OpenAnnotationandDomainOntologies–PaoloCiccarese
Integrating OPEN ANNOTATION
with any DOMAIN ONTOLOGY
Paolo Ciccarese, PhD...
OpenAnnotationandDomainOntologies–PaoloCiccarese
My background
• Evidence-based decision support (integration
of guideline...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotation is emerging as…
• A uniform, pervasive method for describing…
...
OpenAnnotationandDomainOntologies–PaoloCiccarese
… we commonly use annotation
• We annotate prints,
HTML and PDFs
• We boo...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Problem is…
• Most of applications make very hard to export
and aggregate...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Goal: annotation interoperability
… and integration with ontologies
(sema...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotation Ontology (AO) - 2009
• OWL vocabulary for representing and sha...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotation Ontology adopters
The Living Document
Project
Biotea
OpenAnnotationandDomainOntologies–PaoloCiccarese
W3C Open Annotation Community Group
• Started with the reconciliation of ...
OpenAnnotationandDomainOntologies–PaoloCiccarese
W3C Open Annotation Community Group
http://www.w3.org/community/openannot...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Mailing List
OpenAnnotationandDomainOntologies–PaoloCiccarese
Open Annotation Data Model (Feb 2013)
http://www.openannotation.org/spec/...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Open Annotation
Not only for annotating the web!
OpenAnnotationandDomainOntologies–PaoloCiccarese
Open Annotation Model
• An annotation is considered to be a set of connec...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Bodies and Targets
• The Body and Target may be of any media
type, and co...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotation
Body Target
http://coastalnhneurosurgeons.com/http://annonc.ox...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotation
Body
https://www.youtube.com/watch?v=s5RM81_6vC8
http://coasta...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Body
Annotation
Body
Target
MRI scan of a glioblastoma multiforme annotat...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Motivations
• Reasons why the Annotation was created
(describing, tagging...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Motivation modeled as skos:Concepts
You can create a SKOS Schema for your...
OpenAnnotationandDomainOntologies–PaoloCiccarese
anno1
body1 target1
http://coastalnhneurosurgeons.com/http://en.wikipedia...
OpenAnnotationandDomainOntologies–PaoloCiccarese
http://annonc.oxfordjournals.org/content/21/suppl_5/v190.full
anno1
body1...
OpenAnnotationandDomainOntologies–PaoloCiccarese
How to identify
fragments?
OpenAnnotationandDomainOntologies–PaoloCiccarese
Specific Resources
• Identify and describe resource fragments (for
both b...
OpenAnnotationandDomainOntologies–PaoloCiccarese
anno1
body1 sptarget1
http://coastalnhneurosurgeons.com/…jpghttp://annonc...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Example of Selectors for images
Source: http://maphub.github.io/api/
OpenAnnotationandDomainOntologies–PaoloCiccarese
You can create more selectors!
Please contribute them back!
OpenAnnotationandDomainOntologies–PaoloCiccarese
Tagging
OpenAnnotationandDomainOntologies–PaoloCiccarese
anno1
body1
oa:Annotation
rdf:type
oa:hasTarget
oa:hasBody
oa:tagging
oa:...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Adding semantics…
OpenAnnotationandDomainOntologies–PaoloCiccarese
Simplest example: Semantic Tagging
OpenAnnotationandDomainOntologies–PaoloCiccarese
anno1
http://purl.obolibrary.org/obo/DOID_3068 sptarget1
http://coastalnh...
OpenAnnotationandDomainOntologies–PaoloCiccarese
anno1
http://purl.obolibrary.org/obo/GO_0005634
sptarget1
http://nanobiot...
OpenAnnotationandDomainOntologies–PaoloCiccarese
 Web Annotation Tool
• Domeo is a web application for producing and
shari...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Manual and automatic annotation
URLIamannotating
Manualannotationtools
Au...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Semantic tagging
NCBO BioPortal
NIF Registry
Domeo can query external ser...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Semantic tagging
We could refer to diseases, historic figures, galaxies, ...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Text Mining
Service based:
NCBO Annotator
NIF Annotator
UIMA
GATE
OpenAnnotationandDomainOntologies–PaoloCiccarese
Text Mining Results
OpenAnnotationandDomainOntologies–PaoloCiccarese
Crowd sourcing results curation (v.1)
Customizable
SKOS-like… mappings
OpenAnnotationandDomainOntologies–PaoloCiccarese
Images in Domeo
OpenAnnotationandDomainOntologies–PaoloCiccarese
Image annotation
By semantically tagging figures in a paper, I make them ...
OpenAnnotationandDomainOntologies–PaoloCiccarese
OpenAnnotationandDomainOntologies–PaoloCiccarese
Integration with Drupal7 (Semtech 2012)
OpenAnnotationandDomainOntologies–PaoloCiccarese
And more semantics…
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotating with Named Graphs
OpenAnnotationandDomainOntologies–PaoloCiccarese
Intracellular Processing of APP Generates a
Variety of Cleavage Products
...
OpenAnnotationandDomainOntologies–PaoloCiccarese
anno1
sptarget1
oa:Annotation
rdf:type
oa:describing
oa:motivatedBy
sptar...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotation body: Graph1
<http://purl.bioontology.org/ontology/MSH/C096899...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Some examples using graphs
• Antibodies annotation (NIF Antibody registry...
OpenAnnotationandDomainOntologies–PaoloCiccarese
NIF Antibody Registry
http://antibodyregistry.org/
OpenAnnotationandDomainOntologies–PaoloCiccarese
Antibody Registry Integration
• The NIF (https://www.neuinfo.org/) team
m...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Domeo: antibodies
Contributed to PubMed LinkOut through NIF (http://neuin...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Export of the annotation in RDF
• DOMEO can serialize the annotation in s...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Integration with NIF
OpenAnnotationandDomainOntologies–PaoloCiccarese
Domeo: Hypotheses management (v1)
Translates into a formal OWL/RDF repres...
OpenAnnotationandDomainOntologies–PaoloCiccarese
OpenAnnotationandDomainOntologies–PaoloCiccarese
ANNOTOPIA
UNIVERSAL ANNOTATION HUB
Full ‘live’ version of the slides on:
...
OpenAnnotationandDomainOntologies–PaoloCiccarese
What is it Annotopia?
• It is a Universal Annotation Hub
• It provides yo...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Annotopia
Instance 1
Annotopia: De-Siloing Annotation
Aggregated
querying...
OpenAnnotationandDomainOntologies–PaoloCiccarese
Thank you!
paolo.ciccarese@gmail.com
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Integrating OPEN ANNOTATION with any DOMAIN ONTOLOGY

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Integrating OPEN ANNOTATION with any DOMAIN ONTOLOGY

  1. 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. 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. 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. 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. 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. 6. OpenAnnotationandDomainOntologies–PaoloCiccarese Goal: annotation interoperability … and integration with ontologies (semantic annotation)
  7. 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. 8. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotation Ontology adopters The Living Document Project Biotea
  9. 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. 10. OpenAnnotationandDomainOntologies–PaoloCiccarese W3C Open Annotation Community Group http://www.w3.org/community/openannotation/
  11. 11. OpenAnnotationandDomainOntologies–PaoloCiccarese Mailing List
  12. 12. OpenAnnotationandDomainOntologies–PaoloCiccarese Open Annotation Data Model (Feb 2013) http://www.openannotation.org/spec/core/
  13. 13. OpenAnnotationandDomainOntologies–PaoloCiccarese Open Annotation Not only for annotating the web!
  14. 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. 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. 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. 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. 18. OpenAnnotationandDomainOntologies–PaoloCiccarese Body Annotation Body Target MRI scan of a glioblastoma multiforme annotated with surgical footage
  19. 19. OpenAnnotationandDomainOntologies–PaoloCiccarese Motivations • Reasons why the Annotation was created (describing, tagging, commenting, identifying…)
  20. 20. OpenAnnotationandDomainOntologies–PaoloCiccarese Motivation modeled as skos:Concepts You can create a SKOS Schema for your own community
  21. 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. 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. 23. OpenAnnotationandDomainOntologies–PaoloCiccarese How to identify fragments?
  24. 24. OpenAnnotationandDomainOntologies–PaoloCiccarese Specific Resources • Identify and describe resource fragments (for both bodies and targets)
  25. 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. 26. OpenAnnotationandDomainOntologies–PaoloCiccarese Example of Selectors for images Source: http://maphub.github.io/api/
  27. 27. OpenAnnotationandDomainOntologies–PaoloCiccarese You can create more selectors! Please contribute them back!
  28. 28. OpenAnnotationandDomainOntologies–PaoloCiccarese Tagging
  29. 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. 30. OpenAnnotationandDomainOntologies–PaoloCiccarese Adding semantics…
  31. 31. OpenAnnotationandDomainOntologies–PaoloCiccarese Simplest example: Semantic Tagging
  32. 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. 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. 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. 35. OpenAnnotationandDomainOntologies–PaoloCiccarese Manual and automatic annotation URLIamannotating Manualannotationtools Automaticannotationtools Exploration panels
  36. 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. 37. OpenAnnotationandDomainOntologies–PaoloCiccarese Semantic tagging We could refer to diseases, historic figures, galaxies, places, events… APPintheProteinOntology
  38. 38. OpenAnnotationandDomainOntologies–PaoloCiccarese Text Mining Service based: NCBO Annotator NIF Annotator UIMA GATE
  39. 39. OpenAnnotationandDomainOntologies–PaoloCiccarese Text Mining Results
  40. 40. OpenAnnotationandDomainOntologies–PaoloCiccarese Crowd sourcing results curation (v.1) Customizable SKOS-like… mappings
  41. 41. OpenAnnotationandDomainOntologies–PaoloCiccarese Images in Domeo
  42. 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. 43. OpenAnnotationandDomainOntologies–PaoloCiccarese
  44. 44. OpenAnnotationandDomainOntologies–PaoloCiccarese Integration with Drupal7 (Semtech 2012)
  45. 45. OpenAnnotationandDomainOntologies–PaoloCiccarese And more semantics…
  46. 46. OpenAnnotationandDomainOntologies–PaoloCiccarese Annotating with Named Graphs
  47. 47. OpenAnnotationandDomainOntologies–PaoloCiccarese Intracellular Processing of APP Generates a Variety of Cleavage Products SpecificTarget1 SpecificTarget2 alpha-sAPP is derived from APP
  48. 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. 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. 50. OpenAnnotationandDomainOntologies–PaoloCiccarese Some examples using graphs • Antibodies annotation (NIF Antibody registry) • SWAN Ontology for scientific discourse and Micro-publications • Nano-publications
  51. 51. OpenAnnotationandDomainOntologies–PaoloCiccarese NIF Antibody Registry http://antibodyregistry.org/
  52. 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. 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. 54. OpenAnnotationandDomainOntologies–PaoloCiccarese Export of the annotation in RDF • DOMEO can serialize the annotation in several serialization formats.
  55. 55. OpenAnnotationandDomainOntologies–PaoloCiccarese Integration with NIF
  56. 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. 57. OpenAnnotationandDomainOntologies–PaoloCiccarese
  58. 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. 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. 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. 61. OpenAnnotationandDomainOntologies–PaoloCiccarese Thank you! paolo.ciccarese@gmail.com

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