BioCreative XML-RPC MetaService

To invoke the RPC service use an XML-RPC client (library) using this URL and path: http://bcms.bioinfo.cnio.es/xmlrpc/ .

The following methods are available:

• Annotations.getAnnotation - ([string or int], [int]) -> struct{...}

  Return the annotations created by one Annotation Server for the given article. Input is either a positive integer - a valid PubMed ID - or a text string for fulltext annotations.

  Fulltext ([string] input) is currently NOT supported.

  Response struct:

  • Struct of result_type/array key-values.
  • Each result array is either a list of structs containing the raw results, or a two-element array consiting of a boolean and the confidence for the interaction prediction result.
  See getAnnotations() for result_type keys.

• Annotations.getAnnotationServerList - ([string or int]) -> array([int], ...)

  Return the list of all server IDs which should create annotations for the given PMID or fulltext sting (fulltext currently not supported).

• Annotations.getAnnotations - ([string or int]) -> struct{...}

  Return the annotations created by the Annotation Servers for the given article. Input is either a positive integer - a valid PubMed ID - or a text string for fulltext annotations.

  Fulltext ([string] input) is currently NOT supported.

  response struct:

  • Struct of server_id/result key-values.
  • Each value has a struct of result_type/array key-values.
  • Each result array is either a list of structs containing the raw results, or a two-element array consiting of a boolean and the confidence for the interaction prediction result.
  The follwoing result_type keys can be found:
  • mentions (struct)
    • offset (int)
    • section (str)
    • mention (str)
    • confidence (float, optional)
  • normalizations (struct)
    • dbname (str)
    • dbid (str)
    • taxid (int)
    • confidence (float, optional)
  • taxons (struct)
    • taxid (int)
    • confidence (float)
  • interaction (array)
    • 0 (boolean, has interaction)
    • 1 (float, confidence)

• Resources.getServer - ([int]) => struct{...}

  Return a server struct for a server ID describing the current status of the server (ONLINE, OFFLINE, DISABLED) and its annotation capabilities.

  response struct:

  • team_id (int)
  • status (str)
  • fulltext (boolean) - currently meaningless
  • mentions (boolean)
  • normalizations (boolean)
  • taxons (boolean)
  • interaction (boolean)

• Resources.getServerIDs - ([int]) => array([int], ...)

  Return all known server IDs for a team ID.

• Resources.getTeam - ([int]) => struct{...}

  Return a team struct for a team ID giving general information on the team and their annotation system.

  response struct:

  • organization (str)
  • system_description (str)
  • contact_name (str)
  • email_address (str)
  • homepage (str)

• Resources.getTeamID - ([int]) => [int]

  Return the team ID for a server ID.

• Resources.getTeams - () => array([int], ...)

  Return an integer array of all team IDs.

• add - ([int], [int]) -> [int]

  Return the sum of two integers. Default test function for ensuring the connectivity to the XML-RPC server.

  Please do not call the real functions for connectivity testing purposes.

• system.listMethods - system.listMethods() => ['add', 'subtract', 'multiple'] Returns a list of the methods supported by the server.
• system.methodHelp - system.methodHelp('add') => "Adds two integers together" Returns a string containing documentation for the specified method.
• system.methodSignature - system.methodSignature('add') => [double, int, int] Returns a list describing the signature of the method. In the above example, the add method takes two integers as arguments and returns a double result. This server does NOT support system.methodSignature.

More information about XML-RPC can be found here.

Examples

Python

This is an example Python script to access the XML-RPC services of the MetaServer.

#!/usr/bin/env python
# -*- coding: UTF-8 -*-

import sys
import xmlrpclib

url = "http://bcms.bioinfo.cnio.es/xmlrpc/"
method = sys.argv[1]
arguments = sys.argv[2:]
server = xmlrpclib.Server(url, encoding="UTF-8",
                          verbose=True)

cmd = "server." + method + "(" + ", ".join(arguments) + ")"

print >> sys.stderr, "command:", cmd

result = eval(cmd)

print result

You could use it, for example if you named it bcms-xmlrpc.py, like this:

python bcms-xmlrpc.py Annotations.getAnnotations 16212962

Perl

And this is an example of a Perl script with a test option for the XML-RPC or listing the available methods:

#!/usr/bin/env perl

use strict;

require Data::Dumper;
require RPC::XML;
require RPC::XML::Client;

my $conn = RPC::XML::Client->new(
  'http://bcms.bioinfo.cnio.es/xmlrpc/'
);

sub help
{
  print "options: -t | -l | {pmid}\n";
  print "-t   => test\n";
  print "-l   => list XML-RPC methods\n";
  print "pmid => integer\n";
  exit 1;
}

my $req;
for ($ARGV[0]) {
  $req = /^-t$/  && RPC::XML::request->new('add', 23, 32)
      || /^-l$/  && RPC::XML::request->new('system.listMethods')
      || /^\d+$/ && RPC::XML::request->new('Annotations.getAnnotations', 
                                           $ARGV[0])
      || help();
}
print "sending request: '".$req->as_string."'\n";
my $resp = $conn->simple_request($req);

unless (defined $resp) {
  print "Client Error:\n  ".$RPC::XML::fault."\n";
  exit 1;
}
if ($req->name eq "add") {
  if (55 == $resp) {
    print "TEST OK\n";
  } else {
    print "TEST FAILED\n";
    exit 1;
  }
} else {
  print Data::Dumper::Dumper($resp);
}
exit 0;

BioCreative Annotation Servers