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2012 CNI Fall Membership Meeting, Dec 10th 2012, Washington DC  Annotations in Biomedicine&Ongoing Work of the W3C Open An...
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, da...
Limitations of the Web of Documents  • Machines don’t do very well in *understanding*    documents and have difficulties t...
News and Hypotheses  Semantic tagging                                  APP                                                ...
Document Metadata                                  Exchange Organizer  • Domeo is a web application for producing and    s...
Semantic tagging through ontologies         http://purl.obolibrary.org/obo/PR_000004168         Label ‘amyloid beta A4 pro...
APPs for the Semantic Resources Project, May 2010                       2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Reagents (reproducibility)                                                  antibodyregistry.org                       201...
Annotation of Argumentation                                          Semantic Web Applications in Neuromedicine           ...
graph representation                       2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
Annotation Sharing                   Dynamic inventory of Web-based                   neuroscience resources              ...
Annotation Ontology (AO)  • OWL vocabulary for representing and sharing    annotation of digital resources and their    fr...
Annotation Ontology Network                                                           Biotea                              ...
Open Annotation Collaboration  • Focus on interoperability for annotations in    order to allow sharing of annotations acr...
AO+OAC = W3C Open Annotation  • Annotation Ontology and Open Annotation    Collaboration have been merged to create the   ...
W3C Open Annotation                        Community Group  • Is working towards a common, RDF-based,    specification for...
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      ...
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 ...
Acknowledgements  • Tim Clark, Director of MIND Informatics  • Domeo Support: Maryann Martone, Anita    Bandrowski, VadimA...
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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

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Transcript of "2012 CNI Fall Membership Meeting"

  1. 1. 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
  2. 2. Annotation in Biomedicine 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  3. 3. 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
  4. 4. 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
  5. 5. News and Hypotheses Semantic tagging APP Biological Processes ExpertsPathways Videos/images Antibodies 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  6. 6. 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
  7. 7. 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
  8. 8. APPs for the Semantic Resources Project, May 2010 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  9. 9. Reagents (reproducibility) antibodyregistry.org 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  10. 10. 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
  11. 11. graph representation 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  12. 12. 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
  13. 13. 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
  14. 14. Annotation Ontology Network Biotea Annotations at Harvard The Living Document Project 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  15. 15. 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
  16. 16. 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
  17. 17. 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
  18. 18. http://www.w3.org/community/openannotation/ 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  19. 19. Participants 54 Participants From more than 30 institutions Additional users interact through the mailing list 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  20. 20. Public Mailing List 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  21. 21. Specifications (Drafts) 2012 CNI Fall Membership MeetingPaolo Ciccarese, PhD
  22. 22. 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
  23. 23. 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
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