Example Solr Queries
Overview
This page has examples of various kinds of queries possible on the GO Solr document store (GOlr), Preliminary schema information can be found in the repo.
Preliminary information about the schema can be found on SF.net.
Usage
The current testing ground for GOlr is:
http://golr.berkeleybop.org/
This is a naked Solr server; you can access it with any http client, including a web browser. In addition, there is an experimental version of GOOSE that can talk to Solr (select a Solr mirror from the list):
http://amigo2.berkeleybop.org/cgi-bin/amigo2/goose
This method is currently a little slower, but may make learning a little bit easier.
Example Queries
All documents (first 10)
URL
http://golr.berkeleybop.org/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=10&indent=on&q=*:*&start=0
GOOSE
q=*:*
All documents (first 20)
URL
http://golr.berkeleybop.org/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=20&indent=on&q=*:*&start=0
GOOSE
q=*:* rows=20
All bioentities (50-100)
URL
http://golr.berkeleybop.org/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=50&indent=on&q=*:*&fq=document_category:%22bioentity%22&start=50
GOOSE
q=*:* fq=document_category:"bioentity" rows=50 start=50
Find term information for GO ID, for example "GO:0005634"
URL
http://golr.berkeleybop.org/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
q=id:"GO:0005634" fq=document_category:"ontology_class"
Find term by (preferred) name, for example "nucleus"
URL
http://golr.berkeleybop.org/select?qt=standard&fl=*&version=2.2&wt=json&indent=on&rows=1&q=label:%22nucleus%22&fq=document_category:%22ontology_class%22
GOOSE
q=label:"nucleus" fq=document_category:"ontology_class" rows=1
To find (first 50) obsolete terms
URL
http://golr.berkeleybop.org/select?qt=standard&fl=*&version=2.2&wt=json&indent=on&rows=50&q=document_category:%22ontology_class%22&fq=is_obsolete:%22true%22
GOOSE
q=document_category:"ontology_class" fq=is_obsolete:"true" rows=50
Counts of types in IEA annotations (illustrates the use of solr 'facets')
URL
http://golr.berkeleybop.org/select?fq=document_category:annotation&rows=0&json.nl=arrarr&facet.sort=count&q=*:*&indent=on&facet.field=type&fl=*%2Cscore&facet=true&start=0&wt=json&facet.mincount=1
q=*:* fq=document_category:annotation facet=true facet.sort="count" facet.mincount:"1" rows:"0"
IEA Annotations from TAIR (first 10)
URL
http://golr.berkeleybop.org/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=10&indent=on&q=*:*&fq=document_category:annotation&start=0
GOOSE
q=*:* fq=document_category:annotation fq=source:"TAIR" fq=evidence_type:"IEA"
Genes to both "macromolecule biosynthetic process" and "cellular response to stress" (first 10, plus facets)
URL
http://golr.berkeleybop.org/select?qt=standard&indent=on&wt=json&version=2.2&rows=10&start=0&fl=*%2Cscore&facet=true&facet.field=type&facet.field=taxon&facet.field=isa_partof_closure_label&fq=&q=*:*&fq=document_category:"bioentity"&fq=isa_partof_closure_label:"macromolecule biosynthetic process"&fq=isa_partof_closure_label:"cellular response to stress"
GOOSE (facets generated, but not shown)
q=*:* fq=document_category:"bioentity" fq=isa_partof_closure_label:"macromolecule biosynthetic process" fq=isa_partof_closure_label:"cellular response to stress" facet=true facet.field=type facet.field=taxon facet.field=isa_partof_closure_label