SWUG:Meeting 2012 04 11: Difference between revisions
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[[Category:SWUG_Meetings]] | |||
== Action items from previous calls == | == Action items from previous calls == | ||
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* EBI test schema overview (Tony/Carlos) | * EBI test schema overview (Tony/Carlos) | ||
* GOlr schema overview (Seth) | * GOlr schema overview (Seth) | ||
: The current work is on this schema: [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/gold/solr/conf/schema.xml?revision=4422&content-type=text%2Fplain] | |||
: Which is being pieced together with these: [https://code.google.com/p/owltools/source/browse/#svn%2Ftrunk%2FOWLTools-Solr%2Fsrc%2Fmain%2Fresources] with owltools. The command to generate the Solr schema looks like: | |||
: <pre>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</pre> | |||
* Design questions: | * Design questions: | ||
** How much to cache? Graph info? | ** How much to cache? Graph info? | ||
** How generic? E.g. use in PO | |||
* OWLTools loading overview (Seth) | * OWLTools loading overview (Seth) | ||
* Example queries (Mary) | |||
: Looks something like: | |||
: <pre>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</pre> | |||
* Example queries (Mary) [http://wiki.geneontology.org/index.php/Example_Solr_Queries] | |||
** Find term information for GO ID, for example "GO:0005634"<br />URL<br />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<br />GOOSE (http://amigo2.berkeleybop.org/cgi-bin/amigo2/goose)<br /><pre>q=id:"GO:0005634" fq=document_category:"ontology_class"</pre> | |||
** 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) | * Ontology property views - closure facets (Chris) | ||
** https://code.google.com/p/owltools/source/browse/trunk/OWLTools-Core/src/main/java/owltools/mooncat/PropertyViewOntologyBuilder.java | |||
* Client applications. Generic javascript libraries? | |||
* Next steps | * Next steps | ||
** BOSC submission? | ** BOSC submission? | ||
** Hackathon? | ** Hackathon? | ||
** Converge on single schema | ** Converge on single schema | ||
Latest revision as of 18:06, 14 July 2014
Action items from previous calls
- 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.
- Find term information for GO ID, for example "GO:0005634"
- Ontology property views - closure facets (Chris)
- Client applications. Generic javascript libraries?
- Next steps
- BOSC submission?
- Hackathon?
- Converge on single schema