Example Solr Queries: Difference between revisions

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The current testing ground for GOlr is:
The current testing ground for GOlr is:


  http://skewer.lbl.gov:8080/solr/
  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):
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/cgi-bin/amigo2/goose
  http://amigo2.berkeleybop.org/gannet


This method is currently a little slower, but may make learning a little bit easier.
This method is currently a little slower, but may make learning a little bit easier.
Line 23: Line 23:


URL
URL
  http://skewer.lbl.gov:8080/solr/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=10&indent=on&q=*:*&start=0
  http://golr.berkeleybop.org/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=10&indent=on&q=*:*&start=0


GOOSE
Gannet
  q=*:*
  q=*:*


Line 31: Line 31:


URL
URL
  http://skewer.lbl.gov:8080/solr/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=20&indent=on&q=*:*&start=0
  http://golr.berkeleybop.org/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=20&indent=on&q=*:*&start=0


GOOSE
Gannet
  q=*:*
  q=*:*
  rows=20
  rows=20
Line 40: Line 40:


URL
URL
  http://skewer.lbl.gov:8080/solr/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=50&indent=on&q=*:*&fq=document_category:%22bioentity%22&start=50
  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
Gannet
  q=*:*
  q=*:*
  fq=document_category:"bioentity"
  fq=document_category:"bioentity"
  rows=50
  rows=50
  start=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)==
==IEA Annotations from TAIR (first 10)==


URL
URL
  http://skewer.lbl.gov:8080/solr/select?qt=standard&fl=*%2Cscore&version=2.2&wt=json&rows=10&indent=on&q=*:*&fq=document_category:annotation&start=0
  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
Gannet
  q=*:*
  q=*:*
  fq=document_category:annotation
  fq=document_category:annotation
Line 59: Line 102:
  fq=evidence_type:"IEA"
  fq=evidence_type:"IEA"


==Annotations to both "macromolecule biosynthetic process" and "cellular response to stress" (first 10, plus facets)==
==Genes to both "macromolecule biosynthetic process" and "cellular response to stress" (first 10, plus facets)==


URL
URL
  http://skewer.lbl.gov:8080/solr/select?qt=standard&indent=on&wt=json&version=2.2&rows=10&start=0&fl=*%2Cscore&facet=true&facet.field=document_category&facet.field=type&facet.field=evidence_type&facet.field=evidence_closure&facet.field=source&facet.field=taxon&facet.field=isa_partof_label_closure&facet.field=annotation_extension_class_label_closure&fq=&q=*:*&fq=document_category:"annotation"&fq=isa_partof_label_closure:"macromolecule biosynthetic process"&fq=isa_partof_label_closure:"cellular response to stress"
  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)
Gannet (facets generated, but not shown)
  q=*:*
  q=*:*
  fq=document_category:"annotation"
  fq=document_category:"bioentity"
  fq=isa_partof_label_closure:"macromolecule biosynthetic process"
  fq=isa_partof_closure_label:"macromolecule biosynthetic process"
  fq=isa_partof_label_closure:"cellular response to stress"
  fq=isa_partof_closure_label:"cellular response to stress"
  facet=true
  facet=true
facet.field=document_category
  facet.field=type
  facet.field=type
facet.field=evidence_type
facet.field=evidence_closure
facet.field=source
  facet.field=taxon
  facet.field=taxon
  facet.field=isa_partof_label_closure
  facet.field=isa_partof_closure_label
  facet.field=annotation_extension_class_label_closure
 
==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
 


[[Category:Database]]
[[Category:Database]]

Latest revision as of 15:43, 27 May 2015

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