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  • 1. OpenAnnotationandDomainOntologies–PaoloCiccarese Integrating OPEN ANNOTATION with any DOMAIN ONTOLOGY Paolo Ciccarese, PhD Assistant Professor of Neurology at Harvard Medical School Knowledge Architect of the MGH Biomedical Informatics Core Co-chair of the W3C Open Annotation Community Group Ontology and Imaging Informatics, Amherst, NY, June 24-25 2014 Thanks to Tim Clark, MIND Informatics Director
  • 2. OpenAnnotationandDomainOntologies–PaoloCiccarese My background • Evidence-based decision support (integration of guidelines based decision support with patient records and clinical workflows) • Structured Electronic Patient Records (using ontologies and archetypes) • Representation of scientific discourse (claims, hypothesis, evidence) • Annotation of digital content • I build and deliver systems
  • 3. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation is emerging as… • A uniform, pervasive method for describing… bookmarking, integrating, connecting, sharing … a variety of (digital) resources • A starting point and not only an end point • Valuable content.. sometimes even more valuable than the annotated content • Important search/discovery mechanism
  • 4. OpenAnnotationandDomainOntologies–PaoloCiccarese … we commonly use annotation • We annotate prints, HTML and PDFs • We bookmark/tag web pages… • … and publications (citations/references) • We comment on web pages, blogs, forums and emails • youtube, vimeo, flickr slideshare, twitter… http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059717
  • 5. OpenAnnotationandDomainOntologies–PaoloCiccarese Problem is… • Most of applications make very hard to export and aggregate our own annotation • Applications have a life span and they can disappear along with your annotation • No application will cover all the annotation related use cases • Domains are really challenging to regulate • Need for enabling applications developers and researchers to experiment
  • 6. OpenAnnotationandDomainOntologies–PaoloCiccarese Goal: annotation interoperability … and integration with ontologies (semantic annotation)
  • 7. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation Ontology (AO) - 2009 • OWL vocabulary for representing and sharing annotation of digital resources (text, images, audio, video, …) and their fragments in RDF format • It is orthogonal to the domain of interest • A little under-defined and with extension points – pros: easy adoption, extensible, customizable – cons: not always applied correctly, users not always sharing the custom solutions
  • 8. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation Ontology adopters The Living Document Project Biotea
  • 9. OpenAnnotationandDomainOntologies–PaoloCiccarese W3C Open Annotation Community Group • Started with the reconciliation of Annotation Ontology and Open Annotation Collaboration (interoperability starts from people) • 127 participants from around the world: 4th of 181 groups • Adopted by a draft specification for EPUB* • On track to become a W3C Working Group (impacting browsers?) http://www.w3.org/community/openannotation/ *EPUB® is a registered trademark of the International Digital Publishing Forum.
  • 10. OpenAnnotationandDomainOntologies–PaoloCiccarese W3C Open Annotation Community Group http://www.w3.org/community/openannotation/
  • 11. OpenAnnotationandDomainOntologies–PaoloCiccarese Mailing List
  • 12. OpenAnnotationandDomainOntologies–PaoloCiccarese Open Annotation Data Model (Feb 2013) http://www.openannotation.org/spec/core/
  • 13. OpenAnnotationandDomainOntologies–PaoloCiccarese Open Annotation Not only for annotating the web!
  • 14. OpenAnnotationandDomainOntologies–PaoloCiccarese Open Annotation Model • An annotation is considered to be a set of connected resources, it includes body(ies) and target(s), and conveys that the body is related to the target. • Ideally all the resources are identified by URIs
  • 15. OpenAnnotationandDomainOntologies–PaoloCiccarese Bodies and Targets • The Body and Target may be of any media type, and contain any type of content. – Annotate an Image with a video and a comment – Annotate multiple images with a webpage – Annotate an Image and an article with a comment – Annotate an image and a database record with a comment – Annotate annotation(s)
  • 16. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation Body Target http://coastalnhneurosurgeons.com/http://annonc.oxfordjournals.org/content/21/suppl_5/v190.full MRI scan of a glioblastoma multiforme annotated with ESMO Clinical Practice Guidelines
  • 17. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation Body https://www.youtube.com/watch?v=s5RM81_6vC8 http://coastalnhneurosurgeons.com/ Target MRI scan of a glioblastoma multiforme annotated with surgical footage
  • 18. OpenAnnotationandDomainOntologies–PaoloCiccarese Body Annotation Body Target MRI scan of a glioblastoma multiforme annotated with surgical footage
  • 19. OpenAnnotationandDomainOntologies–PaoloCiccarese Motivations • Reasons why the Annotation was created (describing, tagging, commenting, identifying…)
  • 20. OpenAnnotationandDomainOntologies–PaoloCiccarese Motivation modeled as skos:Concepts You can create a SKOS Schema for your own community
  • 21. OpenAnnotationandDomainOntologies–PaoloCiccarese anno1 body1 target1 http://coastalnhneurosurgeons.com/http://en.wikipedia.org/wiki/Glioblastoma_multiforme oa:Annotation rdf:type oa:hasTargetoa:hasBody oa:describing oa:motivatedBy dctypes:Image dctypes:Text
  • 22. OpenAnnotationandDomainOntologies–PaoloCiccarese http://annonc.oxfordjournals.org/content/21/suppl_5/v190.full anno1 body1 target1 http://coastalnhneurosurgeons.com/ oa:Annotation rdf:type oa:hasTargetoa:hasBody oa:describing oa:motivatedBy dctypes:Image dctypes:Text ? ?
  • 23. OpenAnnotationandDomainOntologies–PaoloCiccarese How to identify fragments?
  • 24. OpenAnnotationandDomainOntologies–PaoloCiccarese Specific Resources • Identify and describe resource fragments (for both bodies and targets)
  • 25. OpenAnnotationandDomainOntologies–PaoloCiccarese anno1 body1 sptarget1 http://coastalnhneurosurgeons.com/…jpghttp://annonc.oxfordjournals.org/content/21/suppl_5/v190.full oa:Annotation rdf:type oa:hasTargetoa:hasBody oa:describing oa:motivatedBy SELECTOR oa:hasSource
  • 26. OpenAnnotationandDomainOntologies–PaoloCiccarese Example of Selectors for images Source: http://maphub.github.io/api/
  • 27. OpenAnnotationandDomainOntologies–PaoloCiccarese You can create more selectors! Please contribute them back!
  • 28. OpenAnnotationandDomainOntologies–PaoloCiccarese Tagging
  • 29. OpenAnnotationandDomainOntologies–PaoloCiccarese anno1 body1 oa:Annotation rdf:type oa:hasTarget oa:hasBody oa:tagging oa:motivatedBy oa:Tag cnt:ContentAsText http://coastalnhneurosurgeons.com/…jpg SELECTOR sptarget1 “glioblastoma multiforme” cnt:chars
  • 30. OpenAnnotationandDomainOntologies–PaoloCiccarese Adding semantics…
  • 31. OpenAnnotationandDomainOntologies–PaoloCiccarese Simplest example: Semantic Tagging
  • 32. OpenAnnotationandDomainOntologies–PaoloCiccarese anno1 http://purl.obolibrary.org/obo/DOID_3068 sptarget1 http://coastalnhneurosurgeons.com/ oa:Annotation rdf:type oa:hasTargetoa:hasBody oa:describing oa:motivatedBy oa:SemanticTag SELECTOR Semantic Tagging 1 rdf:type
  • 33. OpenAnnotationandDomainOntologies–PaoloCiccarese anno1 http://purl.obolibrary.org/obo/GO_0005634 sptarget1 http://nanobiotechnews.com/ oa:Annotation rdf:type oa:hasTarget oa:hasBody oa:describing oa:motivatedBy oa:SemanticTag SELECTOR Semantic Tagging 2 rdf:type sptarget2 oa:hasTarget
  • 34. OpenAnnotationandDomainOntologies–PaoloCiccarese Web Annotation Tool • Domeo is a web application for producing and sharing stand-off annotation • Science and semantics linked in a few clicks • Domeo is open source and designed as an open system… – http://annotationframework.org – https://twitter.com/DomeoTool
  • 35. OpenAnnotationandDomainOntologies–PaoloCiccarese Manual and automatic annotation URLIamannotating Manualannotationtools Automaticannotationtools Exploration panels
  • 36. OpenAnnotationandDomainOntologies–PaoloCiccarese Semantic tagging NCBO BioPortal NIF Registry Domeo can query external services and use as qualifiers anything that has a unique identifier.
  • 37. OpenAnnotationandDomainOntologies–PaoloCiccarese Semantic tagging We could refer to diseases, historic figures, galaxies, places, events… APPintheProteinOntology
  • 38. OpenAnnotationandDomainOntologies–PaoloCiccarese Text Mining Service based: NCBO Annotator NIF Annotator UIMA GATE
  • 39. OpenAnnotationandDomainOntologies–PaoloCiccarese Text Mining Results
  • 40. OpenAnnotationandDomainOntologies–PaoloCiccarese Crowd sourcing results curation (v.1) Customizable SKOS-like… mappings
  • 41. OpenAnnotationandDomainOntologies–PaoloCiccarese Images in Domeo
  • 42. OpenAnnotationandDomainOntologies–PaoloCiccarese Image annotation By semantically tagging figures in a paper, I make them discoverable… And we can integrate inference capabilities We have a plugin that integrates to the Yale Image Finder
  • 43. OpenAnnotationandDomainOntologies–PaoloCiccarese
  • 44. OpenAnnotationandDomainOntologies–PaoloCiccarese Integration with Drupal7 (Semtech 2012)
  • 45. OpenAnnotationandDomainOntologies–PaoloCiccarese And more semantics…
  • 46. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotating with Named Graphs
  • 47. OpenAnnotationandDomainOntologies–PaoloCiccarese Intracellular Processing of APP Generates a Variety of Cleavage Products SpecificTarget1 SpecificTarget2 alpha-sAPP is derived from APP
  • 48. OpenAnnotationandDomainOntologies–PaoloCiccarese anno1 sptarget1 oa:Annotation rdf:type oa:describing oa:motivatedBy sptarget2 oa:hasTarget oa:hasTarget Graph1 oa:hasBody alpha-sAPP (depicted bysptarget2) is derived from APP (depicted by sptarget1)
  • 49. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation body: Graph1 <http://purl.bioontology.org/ontology/MSH/C096899> depiction <sptarget2> <http://purl.bioontology.org/ontology/MSH/C096899> preferredName “alpha-sAPP protein, human” <http://purl.obolibrary.org/obo/HGNC_620> depiction <sptarget1> <http://purl.obolibrary.org/obo/HGNC_620> preferredName “APP (human)” <http://purl.bioontology.org/ontology/MSH/C096899> derivedFrom <http://purl.obolibrary.org/obo/HGNC_620>
  • 50. OpenAnnotationandDomainOntologies–PaoloCiccarese Some examples using graphs • Antibodies annotation (NIF Antibody registry) • SWAN Ontology for scientific discourse and Micro-publications • Nano-publications
  • 51. OpenAnnotationandDomainOntologies–PaoloCiccarese NIF Antibody Registry http://antibodyregistry.org/
  • 52. OpenAnnotationandDomainOntologies–PaoloCiccarese Antibody Registry Integration • The NIF (https://www.neuinfo.org/) team made available a web service for searching against the registry • A plug-in for DOMEO has been developed to create antibodies-related annotation: – search the registry and display of the results – selection of the results – specification of the protocol and the subject of the study
  • 53. OpenAnnotationandDomainOntologies–PaoloCiccarese Domeo: antibodies Contributed to PubMed LinkOut through NIF (http://neuinfo.org) Translates into a formal OWL/RDF representation Antibodyregistry.org Paolo Ciccarese, PhD DILS 2013
  • 54. OpenAnnotationandDomainOntologies–PaoloCiccarese Export of the annotation in RDF • DOMEO can serialize the annotation in several serialization formats.
  • 55. OpenAnnotationandDomainOntologies–PaoloCiccarese Integration with NIF
  • 56. OpenAnnotationandDomainOntologies–PaoloCiccarese Domeo: Hypotheses management (v1) Translates into a formal OWL/RDF representation (SWAN Ontology) Possibility for integrating Nanopublications and BEL Data as evidence Paolo Ciccarese, PhD DILS 2013
  • 57. OpenAnnotationandDomainOntologies–PaoloCiccarese
  • 58. OpenAnnotationandDomainOntologies–PaoloCiccarese ANNOTOPIA UNIVERSAL ANNOTATION HUB Full ‘live’ version of the slides on: http://www.slideshare.net/paolociccarese/ This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/
  • 59. OpenAnnotationandDomainOntologies–PaoloCiccarese What is it Annotopia? • It is a Universal Annotation Hub • It provides you with back-end technology so that you can focus on the user interface (client) and the knowledge creation process • It consists of a collections of modules that provide useful services for creating, persisting, searching, sharing and enriching annotation • It is Open Annotation* compliant *Open Annotation Data Model (http://www.openannotation.org/spec/core/) https://github.com/Annotopia
  • 60. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotopia Instance 1 Annotopia: De-Siloing Annotation Aggregated querying and browsing Applications Text Mining Mashups APIs Annotopia Instance 2 APIs JSON-LD JSON-LD
  • 61. OpenAnnotationandDomainOntologies–PaoloCiccarese Thank you! paolo.ciccarese@gmail.com