Example Solr Queries

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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 Gannet that can talk to Solr (select a Solr mirror from the list):

http://amigo2.berkeleybop.org/gannet

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

Gannet

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

Gannet

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

Gannet

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

Gannet

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

Gannet

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

Gannet

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

Gannet

q=*:*
fq=document_category:annotation
facet=true
facet.field=type
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

Gannet

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"

Gannet (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

Distribution by species of annotations to sensory perception of smell

Gannet (facets generated, but not shown)

q=*:*
fq=document_category:"bioentity"
fq=isa_partof_closure_label:"sensory perception of smell"
facet=true
facet.field=taxon_label
facet.mincount=1
rows=0