Agenda
please add or suggest any additional items
Updates
- Brown (Steve) – have altered the model used for ingest of database of legacy data. When the 3rd party contractor went through and parsed the raw text out of the files, did some mapping into the ontology, but the transition was unreliable enough that resulted in unique conferences and organizations for each occurrence. Had collapsed most of that data into a label for a role, not associated with a real event or conference, and hope to go back through and do matching of those strings to capture the host organization, using http://viaf.org for reference. Still have the database from the vendor to go back to and look at the individual fields. From an ontology perspective, the role object was a context node but is functioning as a central object for service to community, at least on a transitional basis until the real event or organization is identified.
- what's happening with updates? Still is faculty access to VIVO but not much editing is happening, so can still focus on legacy data. At least 40 new faculty to enter for fall,so will be focusing on updates then and may be looking at custom forms
- Duke – congratulations on the launch of http://scholars.duke.edu
- Florida (Nicholas) – able to load a couple different parts of the ISF, the clinical modules, into a VIVO instance and run queries against it. Could dynamically query it via Fuseki SPARQL endpoint from other applications. Chris Barnes is using Google JavaScript visualization libraries
- Johns Hopkins (Jing) – attended the Open Annotations workshop at the University of Maryland, including seeing showcasing implementations – e.g, Domeo – interested to see whether this is relevant to the issue of specialization of research interest descriptions – is that an assertion or an annotation, and would this be relevant. Provenance is also referenced in the Open Annotation data model.
- Memorial University
- NARCIS
- North Texas
- Scripps (Michaeleen) – gave a demo on the sample of nearly 500 grants and will be able to ingest the remaining 3000 grants from 2008 forward, including modifying the ontology to represent the NIH award system to be able to link related grants, and potentially make explicit links from grants to publications in PubMed
- (Paul) – has also been working on a way to better represent grants. Looking at NIH exporter, an API for getting normalized grant ids and the PMIDs of publications associated with them.
- (Michaeleen) adding the PMCID to each article in VIVO will help with
- (Jon) – is there an API to get compliance information with the NIH access mandate from myBibliography?
- (Paul) – to be not in compliance, needs to be funded by NIH-funded grant, not have a PMCID, be older than the allowable grace period. Also is only relevant for the corresponding author
, and are hoping to be able to harvest that information from PubMed - (Michaeleen) NIH is starting to enforce at least delays in funding
- UCLA –
- Weill Cornell (Paul) – planning work for the next six months
- Cornell Ithaca (Brian) – working on the code changes to be able to fully test out the Integrated Semantic Framework, especially with respect to dramatic property simplification. Role sub properties are one example – do we want to use the very generic "bearer_of" property from the relations ontology. Making a testbed so we can see what things look like in a VIVO
Discussion Topics
Collaborative ontology development tools
(Jing) Goals are to have a common workspace for the official VIVO ontology and for extensions to it that are under development. The VIVO team at Hopkins will be a decentralized effort and they will need collaborative tools even for their own purposes.
- Web Protégé
- Knoodl has additional features like endpoints and a registry
- Ontobee
- eagle-i ontology browser
Proper use of global citation count
(Paul)
Modeling institutional affiliation
(Paul)
About a year ago, I put in a JIRA ticket to ask how we should model co-author affiliation:
https://issues.library.cornell.edu/browse/VIVOONT-444 (moved to DuraSpace JIRA VIVOONT-5)
That seemed to be a real stumper, because the fix version was delayed until post-1.6. At the time, I put in the ticket our publication ingest wasn't working and the Scopus API was outputting XML showing institutions in a big lump rather than tied to each author. Now though both of those roadblocks have been overcome. Also, unlike before, I have a not terrible approach to this. But I'm not sure if it's ideal.
For every author in the data, there is a Scopus-normalized institutional name (e.g., the author lists "Weill Medical College of Cornell University" and Scopus maps that to "Weill Cornell Medical College"), and a Scopus-generated institutional identifier (e.g., 60007997). In cases of multiple affiliations, you will see multiple institutional names and identifiers.
Here's the approach:
1. Create an object property for InformationResourceInAuthorship called ScopusInstitutionalAffiliationID.
2. ScopusInstitutionalAffiliationID has a range of foaf:organization.
3. Give foaf:organization has a data property of ScopusAffiliationName.
This will be really useful for us if we can bring these data in: it will populate our Dashboard, we can see how often our faculty actually list our institution, and we can identify patterns of inter-institutional collaboration.
discussion
- so much variation in how people list their affiliation – will there be confidence in the identification of the organizations? Paul is primarily interested in querying the changes in affiliation for an author, both for disambiguation. Also wants to flag any document where there's no Weill Cornell affiliation, either because it predates when someone was working at Weill for some other reason.
- will the VCard be ready for 1.6? some trickiness because the VCard spec is changing in a W3C and it's not clear even what namespace it will use. We at least know we want a structured set of strings linked to an authorship that can accommodate name parts, affiliation information, and potentially an institutional identifier.
Review and prioritization of changes for VIVO 1.6
- Publication types and coordination between Sympectic Elements publication types and VIVO/BIBO types
- Research grants – what are the differences between grants, awards, and contracts? How do NIH and NSF (and other funding agencies) model grants, so that VIVO can align data harvested from NIH RePORTER or research.gov?
- Annual amendments, side amendments, the new app R01
- Distinctions among North American, British, continental European, Australian and New Zealand academic position types
- Courses and semester classes – can we finalize the Course as a continuing entity that is realized in Semester Class events?
- Representing and displaying re-publication or performance - the general topic of artistic works
Other recent issues
- Former titles of organizations
- will it work for Brown, as Nicholas suggests, to create a separate organization with the then-current title and link to it from the current organization with the hasPredecessorOrganization property?
- will that solve the problem? anticipate that it will work
WebEx Call-in Information
- Topic: 2013 Bi-weekly VIVO Ontology Call
- Date: Every 2 weeks on Wednesday, from Wednesday, January 23, 2013 with no end date
- Time: 11:00 am, Eastern Standard Time (New York, GMT-05:00)
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