Integrating OPEN ANNOTATION with any DOMAIN ONTOLOGY
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
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
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.
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)
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
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
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