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IRBW2009 workshop presentation Mons
Posted Mon, 08/06/2009 - 12:15 by
Gudmundur A Thorisson
Brief decription of this document
Barend Mons, Netherlands Bioinformatics Centre - Community annotation in WikiProteins
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The ‘Virtual Tech Team’ •Erik van Mulligen •Marco Roos •Scott Marshall •Maarten Hekkelmans •Martijn Schuemie •Ivo Fokkema •Marc van Driel •Barend Mons Financial support •Antoine van Kampen •Ruben Kok •Gert Jan van Ommen •Johan den Dunnen •Bill Melton
Acknowledgem ents
•Nigam Shah •Andrew Gibson •Gerard Meijssen
•Marc Weeber •Christine Chicester •Daniel Kinzler • Ravi
Logistics and advise •Albert Mons •Jan Velterop •Jacintha van Beemen •Geoffrey Bilder •Mark Musen •Carole Goble •Frank van Harmelen
Unique ID Conce pt
‘canc er’
Toke n ‘cancer’ Malignant Neoplasms Krebskrankheit Etc C0-265
Obje ct
Concepts (with Unique Concept Identifiers – CIDs)
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
Digital Objects (with Digital Object Identifiers – DOIs which are a form of Uniform Resource Triples incorporating concept identifiers
Uniform Resource Locators – URLs
URLs incorporating object identifiers (DOIs
URLs not incorporating unique object or concept
Uniform Resource Identifier – URI – is an umbrella term for URNs and URLs
Concept 1
Concept 3
Concept 2
Barend Mons CAPN3_000 265 Dystrophin (Homo Sapiens) Calpain-3 (Homo Sapiens)
‘publish ed’ ‘has pathogenicity’ ‘interacts with’ ‘has GO annotation’
This article (DOI) LGMD2 A S NT3 Proteosome Endopeptid ase activity
Tools, RDF, OWL, OBO, Protege
Communit y Annotatio n
Triple Store <ID1><edge> <ID2> Harmonized data Peregri ne Concept Mapping MRS
Index, virtual concepts
Communit y Annotatio n
Triple construction (unsupervised) Query (expanded)
Commun ity Annotati on
Direct feed Blogs, Daily feed
Uniprot PubMe d
Nextprot CALIPHO
InWe b
WikiPro
SERMO
BioBanks LOVD
GEO
GWA
Information
Under the hood:
<rdf:Description rdf:about="http://www.nbic.nl/cwa/relation/C0035820#C0060383#12 40641052059"> <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>
The resulting triple: reference to annotator
<rdf:Description rdf:about="http://www.nbic.nl/cwa/relation/C0035820#C0060383#12406410 52059"> <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="ht tp://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 ?)
-Self claim -proxy claim (JDD confirms this is JB) -CrossRef/Publisher mark -articles reviewed (Wikipedia Professional) -Unique Triples created -etc.
googl e
L OVD
natur e
PLoS
bioban ks
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
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© 2009
GEN2PHEN Project
.
The
GEN2PHEN Knowledge Centre
has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)
under grant agreement number 200754 - the GEN2PHEN project.
