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: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- usAPPENDIX
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])