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Overview

 The first step of a typical harvest is the get you data from your target source.  We call this the Fetch.  For example, let us suppose we have a VIVO installation containing researchers at our university, and we want to harvest from Pubmed information on publications written by researchers at our university. In this case we would use Harvester's PubmedFetch tool to send a query off to Pubmed, which will return the results of that query to us in its own XML format.  The harvesters Fetch package (org.vivoweb.harvester.fetch) contains various methods for retrieving data from external data sources, including as CSV files, as JSON, through JDBC calls, or via OAI Harvest.Fetch is the first stage in a harvest. It accesses the external source and orders the information in a simple RDF/XML file. The configuration task file determines properties of the fetch (ex. for the JDBCFetch it includes queries, table names, where clauses, fields, delimiters).

Process Diagram

  1. External Data Source - This is the foreign source
  2. Fetch - Retrieves data from foreign source
  3. Raw Data - A simple database or as simple XML
  4. Translate - Turns the raw data into Ontological RDF
  5. RDF - RDF models which can be dumped into RDF/XML.
  6. Score - First find similarities and rate them, second determine and apply matches based on a threshold of difference.
  7. Qualify - Changes any unmatched data
  8. Transfer (Update) - move into a vivo model (through an update process if possible.)
  9. Vivo - Final model in RDF visible from the webapp. |

Tools