2012 CNI Fall Membership Meeting
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2012 CNI Fall Membership Meeting

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Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group, Washington DC, December 2012

Annotations in Biomedicine & Ongoing Work of the W3C Open Annotation Community Group, Washington DC, December 2012

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2012 CNI Fall Membership Meeting 2012 CNI Fall Membership Meeting Presentation Transcript

  • 2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC Annotations in Biomedicine&Ongoing Work of the W3C Open Annotation Community Group Paolo Ciccarese, PhD paolo.ciccarese@gmail.com Mass General Hospital Harvard Medical School
  • Annotation in Biomedicine 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • As (biomedical) scientists… • We deal with an increasing amount of digital resources: documents, images, videos, datasets, vocabul aries, databases, software… – About 150-200 articles a week – 10mins/article ≈ 34 hours/week – How can we manage it? 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Limitations of the Web of Documents • Machines don’t do very well in *understanding* documents and have difficulties to find, present, access, or maintain available electronic information on the web • Need for a data representation to enable software products (agents) to provide access to heterogeneous and distributed information – Tasks often require to combine data on the Web – Humans combine these information easily** even ifdifferent terminologies are used and the information is incomplete, or buried in images and videos 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • News and Hypotheses Semantic tagging APP Biological Processes ExpertsPathways Videos/images Antibodies 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Document Metadata Exchange Organizer • Domeo is a web application for producing and sharing manual and semi-automatic (structured/unstructured) stand-off annotation • Domeo is designed as an open system Ciccarese et al, 2012 Open semantic annotation of scientific publications using DOMEO http://www.jbiomedsem.com/content/3/S1/S1 http://annotationframework.org https://twitter.com/DomeoTool 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Semantic tagging through ontologies http://purl.obolibrary.org/obo/PR_000004168 Label ‘amyloid beta A4 protein’ Exact synonyms ‘APP’, ‘amyloidogenic glycoprotein’, … Related Synonyms ‘A4’, ‘ABPP’, Is a http://purl.obolibrary.org/obo/PR_000000001 Label ‘protein’ Definition ‘An amino acid chain that…’ 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • APPs for the Semantic Resources Project, May 2010 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Reagents (reproducibility) antibodyregistry.org 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Annotation of Argumentation Semantic Web Applications in Neuromedicine (SWAN) project [2007] classic publication scientific discourse ‘semantic’ representation http://tinyurl.com/cgyna2m 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • graph representation 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Annotation Sharing Dynamic inventory of Web-based neuroscience resources Video Annotation http://www.neuinfo.org/ Tools Viz. ann. systems Drupal Framework for building online scientific communities http://sciencecollaboration.org/ Analysis 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Annotation Ontology (AO) • OWL vocabulary for representing and sharing annotation of digital resources and their fragments in RDF format • Focus on biomedicine and sciences. But desire to make the AO framework more broadly usable. Ciccarese et al, 2011 An open annotation ontology for science on web 3.0 http://www.jbiomedsem.com/content/2/S2/S4 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Annotation Ontology Network Biotea Annotations at Harvard The Living Document Project 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Open Annotation Collaboration • Focus on interoperability for annotations in order to allow sharing of annotations across: – Annotation clients; – Content collections; – Services that leverage annotations. • Focus on annotation for scholarly purposes. But desire to make the OAC framework more broadly usable. http://openannotation.org/ 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • AO+OAC = W3C Open Annotation • Annotation Ontology and Open Annotation Collaboration have been merged to create the W3C Open Annotation Community Group • Officially started in February 2012 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD Take Note Site Visit, November 1st 2012
  • W3C Open Annotation Community Group • Is working towards a common, RDF-based, specification for annotating digital resources: – Aligned with WWW Architecture & Linked Open Data best practices – Focus on interoperability – the sharing of annotations across clients, servers, repositories and applications – Annotations are treated as first class Web resources, i.e., referenceable and available to themselves be annotated 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • http://www.w3.org/community/openannotation/ 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Participants 54 Participants From more than 30 institutions Additional users interact through the mailing list 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Public Mailing List 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Specifications (Drafts) 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Plans for Open Annotation 1.0 Release • Currently working on a new draft and a new tutorial that will be published in mid January for collecting further feedback • We are planning a release of Open Annotation Model v. 1.0 for March/April • They will have a new structure that we believe will help lowering the learning and implementation curves 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  • Acknowledgements • Tim Clark, Director of MIND Informatics • Domeo Support: Maryann Martone, Anita Bandrowski, VadimAstakhov, Anita de Waard, Bradley Allen, Keith Gutfreund • W3C Community Group: Robert Sanderson, Herbert van de Sompel and all the members • Funding: National Institutes of Health, Elsevier Laboratories, and Eli Lilly & Co. 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD