Search results for "distribution:Bio-EUtilities CJFIELDS"
Bio::EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils
This distribution encompasses a low-level API for interacting with (and storing) information from) NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::DB::EUtilities - Webagent which interacts with and retrieves data from NCBI's eUtils.
This is a general webagent which posts and retrieves data to NCBI's eUtils service using their CGI interface. A separate project, currently present in BioPerl-Run, utilizes the SOAP-based interface for eUtils. A full explanation of the eUtils interfa...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities - NCBI eutil XML parsers.
Parses NCBI eutils XML output for retrieving IDs and other information. Part of the BioPerl EUtilities system. This is a general parser for eutils XML; data from efetch is NOT parsed (this requires separate format-dependent parsers). All other XML fo...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Link - General API for accessing data retrieved from elink queries.
Bio::Tools::EUtilities::Link is a loadable plugin for Bio::Tools::EUtilities that specifically handles NCBI elink-related data. to_string Title : to_string Usage : $foo->to_string() Function : converts current object to string Returns : none Args : (...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Info - Interface class for storing einfo data.
This class handles data output (XML) from einfo. Einfo is capable of returning two types of information: * A list of all available databases (when called w/o parameters) * Information about a specific database. The latter information includes the dat...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Query - Parse and collect esearch, epost, espell, egquery information.
Pluggable module for handling query-related data returned from eutils....
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::History - Lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
This class extends methods for any EUtilDataI implementation allow instances to dealwith NCBI history data (WebEnv and query_key). These can be used as parameters for further queries against data sets stored on the NCBI server, much like NCBI's Entre...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Summary - Class for handling data output (XML) from esummary.
This class handles data output (XML) from esummary. esummary retrieves information in the form of document summaries (docsums) when passed a list of primary IDs or if using a previous search history. This module breaks down the returned data from esu...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
bp_einfo - Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).
Command line options: -e/--email Valid email (required by NCBI policy) -d/--db/--database NCBI database to query (default = none, which shows available databases) -f/--field print out information about a specific field code (default = none) -l/--link...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::HistoryI - Simple extension of EUtilDataI interface class for classes which hold NCBI server history data.
This class extends methods for any EUtilDataI implementation allow instances to dealwith NCBI history data (WebEnv and query_key). These can be used as parameters for further queries against data sets stored on the NCBI server, much like NCBI's Entre...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::EUtilDataI - EUtil data object interface.
This is a simple interface which allows creation of simple typed object hierarchies. Single layers can be accessed via simple iterators (next_* methods) or retrieved all at once (get_*) methods; nested data can be iterated through nested iterators fo...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Link::UrlLink - Class for EUtils UrlLinks.
# ... get_dbfrom Title : get_dbfrom Usage : Function : Returns : Args : get_attribute Title : get_attribute Usage : Function : Returns : Args : get_icon_url Title : get_icon_url Usage : Function : Returns : Args : get_subject_type Title : Usage : Fun...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Summary::Item - Simple layered object for DocSum item data.
DocSum data, as returned from esummary, normally is a simple list of item-content-content_type groups. However, items can also contain nested data to represent more complex data (such as structural data). Up to three nested layers may appear in any d...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Link::LinkSet - Class for EUtils LinkSets.
# ... get_ids Title : get_ids Usage : my @ids = $linkset->get_ids Function : returns list of retrieved IDs Returns : array of IDs Args : none Notes : Cmd Description acheck same as get_submitted_ids lcheck same as get_submitted_ids ncheck same as get...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Info::LinkInfo - Class for storing einfo link data.
This class handles data output (XML) from both einfo and elink, and centers on describing data that either describes how NCBI databases are linked together via link names, or how databases are linked to outside databases (LinkOut). Further documentat...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Summary::DocSum - Data object for document summary data from esummary.
This is the basic class for Document Summary data from NCBI eUtils, returned from esummary. This implements the simple ItemContainerI interface. new Title : new Usage : Function : Returns : Args : get_ids Title : get_ids Usage : my ($id) = $item->get...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Info::FieldInfo - Class for storing einfo field data.
This class handles simple field data output (XML) from einfo. For more information on einfo see: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html new Title : new Note : *** should not be called by end-users *** Usage : my $ct = Bio:...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::EUtilParameters - Manipulation of NCBI eutil-based parameters for remote database requests.
Bio::Tools::EUtilities::EUtilParameters is-a Bio::ParameterBaseI implementation that allows simple manipulation of NCBI eutil parameters for CGI-based queries. SOAP-based methods may be added in the future. For simplicity parameters do not require da...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Query::GlobalQuery - Container class for egquery data.
This is a simple container class for egquery data. Currently this just contains various accessors for the data, such as get_database(), get_count(), etc. for each item in a global query. get_term Title : get_term Usage : $st = $qd->get_term; Function...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC
Bio::Tools::EUtilities::Summary::ItemContainerI - Abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered).
DocSum data, as returned from esummary, normally is a simple list of item-content-content_type groups. However, items can also contain nested data to represent more complex data (such as structural data). This interface describes the basic methods to...
CJFIELDS/Bio-EUtilities-1.77 - 09 Mar 2020 18:59:57 UTC