniprot.org/uniprot/flnc_human"/></rdf:Description> (free text ?)
Under the hood:
<rdf:Description rdf:about="http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059"><cwa:typeRelation rdf:resource="http://www.nbic.nl/cwa#cooccurrence"/><cwa:strength>0.0625</cwa:strength><cwa:has_query>Limb girdle</cwa:has_query><cwa:annotated_by rdf:resource="http://proteins.wikiprofessional-staging.org/index.php/Concept:85094810"/><cwa:timestamp>1240641052059</cwa:timestamp><cwa:annotation rdf:resource="http://www.uniprot.org/uniprot/flnc_human"/></rdf:Description> (free text ?)
The resulting triple: reference to annotator
-Self claim-proxy claim (JDD confirms this is JB)-CrossRef/Publisher mark-articles reviewed (Wikipedia Professional)-Unique Triples created-etc.
biobanks
PLoS
nature
LOVD
Proposal:• Add all 93,000 (+) mutations to WikiProfessional• display ‘status’ (submitter and curator) in pop up• Link back to relevant ‘LOVD’• Edit in Pop Ups (including research notes• Store each research note (also) in WikiProfessional• Show research notes anywhere• With reference to submitter• Link to unique person page in wikipeople• Have Wikipeople pages authorized by contributors• Have CrossRef certify unique contributor ID• Build tool to approve author self claims on publications• On triples• Enable proxy claims (co-authors)• Enable publisher/CWA approval of claims• Enable nano-credits for contributions• Enable double check by e-mail on ‘identity theft’ • Write/review Wikipedia article on each genetic disease