GOlr

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Revision as of 12:42, 14 March 2012 by Mdolanme (talk | contribs) (Rewriting old GOOSE query examples for the new GOlr Schema)

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Overview

This page describes the status of the public Solr index for the GO. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO and other services.

Implementation Progress

We are currently looking at nginx as a reverse proxy for speed and to prevent unauthorized access to non-select URLs on the Solr server.

Schema Progress

We are currently working towards a flexible schema as defined in the owltools code. As we roll it out for the AmiGO backend and as a replacement for common GOOSE queries, we expect to find holes in the schema, documented below.

Currently, the index is entirely populated by through an owltools command line program, but in the future additional document types may require other scripts for loading.

Rewriting old GOOSE query examples for the new GOlr Schema

  • Example queries [1]
    • Some old queries require the use of Solr facets and some modification of code Seth has written for simpler results queries.
    • Note: hierarchical queries that 'combine' facet queries can be handled by the facet.pivot functionality that is available in Solr 4. In the meantime, we'll see if we can devise a work-around.

Current Issues and Problems with the GOlr Schema

  • No PANTHER data
    • We'll look at creating a new document type from Suzi's PAINT code.
  • A few suggestions to make use of the document categories easier:
    • bioentity 'source' was not loaded correctly in the version I was testing
    • annotation should have 'with' field (I believe Seth said this is coming but thought I'd get it written down here)
    • ontology_class should have 'synonyms' and 'closure' (I believe Seth said this is coming)
    • annotation_aggregate should have 'go_id' as a separate field (I believe Seth said this is coming as 'alternate_id')