1 ORWG and Standards Inventory Resource February 9, 2012

2 ORWG Accomplishments NCBO, NCRI, NCI CBIIT, caBIG – brought these organizations together to solve issues Alignment of goals/Decision matrix for importance of metadata by each organization Research representation of Metadata for vocabularies Suggest OMV, compare OMV to CTS2 and NCBO Bioportal implementation Research Rating Systems Developed a relationship within the OOR and other communities Possible Paper Outline

3 Discovered each Domain WS (ICR, CTMS, Imaging, TBPT) ontologies/terminologies and level of support needs vary Results: QuestionICRTBPTIMGCTMS 1. Where do I start?Yes No 2. What do I use?Yes No 3. Overlap/chooseYes NoYes 4. SynonymsYes 5. Text DefinitionsYes yesYes 6. Do you know the Term to use? NoYes(make own) Yes 7. UML needYes 8. for DiscoveryYes yesYes 9. RelationshipsIncomplete yesYes 10. Retrieve Concepts Incomplete Yes/incompleteNo/Incomplete 11-.ReasoningIncomplete YesNo/Incomplete

4 Research and provide Feedback on a community favorable "Rating System" Received feedback from 3 individuals (separate locations). Comments: Ease of Use - People are not eager to provide comments unless they either get paid to do it or have something to complain about Familiarity - Most people are used to the 5-star rating system that is used on many web pages. Comments - providing a comments fields is common practice - this will allow the users to give detailed input. Needs a prompt question to direct users towards a review Fill in stars is helpful for summarizing Will not trust the community feedback - the quality of comments they cannot judge The number of downloads for the tool will provide helpful feedback

5 Domain WS Interview Comments TBPT WS Most of the end users are informatacists that serve the needs of individual researchers. Want to know the ‘standards” we use (for UML models, for Value sets) they don’t want a bunch of choices CTMS WS These communities usually use vocabularies that are either regulation- induced or come about from best practices. We don’t need to choose from 100s of terminologies, only a handful IMG WS Their needs are more about getting the controlled vocabularies created and ability to use synonyms to search for diseases Help in efforts to interrelate terms (among terminologies) (Mapping)

6 ORWG leading into solutions to OTHER standards Brian discussed “Ontology standards” needs with Domain Workspace Facilitators and our proposed “Roadshow (see script here and feedback here: Clear from Feedback from those representing users, that “Ontology Standards” are Only one of many standards of concern to “users” Users do not differentiate (categorize) standards into “Ontology”, “metadata”, “informational”, etc.) so trying to discuss a narrow view of their over all issues is difficult at best, and counterproductive at worst (we alienate them) Ontology standards, and other standards, do not stand alone, but have relationships (look at our experience with CTS2, OMV, Dublin Core, different iso, etc.) Other standards (eg, metadata, information representation, datatypes, security, interface, etc.) suffer from same issues we have partially solved in ORWG

7 Needs (Near quotes from caBIG participants) “There are so many standards, I don’t know where to start” “ I am using an in-house, legacy system based on homegrown vocabulary for Lab data that I call “Lab test name”, “Lab value”, “Blood count”, “Oxygen content”, etc. How do I transition from the legacy system to LOINC?” “I have a specification for a software application from Stanford. I want to compare it to NCI CBIIT software specifications for LexEVS to see that they’ll be interoperable for some of the data they are going to pass to NCI CBIIT. What standards should I be looking at to make sure they are compliant? “Are there any ontologies that are suitable for annotation of a Nuclear Receptor Signaling Project that I am involved with?” “What are the options for me to represent Protocol Lifecycle objects: as an ontological representation or a UML representation or some other representation? What do you have that I can leverage?” ** green=wholly or partially involving “Ontology standards”

8 Baris Suzek Proposal to caBIG/NCI CBIIT Some Issues on Adopting Standards “There are many types of standards including (but not limited to): Vocabulary Interface Format Messaging Documentation error handling Development Etc….

9 Some Questions on Adopting Standards “What are standards that should be used? what is the value proposition for adopting a standard? does it have community buy-in? are there rules/policies that I need to watch for (e.g. meaningful use) What is the path (tools/process) to adopting this standard? e.g. are there transformations for the terminologies of interest? are there interface engines that do message transformations? What is the cost involved in adopting standards? e.g. are the tools commercial, comprehensive, supported and/or processes around them well-defined/tested? is there a cost associated with the standard?”

10 Proposal elements 1.Use cases from Stakeholders 2.List of Standards (that address stakeholder needs) 3.Information about each standard (that is useful for end user in decision making) 1.Community Driven “Adopters stories/reviews/best practices” associated with each standard ** Novel Aspect (caBIG community) 4.Interface to Standards Resource 1.Organization of the information to address users issues/answer questions

11 List of Stakeholders Leverage some work in ORWG Leverage Work in Roadmaps

12 List of Standards Leverage Work in ORWG Can start with existing documents: Some existing inventory of Standards in caBIG (see ) Existing Standards outlined by ARB (see dEd1aDcwQTE5TEVLM1RiLVZtQ1JYVlE&hl=en_US#gid=0) dEd1aDcwQTE5TEVLM1RiLVZtQ1JYVlE&hl=en_US#gid=0 caDSR metadata standards (see ) Vocabulary Standards (eg, see NCBO BioPortal: see NCI Thesaurus: ) caGrid Standards (eg, see )

13 Interface(s) depend on Use cases (“path”) Leverage Work in ORWG Organization and Multiple Interface options available Cancer Info matrix onix.org.uk/portal/#S24http://ncri- onix.org.uk/portal/#S24 Concept Map (eg: ) Interaction Map (eg: on=map&MIM=replication ) on=map&MIM=replication Web site like NCBO (Ontology BioPortal)

14 Information about each Standard Leverage Work in ORWG Some information probably important for use cases: Standard Name Standard Description Authoritative resource for this standard (eg, URL). Adoption Experience (some contributed by “community”) Level of difficulty in adoption/costs associated with adoption Prerequisites for adoption Level/extent of Adoption Description of Tools associated with Standard Accessibility/availability/Licenses associated with adoption Relationship among standards Regulations (eg, Meaningful use). References to peer-reviewed journals Blogs? Abstracts? Links to other resources.