NAME

Bio::DB::SoapEUtilities - Interface to the NCBI Entrez web service *BETA*

SYNOPSIS

use Bio::DB::SoapEUtilities;

# factory construction

my $fac = Bio::DB::SoapEUtilities->new()

# executing a utility call

#get an iteratable adaptor
my $links = $fac->elink( 
              -dbfrom => 'protein',
              -db => 'taxonomy',
              -id => \@protein_ids )->run(-auto_adapt => 1);

# get a Bio::DB::SoapEUtilities::Result object
my $result = $fac->esearch(
              -db => 'gene',
              -term => 'sonic and human')->run;

# get the raw XML message
my $xml = $fac->efetch(
            -db => 'gene',
            -id => \@gids )->run( -raw_xml => 1 );

# change parameters 
my $new_result = $fac->efetch(
                  -db => 'gene',
                  -id => \@more_gids)->run;
# reset parameters
$fac->efetch->reset_parameters( -db => 'nucleotide',
                                -id => $nucid );
$result = $fac->efetch->run;
               
# parsing and iterating the results

$count = $result->count;
@ids = $result->ids;

while ( my $linkset = $links->next_link ) {
   $submitted = $linkset->submitted_id;
}

($taxid) = $links->id_map($submitted_prot_id);
$species_io = $fac->efetch( -db => 'taxonomy',
                            -id => $taxid )->run( -auto_adapt => 1);
$species = $species_io->next_species;
$linnaeus = $species->binomial;

DESCRIPTION

This module allows the user to query the NCBI Entrez database via its SOAP (Simple Object Access Protocol) web service (described at http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.html). The basic tools (einfo, esearch, elink, efetch, espell, epost) are available as methods off a SoapEUtilities factory object. Parameters for each tool can be queried, set and reset for each method through the Bio::ParameterBaseI standard calls (available_parameters(), set_parameters(), get_parameters(), reset_parameters()). Returned data can be retrieved, accessed and parsed in several ways, according to user preference. Adaptors and object iterators are available for efetch, egquery, elink, and esummary results.

USAGE

The SoapEU system has been designed to be as easy (few includes, available parameter facilities, reasonable defaults, intuitive aliases, built-in pipelines) or as complex (accessors for underlying low-level objects, all parameters accessible, custom hooks for builder objects, facilities for providing local copies of WSDLs) as the user requires or desires. (To the extent that it does not succeed in either direction, it is up to the user to report to the mailing list ("FEEDBACK")!)

Factory

To begin, make a factory:

my $fac = Bio::DB::SoapEUtilities->new();

From the factory, utilities are called, parameters are set, and results or adaptors are retrieved.

If you have your own copy of the wsdl, use

my $fac = Bio::Db::SoapEUtilities->new( -wsdl_file => $my_wsdl );

otherwise, the correct one will be obtained over the network (by Bio::DB::ESoap and friends).

Utilities and parameters

To run any of the standard NCBI EUtilities (einfo, esearch, esummary, elink, egquery, epost, espell), call the desired utility from the factory. To use a utility, you must set its parameters and run it to get a result. TMTOWTDI:

# verbose
my $fetch = $fac->efetch();
$fetch->set_parameters( -db => 'gene', -id => [828392, 790]);
my $result = $fetch->run;

# compact
my $result = $fac->efetch(-db =>'gene',-id => [828392,790])->run;

# change ids
$fac->efetch->set_parameters( -id => 470338 );
$result = $fac->run;

# another util
$result = $fac->esearch(-db => 'protein', -term => 'BRCA and human')->run;

# the utilities are kept separate
%search_params = $fac->esearch->get_parameters;
%fetch_params = $fac->efetch->get_parameters;
$search_param{db}; # is 'protein'
$fetch_params{db}; # is 'gene'

The factory is Bio::ParameterBaseI compliant: that means you can find out what you can set with

@available_search = $fac->esearch->available_parameters;
@available_egquery = $fac->egquery->available_parameters;

For more information on parameters, see http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html.

Results

The "intermediate" object for SoapEU query results is the Bio::DB::SoapEUtilities::Result. This is a BioPerly parsing of the SOAP message sent by NCBI when a query is run(). This can be very useful on it's own, but most users will likely want to proceed directly to "Adaptors", which take a Result and turn it into more intuitive/familiar BioPerl objects. Go there if the following details are too gory.

Results can be highly- or lowly-parsed, depending on the parameters passed to the factory run() method. To get the raw XML message with no parsing, do

my $xml = $fac->$util->run(-raw_xml => 1); # $xml is a scalar string

To retrieve a Bio::DB::SoapEUtilities::Result object with limited parsing, but with accessors to the SOAP::SOM message (provided by SOAP::Lite), do

my $result = $fac->$util->run(-no_parse => 1);
my $som = $result->som;
my $method_hash = $som->method; # etc...

To retrieve a Result object with message elements parsed into accessors, including count() and ids(), run without arguments:

my $result = $fac->esearch->run()
my $count = $result->count;
my @Count = $result->Count; # counts for each member of 
                            # the translation stack
my @ids = $result->IdList_Id; # from automatic message parsing
@ids = $result->ids; # a convenient alias

See Bio::DB::SoapEUtilities::Result for more, even gorier details.

Adaptors

Adaptors convert EUtility Results into convenient objects, via a handle that usually provides an iterator, in the spirit of Bio::SeqIO. These are probably more useful than the Result to the typical user, and so you can retrieve them automatically by setting the run() parameter -auto_adapt = 1>.

In general, retrieve an adaptor like so:

$adp = $fac->$util->run( -auto_adapt => 1 );
# iterate...
while ( my $obj = $adp->next_obj ) {
   # do stuff with $obj
}

The adaptor itself occasionally possesses useful methods besides the iterator. The method next_obj always works, but a natural alias is also always available:

$seqio = $fac->esearch->run( -auto_adapt => 1 );
while ( my $seq = $seqio->next_seq ) {
   # do stuff with $seq
}

In the above example, -auto_adapt = 1> also instructs the factory to perform an efetch based on the ids returned by the esearch (if any), so that the adaptor returned iterates over Bio::SeqI objects.

Here is a rundown of the different adaptor flavors:

efetch, Fetch Adaptors, and BioPerl object iterators

The FetchAdaptor creates bona fide BioPerl objects. Currently, there are FetchAdaptor subclasses for sequence data (both Genbank and FASTA rettypes) and taxonomy data. The choice of FetchAdaptor is based on information in the result message, and should be transparent to the user.
```
 $seqio = $fac->efetch( -db =>'nucleotide',
                        -id => \@ids,
                        -rettype => 'gb' )->run( -auto_adapt => 1 );
 while (my $seq = $seqio->next_seq) {
    my $taxio = $fac->efetch( 
	-db => 'taxonomy', 
	-id => $seq->species->ncbi_taxid )->run(-auto_adapt => 1);
    my $tax = $taxio->next_species;
    unless ( $tax->TaxId == $seq->species->ncbi_taxid ) {
      print "more work for MAJ"
    }
 }
```
See the pod for the FetchAdaptor subclasses (e.g., Bio::DB::SoapEUtilities::FetchAdaptor::seq) for more detail.

elink, the Link adaptor, and the linkset iterator

The LinkAdaptor manages LinkSets. In SoapEU, an elink call always preserves the correspondence between submitted and retrieved ids. The mapping between these can be accessed from the adaptor object directly as id_map()

my $links = $fac->elink( -db => 'protein', 
                         -dbfrom => 'nucleotide',
                         -id => \@nucids )->run( -auto_adapt => 1 );

# maybe more than one associated id...
my @prot_0 = $links->id_map( $nucids[0] );

Or iterate over the linksets:

while ( my $ls = $links->next_linkset ) {
   @ids = $ls->ids;
   @submitted_ids = $ls->submitted_ids;
   # etc.
}

esummary, the DocSum adaptor, and the docsum iterator

The DocSumAdaptor manages docsums, the esummary return type. The objects returned by iterating with a DocSumAdaptor have accessors that let you obtain field information directly. Docsums contain lots of easy-to-forget fields; use item_names() to remind yourself.

my $docs = $fac->esummary( -db => 'taxonomy',
                           -id => 527031 )->run(-auto_adapt=>1);
# iterate over docsums
while (my $d = $docs->next_docsum) {
   @available_items = $docsum->item_names;
   # any available item can be called as an accessor
   # from the docsum object...watch your case...
   $sci_name = $d->ScientificName;
   $taxid = $d->TaxId;
}

egquery, the GQuery adaptor, and the query iterator

The GQueryAdaptor manages global query items returned by calls to egquery, which identifies all NCBI databases containing hits for your query term. The databases actually containing hits can be retrieved directly from the adaptor with found_in_dbs:
```
my $queries = $fac->egquery( 
    -term => 'BRCA and human'
   )->run(-auto_adapt=>1);
my @dbs = $queries->found_in_dbs;
```
Retrieve the global query info returned for any database with query_by_db:
```
my $prot_q = $queries->query_by_db('protein');
if ($prot_q->count) {
   #do something
}
```
Or iterate as usual:
```
while ( my $q = $queries->next_query ) {
   if ($q->status eq 'Ok') {
     # do sth
   }
}
```

Web environments and query keys

To make large or complex requests for data, or to share queries, it may be helpful to use the NCBI WebEnv system to manage your queries. Each EUtility accepts the following parameters:

-usehistory
-WebEnv
-QueryKey

for this purpose. These store the details of your queries serverside.

SoapEU attempts to make using these relatively straightforward. Use Result objects to obtain the correct parameters, and don't forget -usehistory:

my $result1 = $fac->esearch( 
    -term => 'BRCA and human', 
    -db => 'nucleotide',
    -usehistory => 1 )->run( -no_parse=>1 );

my $result = $fac->esearch( 
    -term => 'AND early onset', 
    -QueryKey => $result1->query_key,
    -WebEnv => $result1->webenv )->run( -no_parse => 1 );

my $result = $fac->esearch(
   -db => 'protein',
   -term => 'sonic', 
   -usehistory => 1 )->run( -no_parse => 1 );

# later (but not more than 8 hours later) that day...

$result = $fac->esearch(
   -WebEnv => $result->webenv,
   -QueryKey => $result->query_key,
   -RetMax => 800 # get 'em all
   )->run; # note we're parsing the result...
@all_ids = $result->ids;

Error checking

Two kinds of errors can ensue on an Entrez SOAP run. One is a SOAP fault, and the other is an error sent in non-faulted SOAP message from the server. The distinction is probably systematic, and I would welcome an explanation of it. To check for result errors, try something like:

unless ( $result = $fac->$util->run ) {
   die $fac->errstr; # this will catch a SOAP fault
}
# a valid result object was returned, but it may carry an error
if ($result->count == 0) {
   warn "No hits returned";
   if ($result->ERROR) {
     warn "Entrez error : ".$result->ERROR;
   }
}

Error handling will be improved in the package eventually.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $eutil = new Bio::DB::SoapEUtilities();
Function: Builds a new Bio::DB::SoapEUtilities object
Returns : an instance of Bio::DB::SoapEUtilities
Args    :

run()

Title   : run
Usage   : $fac->$eutility->run(@args)
Function: Execute the EUtility
Returns : true on success, false on fault or error
          (reason in errstr(), for more detail check the SOAP message
           in last_result() )
Args    : named params appropriate to utility
          -auto_adapt => boolean ( return an iterator over results as 
                                   appropriate to util if true)
          -raw_xml => boolean ( return raw xml result; no processing )
          Bio::DB::SoapEUtilities::Result constructor parms

Useful Accessors

response_message()

Title   : response_message
Aliases : last_response, last_result
Usage   : $som = $fac->response_message
Function: get the last response message
Returns : a SOAP::SOM object
Args    : none

webenv()

Title   : webenv
Usage   : 
Function: contains WebEnv key referencing the session
          (set after run() )
Returns : scalar
Args    : none

errstr()

Title   : errstr
Usage   : $fac->errstr
Function: get the last error, if any
Example : 
Returns : value of errstr (a scalar)
Args    : none

Bio::ParameterBaseI compliance

available_parameters()

Title   : available_parameters
Usage   : 
Function: get available request parameters for calling
          utility
Returns : 
Args    : -util => $desired_utility [optional, default is
          caller utility]

set_parameters()

Title   : set_parameters
Usage   : 
Function: 
Returns : none
Args    : -util => $desired_utility [optional, default is 
           caller utility],
          named utility arguments

get_parameters()

Title   : get_parameters
Usage   : 
Function: 
Returns : array of named parameters
Args    : utility (scalar string) [optional]
          (default is caller utility)

reset_parameters()

Title   : reset_parameters
Usage   : 
Function: 
Returns : none
Args    : -util => $desired_utility [optional, default is 
           caller utility],
          named utility arguments

parameters_changed()

Title   : parameters_changed
Usage   : 
Function: 
Returns : boolean
Args    : utility (scalar string) [optional]
          (default is caller utility)

_soap_facs()

Title   : _soap_facs
Usage   : $self->_soap_facs($util, $fac)
Function: caches Bio::DB::ESoap factories for the 
          eutils in use by this instance
Example : 
Returns : Bio::DB::ESoap object
Args    : $eutility, [optional on set] $esoap_factory_object

_caller_util()

Title   : _caller_util
Usage   : $self->_caller_util($newval)
Function: the utility requested off the main SoapEUtilities 
          object
Example : 
Returns : value of _caller_util (a scalar string, a valid eutility)
Args    : on set, new value (a scalar string [optional])

To install Bio::DB::ESoap, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::DB::ESoap

CPAN shell

perl -MCPAN -e shell
install Bio::DB::ESoap

For more information on module installation, please visit the detailed CPAN module installation guide.

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