Introduction

The VIVO Harvester is a library of tools designed to take data from external data sources and ingest it into a semantic system like VIVO. The library was originally developed at the University of Florida during the 2009-2011 NIH Grant. Development of the Harvester at first followed a monthly release cycle. Now a new version of the VIVO Harvester is released alongside each never major version of VIVO.  Use the links below to learn more about individual tools the harvester is comprised of, or read the Harvester User Guide to learn more about using the harvester.

• Typical harvest

Harvester Instructions

Harvester User Guide

Scheduling

Walkthrus for example scripts

JDBC Example Script

Pubmed Example Script

IP Example Script

Deployment

• Execute
• Scheduling
• Configuration

Video Walkthrus

Screencasts of example harvester runs: https://sourceforge.net/projects/vivo/files/VIVO%20Harvester/Demonstration/

Case Studies/Examples

University of Florida PubMed Harvest

University of Florida PeopleSoft Harvest

University of Florida Department of Sponsored Research Harvest

Class Documentation

• Fetch
• Translate
  • GlozeTranslator
  • SPARQLTranslator
  • XSLTranslator
• Score/Match
  • Score
  • Algorithm
  • Match
• Transfer
• Diff
• Qualify
  • ChangeNamespace
  • RenameResources
  • Smush
• Utilities
  • JenaConnect
  • RecordHandler
  • ArgParser
  • Merge
  • DatabaseClone
  • XPathTool
  • XMLGrep
  • CSVtoJDBC

Development Documentation

• Harvester Development Toolkit
• Harvester Documentation Procedures
• Harvester Planned Features
• Advanced PubMed name matching diagram
• New Harvest Workflow Proposal
  • RecordHandler Tool Specification
  • RecordCompare Tool Specification
  • SPARQLFetch Tool Specification
  • Update Tool Specification
• Arbitrary Sparql Structure Scoring

Milestones

• Milestone 1
• Milestone 2
• Milestone 3
• Milestone 4
• Milestone 5
• Milestone 6
• Milestone 7
• Milestone 8
• Milestone 9