SWUG:Meeting 2012 04 11

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Revision as of 05:13, 10 April 2012 by Mdolanme (talk | contribs) (Solr)

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Action items from previous calls

SWUG:Meeting_2012_03_27

  • ACTION: chris, tony and jane to have a call to discuss organization
  • ACTION: Mary to add links to example queries and schema (Mary)
  • ACTION: set up a call with: Carlos, Tony, Seth, Mary (monday?) (Seth)
  • ACTION: docs on how we deal with closures in solr (Seth)

Solr

  • Overview (Seth)
  • EBI test schema overview (Tony/Carlos)
  • GOlr schema overview (Seth)
The current work is on this schema: [1]
Which is being pieced together with these: [2] with owltools. The command to generate the Solr schema looks like:
owltools --solr-config /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ont-config.yaml /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/bio-config.yaml /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ann-config.yaml /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ann_ev_agg-config.yaml --solr-schema-dump
  • Design questions:
    • How much to cache? Graph info?
    • How generic? E.g. use in PO
  • OWLTools loading overview (Seth)
Looks something like:
owltools /srv/tmp/go.owl /srv/tmp/cl.owl /srv/tmp/taxslim.owl --solr-url http://localhost:8080/solr/ --solr-purge --solr-config /home/sjcarbon/local/src/svn/owltools/OWLTools-Solr/src/main/resources/ont-config.yaml --solr-load-ontology --solr-load-gafs /srv/tmp/gene_association.mgi
  • Example queries (Mary) [3]

Find term information for GO ID, for example "GO:0005634"

URL

http://skewer.lbl.gov:8080/solr/select?qt=standard&fl=*&version=2.2&wt=json&indent=on&rows=1&q=id:%22GO:0005634%22&fq=document_category:%22ontology_class%22

GOOSE (http://amigo2.berkeleybop.org/cgi-bin/amigo2/goose)

q=id:"GO:0005634"
fq=document_category:"ontology_class"
    • Some old queries require the use of Solr facets and some modification of code Seth has written to present 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.
  • Ontology property views - closure facets (Chris)
  • Client applications. Generic javascript libraries?
  • Next steps
    • BOSC submission?
    • Hackathon?
    • Converge on single schema