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Erik van M ulligen Marco Roos Scott Marshall Maarten Hekkelmans Martijn Schuemie Ivo Fokkema

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

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Erik van M ulligen Marco Roos Scott Marshall Maarten Hekkelmans Martijn Schuemie Ivo Fokkema

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  1. Acknowledgements The ‘Virtual Tech Team’ • Erik van Mulligen • Marco Roos • Scott Marshall • Maarten Hekkelmans • Martijn Schuemie • IvoFokkema • Marc van Driel • Barend Mons • Marc Weeber • Christine Chicester • Daniel Kinzler • Ravi Kalaputapu • Nigam Shah • Andrew Gibson • Gerard Meijssen • YaronKoren Financial support Logistics and advise • Albert Mons • Jan Velterop • Jacinthavan Beemen • Geoffrey Bilder • Mark Musen • Carole Goble • Frank van Harmelen • Antoine van Kampen • Ruben Kok • Gert Jan van Ommen • Johan den Dunnen • Bill Melton

  2. Unique ID Concept ‘cancer’ Token Object ‘cancer’ Malignant Neoplasms Krebskrankheit Etc C0-265

  3. 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 Concepts (with Unique Concept Identifiers – CIDs) Digital Objects (with Digital Object Identifiers – DOIs which are a form of Uniform Resource Name – URN) Triples incorporating concept identifiers (CIDs) Uniform Resource Locators – URLs URLs incorporating object identifiers (DOIs URNs) URLs not incorporating unique object or concept identifiers Uniform Resource Identifier – URI – is an umbrella term for URNs and URLs

  4. Concept 1 Concept 2 Concept 3 This article (DOI) ‘has pathogenicity’ ‘interacts with’ ‘has GO annotation’ LGMD2A SNT3 Proteosome Endopeptidase activity ‘published’ Barend Mons CAPN3_000265 Dystrophin (Homo Sapiens) Calpain-3 (Homo Sapiens)

  5. Tools, RDF, OWL, OBO, Protege Triple Store Community Annotation (a posteriori) Community Annotation (a posteriori) <ID1><edge><ID2> Harmonized data Community Annotation (a priori) Triple construction (unsupervised) Peregrine Query (expanded) Concept Mapping Direct feed Blogs, etc. MRS Index, virtual concepts Daily feed Nextprot CALIPHO BioBanks LOVD Uniprot PubMed InWeb WikiPro SERMO GEO GWA Information silos

  6. Under the hood: <rdf:Descriptionrdf:about="http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059"> <cwa:typeRelationrdf:resource="http://www.nbic.nl/cwa#cooccurrence"/> <cwa:strength>0.0625</cwa:strength> <cwa:has_query>Limb girdle</cwa:has_query> <cwa:discovered_byrdf:resource="http://www.nbic.nl/cwa#TripleMiner"/> <cwa:timestamp>1240641052059</cwa:timestamp> <cwa:annotationrdf:resource="http://www.uniprot.org/uniprot/flnc_human"/> </rdf:Description> (free text ?)

  7. The resulting triple: reference to annotator <rdf:Descriptionrdf:about="http://www.nbic.nl/cwa/relation/C0035820#C0060383#1240641052059"> <cwa:typeRelationrdf:resource="http://www.nbic.nl/cwa#cooccurrence"/> <cwa:strength>0.0625</cwa:strength> <cwa:has_query>Limb girdle</cwa:has_query> <cwa:annotated_byrdf:resource="http://proteins.wikiprofessional-staging.org/index.php/Concept:85094810"/> <cwa:timestamp>1240641052059</cwa:timestamp> <cwa:annotationrdf:resource="http://www.uniprot.org/uniprot/flnc_human"/> </rdf:Description> (free text ?)

  8. -Self claim -proxy claim (JDD confirms this is JB) -CrossRef/Publisher mark -articles reviewed (Wikipedia Professional) -Unique Triples created -etc.

  9. google LOVD nature PLoS biobanks

  10. 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

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