VIVO Dashboard A Drupal-based tool for harvesting and executing sophisticated queries against data from a VIVO instance

Transcription

1 VIVO Dashboard A Drupal-based tool for harvesting and executing sophisticated queries against data from a VIVO instance! Paul Albert, Miles Worthington and Don Carpenter

2 Chapter I: The Problem

3 Administrators are avid consumers of institutional data.

4 In 2011, the Dean s Office requested the following reports List of publications in which a Weill Cornell author was first or last author List of publications in which a Weill Cornell author was first or last author, appearing in journals of impact factor > 15

5 This is a fairly reasonable request compared to others

6 Chapter II: Legacy Approach

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10 Why this approach is poor Asynchronous, can t sort or facet, and requires a lot of sweat

11 Sample SPARQL query SELECT distinct?article1_pmid?person1_cwid? Authorship1_authorRank! WHERE{?Article1 rdf:type bibo:document.?article1 vivo:informationresourceinauthorship?authorship1.?article1 bibo:pmid?article1_pmid.?authorship1 rdf:type vivo:authorship.?authorship1 vivo:authorrank?authorship1_authorrank.?authorship1 vivo:linkedauthor?person1.?person1 rdf:type foaf:person.?person1 wcmc:cwid?person1_cwid. }!

12 Chapter III: Let s create a prototype

13 Goal of VIVO Dashboard Empower untrained users to run sophisticated semantic queries on Weill Cornell faculty publications * Secondary directive: kill Sarah Connor

14 Publications Graph List Export Date Present The following publications are for all publications by active Weill Cornell Medical College faculty as represented in VIVO Publication Type Research Article (657)! In Process (55)! Review (45)! Clinical Guideline (32)! more... Journal ranking Journal Name 25 Author Name

15 Invention is 1% inspiration and 99% perspiration.! Thomas A. Edison Source: Yahoo Answers

16 Chapter IV: Technology Stack of next version

17 VIVO Dashboard is an installed profile based on Drupal

18 Why Drupal? Familiar platform - Used at many institutions - Developers are familiar with the technology - Easy to host Existing solutions - Many modules available to solve common use cases - Same application could be built with any other web platform, but Drupal saves a huge amount of development effort.

19 VIVO Dashboard leverages existing Drupal modules Faceted search - Search API module - Facet API module Data import - Feeds module - Linked data import module * All of which are actively maintained and supported

20 Key Module: Linked Data Import Feeds plugin for linked data as a data source Uses open source library called ARC2 for requesting and parsing RDF Authored by Miles Worthington Originally created for Cornell's CALS Research & Impact site

21 Key Module: Feeds Offers a generic import system for Drupal Handles scheduling Maps various data sources (RSS, CSV, SQL) into Drupal content (nodes, taxonomy terms) Manages custom data sources via plugins

22 Other technology Stores content using the robust indexing application, Apache Solr AJAX Key modules - Apache Solr - Elysia cron - D3.js (visualization library) - Charts and graphs - VIVO Dashboard Core, Publications, and Import (custom module)

23 Demonstration Demonstration Demonstration Demonstration Demonstration Demonstration Demonstration Demonstration Demonstration Demonstration

24 Chapter V: Import process

25 Get a list of all publication URIs from VIVO

26 Go through list of URIs, request RDF for each

27 Request necessary related data for each article

28 Map VIVO RDF to Drupal structures

29 Repeat for all publication URIs

30 Chapter VI: How to install VIVO Dashboard

31 I am not a smart programmer, but even I can set up a VIVO Dashboard Me

32 Code and instructions github.com/paulalbert1/vivodashboard

33 Install Drush locally and create a repository Install Drush on local machine by following the instructions at: Run following command: drush make vivodashboard/master/distro.make vivo-dashboard

34 Create a new site in Pantheon Also easily done in Acquia

35 Put the Pantheon site in SFTP mode

36 Using SFTP connection info on previous screen, copy local code to Pantheon.

37 Wipe database

38 Visit development site

39 Install profile (resulting screen)

40 You are now taken to VIVO Dashboard s home page.

41 Select a fetcher (VIVO Class Fetcher requires 1.7 if you have > 30,000 objects)

42 Setup the publications import

43 Enter site URL and top level article class

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45 Define URIs of custom classes

46 Hide certain types

47 Journal ranking data can be imported from Scimago Journal Rank (Pearson correlation between Impact Factor and ScImago Journal ranking c is 0.915)

48 Chapter VII: Final Thoughts

49 Advantages with this approach Leverages standard VIVO features No SPARQL endpoint required No authentication necessary Configured through an admin UI All but major ontology changes require code changes

50 You can use VIVO Dashboard s data harvesting approach to create new apps to do other kinds of data visualization and analysis

51 Disadvantages with this approach Takes a long time Drupal/PHP not designed for long-running jobs

52 Future Work Make VIVO Dashboard VIVO-ISF 1.6 compatible

53 Data dashboards tend to elicit a Highlander-type response among administrators