SemTechBiz 2012 San Francisco Annotations

SemTechBiz 2012, San Francisco, June 4th 2012

Domeo: a web-based tool for semantic
annotation of online documents
http://www.annotationframework.org/

Paolo Ciccarese, PhD
http://www.paolociccarese.info/
paolo.ciccarese@gmail.com

Mass General Hospital Harvard Medical School

About Me
• Assistant in Neurology at Mass General Hospital
• Research faculty at Harvard Medical School
• Author of 30+ scientific publications
• Senior software and knowledge engineer
• Member of W3C HCLS Interest Group
• Co-chair of the W3C Open Annotation
Community Group


Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012

As (biomedical) scientists…
• We deal with an increasing amount of digital
resources: documents, images, videos,
datasets, vocabularies, databases, software…
– About 150-200 articles a week
– 10mins/article ≈ 34hours/week?
– How can we manage it?

http://www.ncbi.nlm.nih.gov/pubmed/


… 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
• We tweet…
• …


Are we efficient and effective?
• Can we integrate our annotations?
• Can we leverage machine computation?
• Can we share it easily with our colleagues?
• Can we capitalize on the work of colleagues?
• Can we integrate it with other resources?
• Can we easily observe science evolution?
• Can we easily detect the up-to-date science?
• Can we discover valuable resources?

A ‘semantic’ view of a publication
Semantic Web Applications in Neuromedicine
(SWAN) project [2007]

classic publication

scientific discourse ‘semantic’ representation

http://tinyurl.com/cgyna2m


graph representation


SWAN Creation/Curation Process


How do we empower ‘Joe Scientist’?
• Even simple linking tasks are not ‘standardized’, hard
to share and not easy to perform

http://antibodyregistry.org/antibody17/antibodyform.html?
gui_type=advanced&ab_id=2266850

antibodyregistry.org


Enable manual annotation
of digital resources
• Visually and effectively annotate - better
semantically annotate - any digital resource
and resource fragment, while performing our
regular browsing/reading activities
http://www.ncbi.nlm.nih.gov/pubmed/19822029 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874257/

≈


Leverage text mining and
community curation
• Run text mining and entities recognition
algorithms on scientific documents and persist
the results in a standard format
• Benefit from crowdsourcing by supporting
curation of manual and automatic annotation


Enable semantic tagging (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…’

Source: Protein Ontology (PRO) https://pir5.georgetown.edu/wiki/PRO

APPs for the Semantic Resources Project, May 2010

Zooming in

APPs for the Semantic Resources Project, May 2010


…and more
• Share the annotation in a common format
• Efficiently search (inference, rules) the annotation
• Reuse/integrate the annotation
• Exercise access control
• Subscribe to feeds related to topics of interest
– Proteins, Cells, Authors, Papers…
• Retrieve additional content (mashups)
• Find new resources
• Find collaborators


Annotation Ontology (AO)
• OWL vocabulary for representing and sharing
annotation of digital resources and their fragments
• Not only for biomedicine!

Ciccarese et al, 2011
An open annotation ontology for science on web 3.0
http://www.jbiomedsem.com/content/2/S2/S4

http://purl.org/ao/home (Website/Wiki)


AO Overview
AO allows to annotate:
Resources: Documents (HTML, PDF, Word, Excel), Images,
Databases, Web Services... (and their fragments)
Specifying (or not) an:
Annotation Type: through one of the already available
types (errata, highlight, qualifiers...) or the ones the users
will define.
With (or without) a:
Topic: free text, structured text, URIs, RDF entities,
RDF graphs, domain ontologies…
Tracing:
Provenance: who created what, when, with which
software, with what expectations…

AlzSWAN: http://tinyurl.com/18r
Annotating a document


Annotating a document fragment

Protein Ontology – PRO: http://purl.org/obo/owl/PRO


HyQue triples

Experiments
Workflows

Paolo Ontology 2.0: http://code.google.com/p/swan-ontology/
SWAN Ciccarese, PhD SemTechBiz 2012, June 4th 2012

Annotation Ontology Network

Biotea

The Living Document
Project


Open Annotation Community Group
• Annotation Ontology is going to be replaced in
our applications by the Open Annotation
Model developed through the W3C Open
Annotation Community Group

– Website http://www.w3.org/community/openannotation/
– Core Model http://www.openannotation.org/spec/core/
– Extensions http://www.openannotation.org/spec/extension/


• DOMEO Annotation Toolkit is a web
application for producing and sharing manual,
semi-automatic and automatic annotation

Ciccarese et al, 2012
Open semantic annotation of scientific publications using DOMEO
http://www.jbiomedsem.com/content/3/S1/S1

http://annotationframework.org


DOMEO: Document Metadata Organizer


Semantic Tags or Qualifiers [1]


Domeo and the NCBO Annotator

http://www.bioontology.org/annotator-service
• Domeo allows automatic/manual annotation with
terms coming from selected ontologies managed by
the BioPortal


Running NCBO Annotator

Additional text mining services
will be listed here


NCBO Annotator Results in Domeo

List of recognized
entities


Results Curation

Customizable


Cumulative Results Curation
• One item only
• All instances with the same text match
• All instances independently from the text
match


Serialization in AO/RDF (Share)


http://www.slideshare.net/paolociccarese/domeo-and-text-mining

UIMA, Clerezza and AO

Evaluating Performance
Comparing Algorithms
Learning
…

Text
Curated
Mining
Results
AO RDF Text
Mining
Results

Applications
AO RDF Publishing


SemTechBiz 2012, San Francisco, June 4th 2012

Thank you!
Paolo Ciccarese, PhD
paolo.ciccarese@gmail.com

Mass General Hospital Harvard Medical School

SemTechBiz 2012 San Francisco Annotations

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