GMOD

GMOD RPC API

(Redirected from GMOD REST API

Contents

Document Status

In progress.

Background

This effort was started after Josh Goodman’s talk at the January 2009 GMOD Meeting meeting titled “MOD Web API (A RESTful interface for MODs)”. The main idea is to increase interoperability among the various model organism databases by creating an easy to use high level RESTful API. The queries iterated below are currently in the proposal stage and have no been implemented at any MOD.

Members

Services

Searches

Organism List

Service Name

organisms

Purpose

Provides a list of organisms that are able to be queried with the service provider.

URL

http://yourmod.org/gmodrpc/v<api version>/organisms[.xml | .json]

Return types

XML or JSON

Default return type

XML

Example URLs
XML Result
<?xml version="1.0" encoding="UTF-8"?>
<resultset>
   <api_version>1.1</api_version>
   <data_provider>FlyBase</data_provider>
   <data_version>FB2008_10</data_version>
   <result>
      <organism>
         <genus>Drosophila</genus>
         <species>melanogaster</species>
         <taxonomy_id>7227</taxonomy_id>
      </organism>
   </result>
   <result>
      <organism>
          <species>Drosophila</species>
          <genus>simulans</genus>
          <taxonomy_id>7240</taxonomy_id>
      </organism>
    </result>
</resultset>
JSON Result
{
   resultset:{
       api_version:1.1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       result:[
           {
               organism:{
                   genus:'Drosophila',
                   species:'melanogaster',
                   taxonomy_id:7227
               }
           },
           {
               organism:{
                   species:'Drosophila',
                   genus:'simulans',
                   taxonomy_id:7240
               }
           }
       ]
   }
}

Gene full text search

Service Name

fulltext

Purpose

Performs a full text search on records and returns the IDs for matching records.

Description

This service returns features that contain the search term anywhere in the gene record. Results can be restricted to a specific organism by supplying the NCBI taxonomy id.

URL

http://yourmod.org/gmodrpc/v<api version>/fulltext/<search term>[.xml | .json]?[type=<SO term ID>][taxid=<taxid>][genus=<genus>][species=<species>]

Return types

XML or JSON

Default return type

XML

Example URLs
XML Result
<?xml version="1.0" encoding="UTF-8"?>
<resultset>
   <api_version>1.1</api_version>
   <data_provider>FlyBase</data_provider>
   <data_version>FB2008_10</data_version>
   <query_time>2009-01-15 09:03:00</query_time>
   <query_url>http://flybase.org/gmodrpc/v1.1/fulltext/cotransfection?type=SO:0000704</query_url>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0085432</accession>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0085432</url>
      </dbxref>
      <date_created>2003-03-08 00:00:00</date_created>
      <last_modified>2005-01-15 09:03:00</last_modified>
   </result>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0004364</accession>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0004364</url>
      </dbxref>
      <date_created>2005-01-08 00:00:00</date_created>
      <last_modified>2009-01-01 00:00:00</last_modified>
   </result>
</resultset>
JSON Result
{
   resultset:{
       api_version:1.1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrpc/v1.1/fulltext/cotransfection?type=SO:0000704',
       result:[
           {
               dbxref:{
                   db:'FlyBase',
                   accession:'FBgn0085432',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0085432'
               },
               date_created:'2003-03-08 00:00:00',
               last_modified:'2005-01-15 09:03:00'
           },
           {
               dbxref:{
                   db:'FlyBase',
                   accession:'FBgn0004364',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0004364'
               },
               date_created:'2005-01-08 00:00:00',
               last_modified:'2009-01-01 00:00:00'
           }
       ]
   }
}

Gene location

Service Name

location

Purpose

Retrieves a list of features that lie within a specific sequence range.

Description

This service returns features that lie within a specific sequence range. Arguments include the name of the largest assembled unit (i.e. chromosome, scaffold, etc…), location start (fmin), location stop (fmax), and strand. Results can be restricted to a specific organism by supplying the NCBI taxonomy id.

URL

http://yourmod.org/gmodrpc/v<api version>/location/chromosome/<name>[.xml | .json]?[type=<SO term ID>][fmin=<int>][fmax=<int>][strand=(1 | -1)][taxid=<taxid>][genus=<genus>][species=<species>]

Return types

XML or JSON

Default return type

XML

Example URLs
XML Result
<?xml version="1.0" encoding="UTF-8"?>
<resultset>
   <api_version>1.1</api_version>
   <data_provider>FlyBase</data_provider>
   <data_version>FB2008_10</data_version>
   <query_time>2009-01-15 09:03:00</query_time>
   <query_url>http://flybase.org/gmodrpc/v1.1/location/chromosome/2L?type=SO:0000704&amp;fmin=12587000&amp;fmax=12629000&amp;taxid=7227</query_url>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0085424</accession>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0085424</url>
      </dbxref>
      <date_created>2003-03-08 00:00:00</date_created>
      <last_modified>2005-01-15 09:03:00</last_modified>
   </result>
</resultset>
JSON Result
{
   resultset:{
       api_version:1.1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrpc/v1.1/location/chromosome/2L?type=SO:0000704&fmin=12587000&fmax=12629000&taxid=7227',
       result:[
           {
               dbxref:{
                   db:'FlyBase',
                   accession:'FBgn0085424',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0085424'
               },
               date_created:'2003-03-08 00:00:00',
               last_modified:'2005-01-15 09:03:00'
           }
       ]
   }
}
Service Name

ontology

Purpose

Search for genes that have been annotated with a particular gene ontology ID.

Description

This service returns genes that have been annotated with a particular ontology term. Results can be restricted to a specific organism by supplying the NCBI taxonomy id.

URL

http://yourmod.org/gmodrpc/v<api version>/ontology/gene/<ontology ID>[.xml | .json]?[taxid=<taxid>][genus=<genus>][species=<species>]

Return types

XML or JSON

Default return type

XML

Example URLs
XML Result
<?xml version="1.0" encoding="UTF-8"?>
<resultset>
   <api_version>1.1</api_version>
   <data_provider>FlyBase</data_provider>
   <data_version>FB2008_10</data_version>
   <query_time>2009-01-15 09:03:00</query_time>
   <query_url>http://flybase.org/gmodrpc/v1.1/ontology/gene/GO:0005515</query_url>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0085432</accession>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0085432</url>
      </dbxref>
      <date_created>2003-03-08 00:00:00</date_created>
      <last_modified>2005-01-15 09:03:00</last_modified>
   </result>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0004364</accession>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0004364</url>
      </dbxref>
      <date_created>2005-01-08 00:00:00</date_created>
      <last_modified>2009-01-01 00:00:00</last_modified>
   </result>
</resultset>
JSON Result
{
   resultset:{
       api_version:1.1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrpc/v1.1/ontology/gene/GO:0005515',
       result:[
           {
               dbxref:{
                   db:'FlyBase',
                   accession:'FBgn0085432',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0085432'
               },
               date_created:'2003-03-08 00:00:00',
               last_modified:'2005-01-15 09:03:00'
           },
           {
               dbxref:{
                   db:'FlyBase',
                   accession:'FBgn0004364',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0004364'
               },
               date_created:'2005-01-08 00:00:00',
               last_modified:'2009-01-01 00:00:00'
           }
       ]
   }
}
Service name

orthologs/gene

Purpose

Search for orthologs of the supplied gene ID.

Description

This service returns genes that have been determined by some means to be orthologous to the supplied gene ID. If the supplied gene ID is within the namespace of the web service provider then all known orthologs of that gene are returned. If the supplied gene ID is not within the namespace of the web service provider then it only returns genes for organisms that are offered by the service provider.

For example, for a given gene FlyBase stores orthology calls to other FlyBase genes and non FlyBase genes. Thus, given a FlyBase gene ID you can obtain a list of gene IDs for genes within FlyBase and to other non Drosophila species. In addition, given a non FlyBase gene ID you can obtain a list of FlyBase genes that are orthologous to it.

Results can be restricted to a specific organism by supplying the NCBI taxonomy ID.

URL

http://yourmod.org/gmodrpc/v<api version>/orthologs/gene/<gene ID>[.xml | .json]?[taxid=<taxid>][genus=<genus>][species=<species>]

Return types

XML or JSON

Default return type

XML

Example URLs
XML Result:
<?xml version="1.0" encoding="UTF-8"?>
<resultset>
   <api_version>1.1</api_version>
   <data_provider>FlyBase</data_provider>
   <data_version>FB2008_10</data_version>
   <query_time>2009-01-15 09:03:00</query_time>
   <query_url>http://flybase.org/gmodrpc/v1.1/orthologs/gene/FBgn0000490</query_url>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0097591</accession>
         <data_provider>FlyBase</data_provider>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0097591</url>
      </dbxref>
   </result>
   <result>
      <dbxref>
          <db>ENSEMBL</db>
          <accession>ENSBTAP00000004992</accession>
          <data_provider>InParanoid</data_provider>
      </dbxref>
   </result>
</resultset>
JSON Result
{
   resultset:{
       api_version:1.1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrpc/v1.1/orthologs/gene/FBgn0000490',
       result:[
           {
               dbxref:{
                   db:'FlyBase',
                   accession:'FBgn0097591',
                   data_provider:'FlyBase'
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0097591'
               }
           },
           {
               dbxref:{
                   db:'ENSEMBL',
                   accession:'ENSBTAP00000004992',
                   data_provider:'InParanoid'
               }
           }
       ]
   }
}
Service name

orthologs/organism

Purpose

Returns a list of orthologs between an organism and one or more other organisms.

Description

This service returns genes that have been determined by some means to be orthologous between a single organism and one or more other organisms. The organisms are specified by providing taxonomy IDs.

URL

http://yourmod.org/gmodrpc/v<api version>/orthologs/organism[/<taxid>][/genus/<genus>/species/<species>][.xml | .json]?[to_taxid=<taxid>][to_genus=<genus>&to_species=<species>]

Return types

XML or JSON

Default return type

XML

Example URLs
XML Result:
<?xml version="1.0" encoding="UTF-8"?>
<resultset>
   <api_version>1.1</api_version>
   <data_provider>FlyBase</data_provider>
   <data_version>FB2008_10</data_version>
   <query_time>2009-01-15 09:03:00</query_time>
   <query_url>http://flybase.org/gmodrpc/v1.1/orthologs/organism/genus/Drosophila/species/melanogaster</query_url>
   <result>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0000490</accession>
         <taxonomy_id>7227</taxonomy_id>
         <data_provider>FlyBase</data_provider>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0000490</url>
      </dbxref>
      <dbxref>
         <db>FlyBase</db>
         <accession>FBgn0015673</accession>
         <taxonomy_id>7240</taxonomy_id>
         <data_provider>FlyBase</data_provider>
         <url>http://flybase.org/gmodrpc/v1.1/fetch/FBgn0015673</url>
      </dbxref>
      <dbxref>
         <db>WormBase</db>
         <accession>WBGene00006570</accession>
         <taxonomy_id>6239</taxonomy_id>
         <data_provider>InParanoid</data_provider>
         <url>http://wormbase.org/gmodrpc/v1.1/fetch/WBGene00006570</url>
      </dbxref>
   </result>
...
</resultset>
JSON Result
{
   resultset:{
       api_version:1.1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrpc/v1.1/orthologs/organism/genus/Drosophila/species/melanogaster',
       result:[
         {
           dbxref:[
               {
                   db:'FlyBase',
                   accession:'FBgn0000490',
                   taxonomy_id:7227,
                   data_provider:'FlyBase',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0000490'
               },
               {
                   db:'FlyBase',
                   accession:'FBgn0015673'
                   taxonomy_id:7240,
                   data_provider:'FlyBase',
                   url:'http://flybase.org/gmodrpc/v1.1/fetch/FBgn0015673'
               },
               {
                   db:'WormBase',
                   accession:'WBGene00006570',
                   taxonomy_id:6239,
                   data_provider:'InParanoid',
                   url:'http://wormbase.org/gmodrpc/v1.1/fetch/WBGene00006570'
               }
           ]
         }
       ]
   }
}

Fetching

Gene records

Service name

fetch/gene

Purpose

To fetch gene records in the Generic gene page XML format as implemented by Bio GMOD GenericGenePage.

Description
URL

http://yourmod.org/gmodrpc/v<api version>/fetch/gene/<gene ID>

Return types

XML

Default return type

XML

Example URLs
XML Result

See Bio GMOD GenericGenePage for example XML.

Sequence

Service name

fetch/seq

Purpose

Returns FASTA sequence for the specified query.

Description
URL

http://yourmod.org/gmodrpc/v<api version>/fetch/seq/<ID>[/<SO term ID of subtype>]

Return types

FASTA

Example URLs
FASTA Result:

TODO

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