Erik van Mulligen Marco Roos Scott Marshall Maarten Hekkelmans Martijn Schuemie Ivo Fokkema Marc van...

• 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

google

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