Difference between revisions of "GMOD RPC API"

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m (Brief note about compression.)
(Added more specs.)
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 +
= Document Status =
 +
In progress.
 +
 
= Background =
 
= Background =
 
This effort was started after [[User:Jogoodma|Josh Goodman]]'s talk at the [[January 2009 GMOD Meeting]] meeting titled "MOD Web API (A RESTful interface for [[MOD]]s)".  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]].
 
This effort was started after [[User:Jogoodma|Josh Goodman]]'s talk at the [[January 2009 GMOD Meeting]] meeting titled "MOD Web API (A RESTful interface for [[MOD]]s)".  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]].
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For example, [[FlyBase]] releases its data on a roughly monthly basis and tags all data contained in that release with a release number (e.g. FB2008_10).  If a release number was not used then a date stamp for when the entire genes data class was updated should be used.  If this is not available or if individual genes are updated in a piecemeal fashion then a timestamp based on the query execution time should be used.
 
For example, [[FlyBase]] releases its data on a roughly monthly basis and tags all data contained in that release with a release number (e.g. FB2008_10).  If a release number was not used then a date stamp for when the entire genes data class was updated should be used.  If this is not available or if individual genes are updated in a piecemeal fashion then a timestamp based on the query execution time should be used.
 +
 +
= Result dates =
 +
 +
The individual search results must provide a creation and last modified timestamp via the '''date_created''' and '''last_modified''' XML tags respectively.
 +
If this information is not available then the current timestamp at query execution should be used.
  
 
= Return types =
 
= Return types =
Line 38: Line 46:
 
== Searches ==
 
== Searches ==
 
=== Organism List ===
 
=== Organism List ===
−
'''Purpose:''' Obtain a list of organisms that are able to be queried with the service provider.<br/>
+
==== Purpose ====
−
'''URL:''' <nowiki>http://yourmod.org/gmodrest/v<api version>/organisms[.xml | .json]</nowiki><br/>
+
Provides a list of organisms that are able to be queried with the service provider.
−
'''Return types:''' XML or JSON<br/>
+
 
−
'''Default return type:''' XML<br/>
+
==== URL ====
−
'''Example URLs:'''
+
<nowiki>http://yourmod.org/gmodrest/v<api version>/organisms[.xml | .json]</nowiki>
 +
 
 +
==== Return types ====
 +
XML or JSON
 +
 
 +
==== Default return type ====
 +
XML
 +
 
 +
==== Example URLs ====
 +
* <nowiki>http://flybase.org/gmodrest/v1/organisms</nowiki>
 
* <nowiki>http://flybase.org/gmodrest/v1/organisms.xml</nowiki>
 
* <nowiki>http://flybase.org/gmodrest/v1/organisms.xml</nowiki>
 
* <nowiki>http://flybase.org/gmodrest/v1/organisms.json</nowiki>
 
* <nowiki>http://flybase.org/gmodrest/v1/organisms.json</nowiki>
−
'''XML Result:'''
+
 
 +
==== XML Result ====
 
<xml>
 
<xml>
 
<?xml version="1.0" encoding="UTF-8"?>
 
<?xml version="1.0" encoding="UTF-8"?>
Line 64: Line 82:
 
</resultset>
 
</resultset>
 
</xml>
 
</xml>
−
'''JSON Result:'''
+
 
 +
==== JSON Result ====
 
  {
 
  {
 
     resultset:{
 
     resultset:{
Line 86: Line 105:
  
 
=== Gene full text search ===
 
=== Gene full text search ===
−
'''Purpose:''' Obtain a list of IDs that match a gene full text query.<br/>
+
==== Purpose ====
−
'''URL:''' <nowiki>http://yourmod.org/gmodrest/v<api version>/fulltext/gene/<search term>[+<search term>][/species/<species>][/genus/<genus>][.xml | .json]</nowiki><br/>
+
Performs a full text search on gene records and returns the IDs for matching reocrds.
−
'''Return types:''' XML or JSON<br/>
+
−
'''Default return type:''' XML<br/>
+
−
'''Example URLs:'''
+
−
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection</nowiki>
+
−
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection/species/drosophila/genus/melanogaster</nowiki>
+
−
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/AE003845.json</nowiki>
+
−
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/IPR000483/species/drosophila/genus/simulans.json</nowiki>
+
−
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/egg+expression.xml</nowiki>
+
  
−
'''XML Result:'''
+
==== Description ====
 +
This service returns genes 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====
 +
<nowiki>http://yourmod.org/gmodrest/v<api version>/fulltext/gene/<search term>[/organism/<taxonomy id>][.xml | .json]</nowiki>
 +
 
 +
==== Return types====
 +
XML or JSON
 +
 
 +
==== Default return type ====
 +
XML
 +
 
 +
==== Example URLs ====
 +
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection</nowiki> - Find genes that contain the term cotransfection.
 +
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection/organism/7227</nowiki> - Find Drosophila melanogaster genes that contain the term cotransfection.
 +
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/AE003845.json</nowiki> - Find genes that contain the term AE003845 and return a JSON result.
 +
* <nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/IPR000483/organism/7240.json</nowiki> - Find Drosophila simulans genes that are labeled with InterPro ID IPR000483.
 +
 
 +
==== XML Result ====
 
<xml>
 
<xml>
 
<?xml version="1.0" encoding="UTF-8"?>
 
<?xml version="1.0" encoding="UTF-8"?>
Line 104: Line 134:
 
   <data_provider>FlyBase</data_provider>
 
   <data_provider>FlyBase</data_provider>
 
   <data_version>FB2008_10</data_version>
 
   <data_version>FB2008_10</data_version>
 +
  <query_time>2009-01-15 09:03:00</query_time>
 +
  <query_url>http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection</query_url>
 
   <result>
 
   <result>
 
       <id>FBgn0085432</id>
 
       <id>FBgn0085432</id>
Line 116: Line 148:
 
</resultset>
 
</resultset>
 
</xml>
 
</xml>
−
'''JSON Result:'''
+
 
 +
==== JSON Result ====
 
  {
 
  {
 
     resultset:{
 
     resultset:{
Line 122: Line 155:
 
         data_provider:'FlyBase',
 
         data_provider:'FlyBase',
 
         data_version:'FB2008_10',
 
         data_version:'FB2008_10',
 +
        query_time:'2009-01-15 09:03:00',
 +
        query_url:'<nowiki>http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection.json</nowiki>',
 
         result:[
 
         result:[
 
             {
 
             {
Line 135: Line 170:
 
         ]
 
         ]
 
     }
 
     }
−
}
+
}
  
 +
=== Gene ontology search ===
 +
==== Purpose ====
 +
Searches for genes that have a particular 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.
  
−
== Fetching ==
+
==== URL ====
 +
<nowiki>http://yourmod.org/gmodrest/v<api version>/ontology/gene/<ontology ID>[/organism/<taxonomy id>][.xml | .json]</nowiki>
  
 +
==== Return types ====
 +
XML or JSON
 +
 +
==== Default return type ====
 +
XML
 +
 +
==== Example URLs ====
 +
* <nowiki>http://flybase.org/gmodrest/v1/ontology/gene/GO:12345</nowiki> - Find all genes annotated with GO:12345.
 +
* <nowiki>http://flybase.org/gmodrest/v1/ontology/gene/GO:12345/organism/7227</nowiki> - Find all Drosophila melanogaster genes annotated with GO:12345.
 +
* <nowiki>http://flybase.org/gmodrest/v1/ontology/gene/GO:12345.json</nowiki> - Find all genes annotated with GO:12345 and return a JSON result.
 +
 +
==== XML Result ====
 +
<xml>
 +
<?xml version="1.0" encoding="UTF-8"?>
 +
<resultset>
 +
  <api_version>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/gmodrest/v1/ontology/gene/GO:12345</query_url>
 +
  <result>
 +
      <id>FBgn0085432</id>
 +
      <date_created>2003-03-08 00:00:00</date_created>
 +
      <last_modified>2005-01-15 09:03:00</last_modified>
 +
  </result>
 +
  <result>
 +
      <id>FBgn0004364</id>
 +
      <date_created>2005-01-08 00:00:00</date_created>
 +
      <last_modified>2009-01-01 00:00:00</last_modified>
 +
  </result>
 +
</resultset>
 +
</xml>
 +
 +
==== JSON Result ====
 +
{
 +
    resultset:{
 +
        api_version:1,
 +
        data_provider:'FlyBase',
 +
        data_version:'FB2008_10',
 +
        query_time:'2009-01-15 09:03:00',
 +
        query_url:'<nowiki>http://flybase.org/gmodrest/v1/ontology/gene/GO:12345.json</nowiki>',
 +
        result:[
 +
            {
 +
                id:'FBgn0085432',
 +
                date_created:'2003-03-08 00:00:00',
 +
                last_modified:'2005-01-15 09:03:00'
 +
            },
 +
            {
 +
                id:'FBgn0004364',
 +
                date_created:'2005-01-08 00:00:00',
 +
                last_modified:'2009-01-01 00:00:00'
 +
            }
 +
        ]
 +
    }
 +
}
 +
 +
=== Gene ortholog search ===
 +
==== 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 ====
 +
<nowiki>http://yourmod.org/gmodrest/v<api version>/ortholog/gene/<gene ID>[/organism/<taxonomy id>][.xml | .json]</nowiki>
 +
 +
==== Return types ====
 +
XML or JSON
 +
 +
==== Default return type ====
 +
XML
 +
 +
==== Example URLs ====
 +
* <nowiki>http://flybase.org/gmodrest/v1/ortholog/gene/FBgn0004364</nowiki> - Find all FlyBase and non FlyBase genes that are orthologous to FBgn0004364.
 +
* <nowiki>http://flybase.org/gmodrest/v1/ortholog/gene/FBgn0004364/organism/7240</nowiki> - Find out if FBgn0004364 has an ortholog in Drosophila simulans.
 +
* <nowiki>http://flybase.org/gmodrest/v1/ortholog/gene/WBGene12345.json</nowiki> - Find all FlyBase genes that are orthologous to WBGene12345 and return a JSON result.
 +
 +
==== XML Result: ====
 +
<xml>
 +
<?xml version="1.0" encoding="UTF-8"?>
 +
<resultset>
 +
  <api_version>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/gmodrest/v1/ortholog/gene/FBgn0000490</query_url>
 +
  <result>
 +
      <id>FBgn0097591</id>
 +
      <date_created>2003-03-08 00:00:00</date_created>
 +
      <last_modified>2005-01-15 09:03:00</last_modified>
 +
  </result>
 +
  <result>
 +
      <id>ENSBTAP00000004992</id>
 +
      <date_created>2005-01-08 00:00:00</date_created>
 +
      <last_modified>2009-01-01 00:00:00</last_modified>
 +
  </result>
 +
</resultset>
 +
</xml>
 +
 +
==== JSON Result ====
 +
{
 +
    resultset:{
 +
        api_version:1,
 +
        data_provider:'FlyBase',
 +
        data_version:'FB2008_10',
 +
        query_time:'2009-01-15 09:03:00',
 +
        query_url:'<nowiki>http://flybase.org/gmodrest/v1/ortholog/gene/FBgn0000490.json</nowiki>',
 +
        result:[
 +
            {
 +
                id:'FBgn0097591',
 +
                date_created:'2003-03-08 00:00:00',
 +
                last_modified:'2005-01-15 09:03:00'
 +
            },
 +
            {
 +
                id:'ENSBTAP00000004992',
 +
                date_created:'2005-01-08 00:00:00',
 +
                last_modified:'2009-01-01 00:00:00'
 +
            }
 +
        ]
 +
    }
 +
}
 +
 +
 +
 +
== Fetching ==
  
 
= TODO =
 
= TODO =
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* Write schemas for the XML formats.
 
* Write schemas for the XML formats.
 
* Double check REST compliance.
 
* Double check REST compliance.
−
* Do we need additional fields for full text result format?
+
* Do we need additional fields for full text result format (organism, etc...)?
−
* Timestamp format?
+
* Specify a timestamp format.
 
* Add more details on HTTP headers required to use compression.
 
* Add more details on HTTP headers required to use compression.
 +
* Add ability to use multiple search and ontology terms in one query and perform basic logical operations (AND, OR, NOT).
 +
* Add support for GO's NOT operator.
 +
* Need a null result format.
  
 
[[Category:REST]]
 
[[Category:REST]]
 
[[Category: Web services]]
 
[[Category: Web services]]

Revision as of 06:22, 18 January 2009

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

Goals

  • Data model agnostic
  • Language agnostic
  • Easy to use
  • Versioned URLs for API stability over time

Data classes

At present, this API only covers querying and retrieving information for the gene data class.

API Version

In order to provide a stable URL API all web calls should be versioned according to what version of the GMOD REST API they are using. The version number included in the URLs corresponds to the API version and not the data version. As changes to the API are made the version number will be incremented. Access to the older API versions should be provided indefinitely.

Current GMOD REST API Version: 1

Data version

The search results must contain an XML tag called data_version that contains the database release number. If the database does not use release numbers then the date for when the entire data class was updated should be used. If that is not available or if individual records within a data class are updated and released asynchronously then a timestamp derived from the time of query execution should be used.

For example, FlyBase releases its data on a roughly monthly basis and tags all data contained in that release with a release number (e.g. FB2008_10). If a release number was not used then a date stamp for when the entire genes data class was updated should be used. If this is not available or if individual genes are updated in a piecemeal fashion then a timestamp based on the query execution time should be used.

Result dates

The individual search results must provide a creation and last modified timestamp via the date_created and last_modified XML tags respectively. If this information is not available then the current timestamp at query execution should be used.

Return types

Each service may define its own return types. The client may request a specific return type by appending the appropriate file extension to the URL. If no file extension is appended then the default return type for that service is used.

Compression

Sending of compressed XML and JSON results should be dictated by the same rules used for HTTP communication.

Services

Searches

Organism List

Purpose

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

URL

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

Return types

XML or JSON

Default return type

XML

Example URLs

  • http://flybase.org/gmodrest/v1/organisms
  • http://flybase.org/gmodrest/v1/organisms.xml
  • http://flybase.org/gmodrest/v1/organisms.json

XML Result

<xml> <?xml version="1.0" encoding="UTF-8"?> <resultset> 

  <api_version>1</api_version>
  <data_provider>FlyBase</data_provider>
  <data_version>FB2008_10</data_version>
  <organism>
      <genus>Drosophila</genus>
      <species>melanogaster</species>
      <taxonomy_id>7227</taxonomy_id>
  </organism>
  <organism>
      <species>Drosophila</species>
      <genus>simulans</genus>
      <taxonomy_id>7240</taxonomy_id>
  </organism>

</resultset> </xml>

JSON Result

{
   resultset:{
       api_version:1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       organism:[
           {
               genus:'Drosophila',
               species:'melanogaster',
               taxonomy_id:7227
           },
           {
               species:'Drosophila',
               genus:'simulans',
               taxonomy_id:7240
           }
       ]
   }
}

Gene full text search

Purpose

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

Description

This service returns genes 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/gmodrest/v<api version>/fulltext/gene/<search term>[/organism/<taxonomy id>][.xml | .json]

Return types

XML or JSON

Default return type

XML

Example URLs

  • http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection - Find genes that contain the term cotransfection.
  • http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection/organism/7227 - Find Drosophila melanogaster genes that contain the term cotransfection.
  • http://flybase.org/gmodrest/v1/fulltext/gene/AE003845.json - Find genes that contain the term AE003845 and return a JSON result.
  • http://flybase.org/gmodrest/v1/fulltext/gene/IPR000483/organism/7240.json - Find Drosophila simulans genes that are labeled with InterPro ID IPR000483.

XML Result

<xml> <?xml version="1.0" encoding="UTF-8"?> <resultset> 

  <api_version>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/gmodrest/v1/fulltext/gene/cotransfection</query_url>
  <result>
     <id>FBgn0085432</id>
     <date_created>2003-03-08 00:00:00</date_created>
     <last_modified>2005-01-15 09:03:00</last_modified>
  </result>
  <result>
     <id>FBgn0004364</id>
     <date_created>2005-01-08 00:00:00</date_created>
     <last_modified>2009-01-01 00:00:00</last_modified>
  </result>

</resultset> </xml>

JSON Result

{
   resultset:{
       api_version:1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrest/v1/fulltext/gene/cotransfection.json',
       result:[
           {
               id:'FBgn0085432',
               date_created:'2003-03-08 00:00:00',
               last_modified:'2005-01-15 09:03:00'
           },
           {
               id:'FBgn0004364',
               date_created:'2005-01-08 00:00:00',
               last_modified:'2009-01-01 00:00:00'
           }
       ]
   }
}

Gene ontology search

Purpose

Searches for genes that have a particular 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/gmodrest/v<api version>/ontology/gene/<ontology ID>[/organism/<taxonomy id>][.xml | .json]

Return types

XML or JSON

Default return type

XML

Example URLs

  • http://flybase.org/gmodrest/v1/ontology/gene/GO:12345 - Find all genes annotated with GO:12345.
  • http://flybase.org/gmodrest/v1/ontology/gene/GO:12345/organism/7227 - Find all Drosophila melanogaster genes annotated with GO:12345.
  • http://flybase.org/gmodrest/v1/ontology/gene/GO:12345.json - Find all genes annotated with GO:12345 and return a JSON result.

XML Result

<xml> <?xml version="1.0" encoding="UTF-8"?> <resultset> 

  <api_version>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/gmodrest/v1/ontology/gene/GO:12345</query_url>
  <result>
     <id>FBgn0085432</id>
     <date_created>2003-03-08 00:00:00</date_created>
     <last_modified>2005-01-15 09:03:00</last_modified>
  </result>
  <result>
     <id>FBgn0004364</id>
     <date_created>2005-01-08 00:00:00</date_created>
     <last_modified>2009-01-01 00:00:00</last_modified>
  </result>

</resultset> </xml>

JSON Result

{
   resultset:{
       api_version:1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrest/v1/ontology/gene/GO:12345.json',
       result:[
           {
               id:'FBgn0085432',
               date_created:'2003-03-08 00:00:00',
               last_modified:'2005-01-15 09:03:00'
           },
           {
               id:'FBgn0004364',
               date_created:'2005-01-08 00:00:00',
               last_modified:'2009-01-01 00:00:00'
           }
       ]
   }
}

Gene ortholog search

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/gmodrest/v<api version>/ortholog/gene/<gene ID>[/organism/<taxonomy id>][.xml | .json]

Return types

XML or JSON

Default return type

XML

Example URLs

  • http://flybase.org/gmodrest/v1/ortholog/gene/FBgn0004364 - Find all FlyBase and non FlyBase genes that are orthologous to FBgn0004364.
  • http://flybase.org/gmodrest/v1/ortholog/gene/FBgn0004364/organism/7240 - Find out if FBgn0004364 has an ortholog in Drosophila simulans.
  • http://flybase.org/gmodrest/v1/ortholog/gene/WBGene12345.json - Find all FlyBase genes that are orthologous to WBGene12345 and return a JSON result.

XML Result:

<xml> <?xml version="1.0" encoding="UTF-8"?> <resultset> 

  <api_version>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/gmodrest/v1/ortholog/gene/FBgn0000490</query_url>
  <result>
     <id>FBgn0097591</id>
     <date_created>2003-03-08 00:00:00</date_created>
     <last_modified>2005-01-15 09:03:00</last_modified>
  </result>
  <result>
     <id>ENSBTAP00000004992</id>
     <date_created>2005-01-08 00:00:00</date_created>
     <last_modified>2009-01-01 00:00:00</last_modified>
  </result>

</resultset> </xml>

JSON Result

{
   resultset:{
       api_version:1,
       data_provider:'FlyBase',
       data_version:'FB2008_10',
       query_time:'2009-01-15 09:03:00',
       query_url:'http://flybase.org/gmodrest/v1/ortholog/gene/FBgn0000490.json',
       result:[
           {
               id:'FBgn0097591',
               date_created:'2003-03-08 00:00:00',
               last_modified:'2005-01-15 09:03:00'
           },
           {
               id:'ENSBTAP00000004992',
               date_created:'2005-01-08 00:00:00',
               last_modified:'2009-01-01 00:00:00'
           }
       ]
   }
}


Fetching

TODO

  • Should we use the NCBI eUtils XML formats?
  • Write schemas for the XML formats.
  • Double check REST compliance.
  • Do we need additional fields for full text result format (organism, etc...)?
  • Specify a timestamp format.
  • Add more details on HTTP headers required to use compression.
  • Add ability to use multiple search and ontology terms in one query and perform basic logical operations (AND, OR, NOT).
  • Add support for GO's NOT operator.
  • Need a null result format.
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