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Semtech web-protege-tutorial

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Slides for the hands on WebProtégé tutorial held at Semtech 2013.

Slides for the hands on WebProtégé tutorial held at Semtech 2013.

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  • 1. Collaborative Editing ofLightweight OntologieswithWebProtégéNatasha NoyMatthew HorridgeTaniaTudoracheStanford University
  • 2. Download the slideshttp://tinyurl.com/semtech-webprotege
  • 3. Plan•Introduction•What is collaborative ontology editing?•A guided tour of WebProtégé•Hands-on exercise•Discussion, Roadmap and Wrap up
  • 4. What is Protégé?• An open-source ontology editor• developed at Stanford University• has more than 200,00 registered users• has dozens of plugins for• visualization• inference• import and export• ….• has an API for developers
  • 5. A bit of Protégé history• Started more than 20 years ago• Has gone through many iterations• Was the first editor to support OWL 1• Informed the design of OWL 2• Has a thriving user community:• conferences• mailing list• short courses
  • 6. Protégé short course:Vienna, September 2-4Texthttp://protege.stanford.edu/shortcourse/protege-owl/201309/
  • 7. The “Classic” ProtégéNot what this tutorial is about!
  • 8. WebProtégé•A Web-based application•edit ontologies in your Web browser•nothing to install•Supports distributed editing•multiple editors can make changes at thesame time•Includes many collaboration features•discussion, watches, feeds
  • 9. Plan•Introduction•Collaborative ontology editing•Hands-on•WebProtégé in large projects•Discussion, Roadmap and Wrapup
  • 10. Collaborative Ontology Development
  • 11. Collaborative Ontology DevelopmentCollaboration: several users contribute to thedevelopment of one ontology– Small group → larger community– Larger ontologies that concern a certain community– Individual process → social processEach community does it its own way
  • 12. Use cases of collaborative development inbiomedical domain• Gene Ontology (GO)• NCI Thesaurus• BiomedGT• OBI, BIRNLex, RadLex• Open Biomedical Ontologies (OBO)• International Classification:– of Diseases (ICD-11)– of Traditional Medicine (ICTM)– of Patient Safety (ICPS)
  • 13. The NCI Thesaurus collaborativedevelopment process●Simultaneous editing in Protégéclients●Custom UI for restricting userinput and enforcing businessrules●Development cycle begins afterbaseline●~20 full-time editors makingchanges; 1 “lead editor” whoapproves the changes, andassigns new tasks●Released version on NCIwebsite and BioPortalReference ontology for cancer biology, translational science, and clinicaloncology
  • 14. ICD-11● 11th Revision of the InternationalClassification of Diseases● Over 10.000 categories used for coding,billing, statistics, policy making all over theworld● Collaborative and international effort● Current version: published as books● Goal for the new version: use a more formalrepresentation and published in electronicalformat; use Web-based collaboration andsocial platforms for editing
  • 15. Construction of ICD-10:Revision Process in the 20thCentury● 8 Annual Revision Conferences (1982- 89)● 17 – 58 Countries participated– 1- 5 person delegations– Mainly Health Statisticians● Manual curation– List exchange– Index was done later● "Decibel” Method of discussion● Output: Paper Copy● Work in English only● Limited testing in the field
  • 16. ICD-11 process today● Over 250 domain experts from around the world● Organized in groups, which edit different parts of the ontology
  • 17. ICD-11 process today (cont.)● Each night a snapshot of the commonly edited ontology ispublished in a public platform to encourage feedback fromthe larger communityhttp://apps.who.int/classifications/icd11/browse/f/en● Editorial workflow● Centrally overseen by WHO● Peer-reviewed process for the content and structure● WebProtégé used as the collaborative ontologydevelopment platform
  • 18. Other ways of collaborating: Wikis● Wikis are well known; Wikipedia● Semantic Wikis – add semantic extensions to the wikiplatforms● Assign a wiki page to an entity in the ontology (e.g. theclass “Mountain”)● Export/import RDF
  • 19. Semantic Wiki: MoKiSource: https://moki.fbk.eu/website/userfiles/image/entmod.png
  • 20. The challenge with wikisSource: Hoehndorf, Robert, et al. "BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology."BMC bioinformatics 10.Suppl 5 (2009): S5.
  • 21. Using sourceforge to manage change proposals for the Gene Ontology
  • 22. myexperiment: social platform for sharing scientific workflows
  • 23. Other collaboration processes● Use source control repositories – SVN, CVS– Text based mechanisms– Hard to merge local copies in the shared copy● Locking mechanisms (lock parts of an ontology for editing)● Use specialized (domain dependent) ontology repositories,e.g., BioPortal
  • 24. BioPortal● An open repository of biomedical ontologies developed by NCBO atStanford● Publishing of ontologies, versioning (over 350 ontologies)● Discussions and structured proposals● Mappings, views● Storing metadata● Search over all ontologies● Browsing different versions of an ontology● All content and functionality also available as REST Web services →mash-up of applications● Technology is domain independent● http://bioportal.bioontology.org
  • 25. BioPortal Statistics
  • 26. Ontology list in BioPortal
  • 27. NCI Thesaurus details in BioPortal
  • 28. Useful features for collaboration● Tools for discussion and reaching consensus– Add notes to ontology entities (classes, properties, individuals,axioms)– Add reviews and change proposals anywhere in the ontology– Document the decision process and final decisions● Complete Change history– Establish provenance– Retrieve ontology snapshots at any time– Implement different conflict resolution mechanisms● Personalized views of an ontology based on:– User’s role and tasks– User’s level of expertise
  • 29. Useful features for collaboration (cont.)● User roles and access control– Fine-grained control for editing and viewing rights– Sharing of ontologies● Publishing released versions of an ontology in a centrallocation,e.g. a repository● Scalability, reliability and robustness
  • 30. WebProtégéA QuickTour of the UI
  • 31. Creating an Account ICreate a new account
  • 32. Creating an Account IIEmail address - used for notifications such as ontology changesUser name - displayed next to changes you make and notes that you post
  • 33. The “Home Screen”Side barProject list. Click projectname to openCreate projectDownload projectSign In/Sign OutTrash projectUpload project
  • 34. The Side BarAll public projects plus your projects that are not in the trashYour projects that are in the trashOnly projects owned by you that are not in the trash
  • 35. ProjectsA project encompasses: A collection of ontologiesNotes & discussions and watchesSome user interface settingsSome sharing settingsA list of revisions and a log of changes
  • 36. Creating a ProjectCreate New ProjectProject name - does not need to be uniqueProject description - appears in the project list
  • 37. Uploading a ProjectUpload ProjectProject name - does not need to be uniqueProject description - appears in the project listLocal OWL file name
  • 38. SharingShare link (top right corner)
  • 39. Public Projects➊ Select public➋ Assign permissions for anyone including guests➌ Assign more fine-grained access for specific usersEnter names in list and press “Add”
  • 40. Private Projects➊ Select publicAccess is restricted to specific users➋ Assign more permissions for specific users.Enter names in list and press “Add”
  • 41. Class tree Editor (similar for properties and individuals) Notes & DiscussionsProject feedEditing Class Descriptions
  • 42. Adding SubclassesCreate subclasses buttonEnter one or more names. Press CTRL+Enter to accept and close(one class name per line)
  • 43. Editing Class DescriptionsDisplay name - corresponds to the value of rdfs:label hereIRI - Internationalized Resource Identifier. Auto-generated, globally unique“Property values”(Class expressions under the hoodowl:subClassOf)Annotation assertionsValues can be class names, datatype names,individual names, numbers, dates and stringsLanguage editor for plain literalsDelete row
  • 44. Auto-CompletionType in name. Popup shows possible matches.Dublin Core and SKOS properties “recognised”
  • 45. On-the-Fly CreationNew property warning(helps prevent typos!)Press the tab key and enter value to create property(property type will be determined from the value)
  • 46. Editing Individual DescriptionsClass tree Editor Notes & DiscussionsProject feed
  • 47. Display name - corresponds to the value of rdfs:label hereIRI - Internationalized Resource Identifier. Auto-generated, globally unique“Property values”(Annotations, property assertions orclass expressions under the hood -owl:subClassOf)Type assertions(rdf:type)Values can be class names, datatype names,individual names, numbers, dates and stringsDelete rowSame individuals(owl:sameAs)Editing Individual Descriptions
  • 48. Icon Cheat SheetClassIndividual (named)Datatype (xsd:integer, xsd:double etc.)Property (object/data property)Annotation propertyNumberDate-TimeLiteralLink (http:)IRI
  • 49. Hands OnOnline Newspaper
  • 50. ModellingTaskBuild an ontology to describe an online newspaperor news website e.g. www.nyt.com or www.bbc.comGoal: Become familiar with WebProtégéand some aspects of collaborative ontology editing
  • 51. ContentArticles:title, author, date published, edited by, keywords/topics,published in section, media (pictures, video), external linksetc.Advertisements:Standard ad, personal ad, Service ad etc.Model different kinds of articles and their properties. For example,
  • 52. StructureNewspaper:date published, issue, front matter etc.Sections:Domestic News,World News, Editorial, Magazine, Letters,Commentary,Television Listings,Advertisements,Appointments/Jobs, Sport, Business etc.Sections and subsectionsModel the structure of a news paper - different sections and how theyfit together. For example,
  • 53. PeopleEmployees:Columnist, Editor, Section Editor, Reporter, InternationalReporter, Managername, contact details: email, phone number, roleOther people:Politician, President,Actor etc. Individual people, e.g.Barack Obama.Model the people who contribute to the news paper and people whoare the subject of articles. For example,
  • 54. Custom entry forms for editing the ontologycontent● Easy to create user interfaces for the domain experts● Use common entry forms, but still keep the ontology“intelligence” behind it● A form widget (e.g., text field) is linked to a property in theontology● Easy to create custom forms with different views fordifferent users● Hides complex ontology stuff
  • 55. Form configuration in WebProtégéForm-based editing and configuration of the user interface for the development of ICD-11http://icatdemo.stanford.edu
  • 56. Examples of form-based editing
  • 57. Importing BioPortal terms intoWebProtégé(1) Search term in BioPortal ontologies(2) Getsearchresults(3) Browsedetails ofresults(4) Import into WebProtégé withsingle click
  • 58. WebProtégé – Make UpProtégé CollaborationFrameworkWebProtégéWebProtégé ServerGWT RPCServer sideClient sideJavaJavaJava atdevelopment timeJavaScript atrun- time2 parts: server and clientServer is completelyimplemented in Java and makesAPI calls to the OWL-API andother librariesClient side is developed in Java,and later compiled by GWT intoJavaScriptCommunication between serverclient is done via GWT RPC orsimple HTTP calls
  • 59. WebProtégé is pluggableWebProtégé User Interface(GWT)PortletsEvent manager Other managersWebProtégé Server (Java)Access policiesservice...OntologyServiceNotes andchanges Servicepluggablepluggable
  • 60. Extending WebProtégéPlug-in infrastructure very similar to Protégés: create yourown tabs and portletsExtend: AbstractTab or AbstractEntityPortletImplement your own RPCs, if neededReuse existing portlet codeWriting a tab – as easy as creating an empty class thatextends AbstractTabhttp://protegewiki.stanford.edu/wiki/WebProtegeImplementationGuide
  • 61. Resources●Online WebProtégé server: http://webprotege.stanford.edu●WebProtégé documentation:http://protegewiki.stanford.edu/wiki/WebProtege●WebProtégé paper: “WebProtégé: A Collaborative Ontology Editor and KnowledgeAcquisition Tool for the Web”, Tania Tudorache, Csongor Nyulas, Natalya F. Noy,Mark A. Musen, Semantic Web Journal (SWJ) 4 (Number 1 / 2013), 89 - 99●WebProtégé in use: “Will Semantic Web Technologies Work for the Development ofICD-11?”, T. Tudorache, S. M. Falconer, C. I. Nyulas, N. F. Noy, M. A. Musen. The 9thInternational Semantic Web Conference, ISWC 2010 (In-Use track), Shanghai,China, Springer. Published in 2010.http://bmir.stanford.edu/file_asset/index.php/1646/BMIR-2010-1427.pdf●Other References: http://protegewiki.stanford.edu/wiki/WebProtege#References