![A ‘semantic’ view of a publication
Semantic Web Applications in Neuromedicine
(SWAN) project [2007]
classic publication
scientific discourse ‘semantic’ representation
http://tinyurl.com/cgyna2m
Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012](https://image.slidesharecdn.com/semtechbiz-120604125542-phpapp01/75/SemTechBiz-2012-Domeo-a-web-based-tool-for-semantic-annotation-of-online-documents-6-2048.jpg)
![Semantic Tags or Qualifiers [1]
Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012](https://image.slidesharecdn.com/semtechbiz-120604125542-phpapp01/75/SemTechBiz-2012-Domeo-a-web-based-tool-for-semantic-annotation-of-online-documents-25-2048.jpg)
![Semantic Tags or Qualifiers [2]
Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012](https://image.slidesharecdn.com/semtechbiz-120604125542-phpapp01/75/SemTechBiz-2012-Domeo-a-web-based-tool-for-semantic-annotation-of-online-documents-26-2048.jpg)
![Semantic Tags or Qualifiers [3]
Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012](https://image.slidesharecdn.com/semtechbiz-120604125542-phpapp01/75/SemTechBiz-2012-Domeo-a-web-based-tool-for-semantic-annotation-of-online-documents-27-2048.jpg)
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SemTechBiz 2012: Domeo: a web-based tool for semantic annotation of online documents
The document discusses Domeo, a web-based tool for semantic annotation of online documents, created by Paolo Ciccarese, who highlights the challenges faced by biomedical scientists in managing increasing amounts of digital resources. It emphasizes the importance of effective annotation practices, integration of various resources, and the potential for utilizing semantic tagging and community curation to improve collaboration and resource discovery. The documentation also outlines the features of the annotation ontology and the functionalities of the Domeo annotation toolkit, promoting enhanced annotation capabilities in scientific publications.
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SemTechBiz 2012: Domeo: a web-based tool for semantic annotation of online documents
- 1. SemTechBiz 2012, SanFrancisco, 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/ [email protected] Mass General Hospital Harvard Medical School
- 2. 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 http://www.paolociccarese.info/ Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 3. 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/ Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 4. … we commonlyuse 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… • … Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 5. Are we efficientand 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? Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 6. A ‘semantic’ viewof a publication Semantic Web Applications in Neuromedicine (SWAN) project [2007] classic publication scientific discourse ‘semantic’ representation http://tinyurl.com/cgyna2m Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 7. graph representation Paolo Ciccarese,PhD SemTechBiz 2012, June 4th 2012
- 8. SWAN Creation/Curation Process PaoloCiccarese, PhD SemTechBiz 2012, June 4th 2012
- 9. How do weempower ‘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 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 10. 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/ ≈ Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 11. Leverage text miningand 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 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 12. 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 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 13. APPs for theSemantic Resources Project, May 2010 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 14. Zooming in APPs for the Semantic Resources Project, May 2010 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 15. …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 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 16. 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) Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 17. 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… Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 18. AlzSWAN: http://tinyurl.com/18r Annotating a document Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 19. Annotating a documentfragment Protein Ontology – PRO: http://purl.org/obo/owl/PRO Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 20. HyQue triples Experiments Workflows Paolo Ontology 2.0: http://code.google.com/p/swan-ontology/ SWAN Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 21. Annotation Ontology Network Biotea The Living Document Project Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 22. Open Annotation CommunityGroup • 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/ Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 23. • DOMEO AnnotationToolkit 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 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 24. DOMEO: Document MetadataOrganizer Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 25. Semantic Tags orQualifiers [1] Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 26. Semantic Tags orQualifiers [2] Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 27. Semantic Tags orQualifiers [3] Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 28. Domeo and theNCBO Annotator http://www.bioontology.org/annotator-service • Domeo allows automatic/manual annotation with terms coming from selected ontologies managed by the BioPortal Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 29. Running NCBO Annotator Additional text mining services will be listed here Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 30. NCBO Annotator Resultsin Domeo List of recognized entities Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 31. Results Curation Customizable Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 32. Cumulative Results Curation • One item only • All instances with the same text match • All instances independently from the text match Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 33. Serialization in AO/RDF(Share) Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 34. 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 Paolo Ciccarese, PhD SemTechBiz 2012, June 4th 2012
- 35. SemTechBiz 2012, SanFrancisco, June 4th 2012 Thank you! Paolo Ciccarese, PhD http://www.paolociccarese.info/ [email protected] Mass General Hospital Harvard Medical School
Editor's Notes
- #19 The topic can be an antibody (NIF Antibody registry)