Challenges and Opportunities

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Looking Ahead:

Challenges and Opportunities

in VIVO Development

Jim Blake, Brian Caruso, Jon Corson
-
Rikert
,
Huda Khan, Brian Lowe, and Stella Mitchell


August 24, 2012

Outline


Introduction to the VIVO development
community


Dashboards and external content


Scenarios for interconnectivity & search


Reasoning and the application ontology


Semantic features


Modularity, extensibility and collaborative
development


Questions and discussion


The VIVO development community


Developers within VIVO project


UF Harvester, virtual installations, logging, DV
-
Docs


Indiana visualization team


Contributions above & beyond the project


All the 2011 mini
-
grant projects (Duke widgets, ORCID,
Google Refine, DV
-
Docs, HUBzero, UMLS vocabulary
service)


Semantic web services


Drupal connectivity for display and reporting


OpenSocial integration


ANDS/VIVO effort and VIVO at Melbourne, Griffith, QUT


Sakai integration via Solr and caching explorations



Connecting to external data


Linking to vocabulary services as of 1.4


Generalizing this capability to work with any
vocabulary or thesaurus available as RDF


Support for navigating broader and narrower
terms


Applying to other shared external resources


People


Organizations


Journals


Geographic locations


Events


New page types in VIVO 1.5


Static HTML pages


Pages incorporating SPARQL queries for
embedded summary reports


E.g., latest publications, agencies currently funding
research anywhere in an institution


A little more work delivers contextualized reports
within individual page templates


E.g., a consolidated list of the research areas of faculty
members represented in any department


Datastar example

Data interconnectivity in one institution


Feeding downstream websites and apps


Central source of faculty directory and profiles
(CommonSpot)


Impact via maps of projects by legislative districts
(Drupal)


Faculty expertise & library liaisons in library search


Augmenting one VIVO with another


Reuse of Weill Cornell VIVO profiles in CTSC


Colorado Lab for Astronomy and Space Physics
supplementing university VIVO data with discipline
specific project and research resource data

Connecting campuses


Weill Cornell and Cornell Ithaca campus


Now include stub entries with name & title that resolve
directly from Ithaca to Weill


Want to make bi
-
directional and more granular


Joint search index may simplify discovery, but direct
linkages should also be represented


Other use cases


Stony Brook and SUNY REACH (6 medical centers)


Multiple University of Colorado campuses plus federal
labs


30+ information schools, led by N. Texas and Indiana


Sharing curricular resources, not just profiles


vivosearch.org prototype


Reusable technology demonstrated at 2011
conference


Linked data index builder


Drupal module & interface


Can be extended to support lookups of people,
organizations or other data across institutions
represented in the index

Scaling up


CTSA PIs voted in October, 2011to recommend
using RDF and the VIVO ontology


Multiple platforms making or planning to make
VIVO RDF available


VIVO DuraSpace anticipates offering hosting
and expanded participation


Will require evaluation of linked data from each
new source for consistency & completeness


Likely to grow via disciplines, regions, or consortia




Internationalization


Several dimensions


content and UI


VIVO 1.5 has basic support for language tags
keyed off browser language preference


VIVO 1.6 anticipates a UI to manage multi
-
lingual
content


A framework for internationalization of the UI and
system messages is also needed


This is a prime area for participation in VIVO
development even without specialized skills

RDF API


Triple store independence


For scalability


For other reasoning features


Enables closer integration with the Harvester and
other ingest tools


Will make it possible to submit edits/updates from
outside VIVO


E.g., two
-
way communication with Drupal

Named graphs and provenance


Keep data from each source separate


Store metadata about each graph


Give users the ability to ask

where did this come
from?



Heavy use of named graphs will require triple
stores designed for that purpose


Notably not Jena SDB


Implications for reasoning

OWL sameAs and related features


VIVO 1.5 reasoner fills in triples using other URIs


This needs UI work for 1.6


The goal is to show only one individual to users


Which URI to choose?


Keep all the information in linked data


Removing the sameAs statement leaves
statements associated with original URI

Reasoning


VIVO

s built
-
in reasoner


Enhancements with 1.5


sameAs, inverse property, remove inferences if asserted


What kinds of reasoning might we want to do?


Sub property inference


Full realization of types for all the axioms of OWL


How much should the reasoner within VIVO do?


Reasoning over distributed data

Application configuration ontology


Vitro is designed to store and display data for
any ontology


Goal to adapt the interface readily to accommodate
different data schemas



Mechanism that is flexible, extensible, and
permits fine
-
grained control, and allows
inheritance of settings



How far to go?


Specifying behavior for individuals

Application configuration ontology

Application configuration ontology


Use ontology approach to solve a software
engineering challenge


Represent the contexts in which given
configurations apply as OWL classes and axioms


Transformation of configuration instance data


Reasoner sorts them into a hierarchy

Ontology editor


One of Vitro main functions


create and edit the ontology before then adding data
and displaying/retrieving it


Least emphasis on the ontology editor in the past few
years


New class and property hierarchy displays in 1.5


Improved metadata and interaction


Expand all to see more context


Complex class expression editor

Complex class expression editor

Modularity and extension


Modularity


Improves organization of the code


Makes it easier to modify the code


Allows alternate implementation of core modules


Extension


Built on modularity and well
-
defined interfaces


Allows easy addition of new functionality

OpenSocial for extension


Collaboration with Eric Meeks at UCSF and others


Add new features


With the power of JavaScript and access to VIVO RDF
(ORNG)


Develop extensions for multiple platforms


VIVO, Profiles, perhaps others


Well
-
defined API and enforced modularity

OSGi for modularity and extension


Encourage modular architecture


Develop explicit interfaces and dependencies


Provide a packaging mechanism for extensions
and alternate implementations


E.g., a different search functionality under
development at NYU

Developer community tools


Reassessing our tool set


SourceForge is discontinuing hosted apps such as
MediaWiki


Moving some tools to DuraSpace


Generally moving with the open source
development community


E.g., considering migrating from Subversion to Git


What ancillary services belong with the code and what
are independent?


Advantages of linking code repository with issue tracking


But specialized issue trackers have agile features

Supporting all of these paths


VIVO communities


Ontology


Implementation


Outreach


Development


Gaining the experience of DuraSpace


Dspace and Fedora communities


Newer cloud services

Many ways to contribute


User scenarios and use cases


Requirements analysis and design


Voting on features (http://vivo.ideascale.com)


Responding on the lists


Documentation


Testing


Implementation support


Internationalization


Development from the simple to the complex


We are you


Help us understand your needs


Help us promote open data and open software


Definitive, shared URIs for people/orgs/journals/events


Let us know about new tools and data


Show us your work


http://vivo.vivoweb.org

is a way to find VIVO activity
around the world at any stage of implementation


Contribute to our web presence


Participate via social media

Questions and Discussion



Thank you