man Bio::DB::SoapEUtilities (3): 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 "Result"s 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.

  [email protected]                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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])