AO: Annotation Ontology for science on the web

AO: an open Annotation Ontology for science on the web
Bio-Ontologies 2010: Semantic Applications in Life Sciences
Paolo Ciccarese, PhD
July 9, 2010
Mass General Hospital
Harvard Medical School
paolo.ciccarese@gmail.com
http://code.google.com/p/annotation-ontology/

Background
Collaboration with a major pharma (hypothesis management for drug discovery)
Capitalizes the experience we accumulated with the SWAN project (hypothesis based representation of scientific discourse)
Is meant to serve scientific online communities such as
PDOnline http://www.pdonlineresearch.org
StemBook http://www.stembook.org
Science Collaboration Framework 2.0

Annotation Framework Brief Demo
Annotation Ontology at work

Annotation Ontology Features 1
Annotate any document on the web (text, images, audio, video, …) and their parts
Perform different kind of annotations: notes, semantic tags, errata, examples, hypotheses, citations…
Use existing domain ontologies (AO is a catalyst for the Semantic Web world)
Allow creation of manual annotation and integration of text mining results

Annotation Ontology Features 2
Persist the annotation
Allow multiple annotation perspectives on the document at the same time
Allow curation of manual and automatic annotation
Allow organizing the annotation in various ways for improving the authoring and the publication process

Starting from Annotea…
1
1
annotates
context (XPointer)
2
2
3
body
3
4
4
hasTopic
recalls
5
http://www.w3.org/2001/Annotea/
5
6
description
6

… here comes AO
Annotation and Bookmark are combined in the same model
the context can be still defined through pure XPointer but we provide a consistent mechanism for referring to parts of text, images, audio files, video files...
it is possible to create annotation types not only by sub-classing but also by composition
we provide mechanisms for managing annotation curation
we provide mechanisms for managing collections of annotation items
we provide mechanisms for managing annotation publishing
http://code.google.com/p/annotation-ontology/wiki/Background

Before looking into the details
AO is reusing the following ontologies:
Annotea/Bookmarks
PAV (Provenance, Authoring and Versioning) or DC (Dublin Core)/DCT (Dublin Core Terms)
FOAF (Friend Of A Friend)
And integrating with the following ontologies:
SKOS (Simple Knowledge Organization System)
SIOC (Semantically-Interlinked Online Communities)
Tag Ontology
MOAT (Meaning Of A Tag)
SWAN (Semantic Web Applications in Neuromedicine)
CiTO coming soon

Annotation Example
http://code.google.com/p/annotation-ontology/wiki/Annotation

Annotation of a document

Document Provenance
http://code.google.com/p/annotation-ontology/wiki/SourceDocument

Annotation Provenance

Annotation Type

Context and Selectors
In AO we can still use XPointer as Annotea was doing
But Selectors are the real AO way to define the context within a document (text, image, audio, video…)
Multiple kinds of selectors can be defined for each kind of document
http://code.google.com/p/annotation-ontology/wiki/Selectors

Example with Text Selector
http://code.google.com/p/annotation-ontology/wiki/Qualifiers

Example with Image Selector
http://code.google.com/p/annotation-ontology/wiki/Qualifiers

Annotation Types
As it was happening in Annotea, in AO the Annotation can be sub-classed in more specific annotation types:
Comment
Erratum
Question
Explanation
Definition
Note
Qualifier:
ExactQualifier
BroadQualifier
NarrowQualifier
CloseQualifier
http://code.google.com/p/annotation-ontology/wiki/AnnotationTypes
Parallel to SKOS

Example of Note

Example of Qualifiers usage
http://code.google.com/p/annotation-ontology/wiki/SKOS

We could infer that
BroadQualifier for
BACE1
BIRNLex:Protein
PRO:BetaSecretase 1
BACE1
ExactQualifier for
BIRNLex:Protein
skos:broadMatch
PRO:BetaSecretase 1
Also: BACE1 possible synonym for ‘Beta-Secretase 1’

Annotation by Composition
Annotation types can be sub-classed or created by composition (like multiple inheritance). SWAN Example:
http://hypothesis.alzforum.org/
HP:Human Phenotype Ontology

Annotation Curation
http://code.google.com/p/annotation-ontology/wiki/Curation

Annotation Curation Tokens
http://code.google.com/p/annotation-ontology/wiki/Curation

Annotation Sets 1
Are grouping annotation items
Can be useful for grouping annotation items with the same provenance (for example the annotation produced by text mining services)
Can be useful for grouping annotation items with the same topic (for example the annotation regarding life science entities)
Allow to define access restrictions for the grouped annotation
http://code.google.com/p/annotation-ontology/wiki/AnnotationSet

Annotation Sets 2

Annotation Perspective or Document Annotation 1
Is a collections of annotation sets – within all those available - that have been combined for a specific purpose – usually for publication - by a particular user/group/content provider
Multiple ‘Document Annotation’ instances can be defined for the same document by the same of different publishers

Annotation Perspective or Document Annotation 2

Acknowledgements
Tim Clark, Marco Ocana, Sudeshna Das
LeylaJaelGarcía Castro (E-Business & Web Science Research Group, UniversitätderBundeswehr) and Alexander García Castro (Computational Linguistics Department, University of Bremen) for additional use cases
Jonathan Rees (Science Commons) and Eric Prud'hommeaux (W3C) for fruitful discussions
Anita de Waard (Elsevier) for the support

AO: Annotation Ontology for science on the web

by Paolo Ciccarese

Accessibility

Categories

Upload Details

Usage Rights

3 Embeds 8

Statistics