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Bio-EUtilities-1.74
River stage zero No dependents
2 ++

Changes for version 1.74 - 2016-09-25

  • NCBI related change from HTTP to HTTPS
  • Add preliminary 'idtype' attribute for some eutils, which will be needed for upcoming NCBI changes with migration of GI to Accession.Version
  • Remove usage of 'given' and 'when' which have been downgraded to experimental on perl 5.18.
  • Fixed released tarball so it installs its programs `bp_einfo` and `bp_genbank_ref_extractor`

Documentation

bp_einfo
Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).
bp_genbank_ref_extractor
Retrieves all related sequences for a list of searches on Entrez gene

Modules

Bio::DB::EUtilities
Webagent which interacts with and retrieves data from NCBI's eUtils.
Bio::Tools::EUtilities
NCBI eutil XML parsers.
Bio::Tools::EUtilities::EUtilDataI
EUtil data object interface.
Bio::Tools::EUtilities::EUtilParameters
Manipulation of NCBI eutil-based parameters for remote database requests.
Bio::Tools::EUtilities::History
Lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
Bio::Tools::EUtilities::HistoryI
Simple extension of EUtilDataI interface class for classes which hold NCBI server history data.
Bio::Tools::EUtilities::Info
Interface class for storing einfo data.
Bio::Tools::EUtilities::Info::FieldInfo
Class for storing einfo field data.
Bio::Tools::EUtilities::Info::LinkInfo
Class for storing einfo link data.
Bio::Tools::EUtilities::Link
General API for accessing data retrieved from elink queries.
Bio::Tools::EUtilities::Link::LinkSet
Class for EUtils LinkSets.
Bio::Tools::EUtilities::Link::UrlLink
Class for EUtils UrlLinks.
Bio::Tools::EUtilities::Query
Parse and collect esearch, epost, espell, egquery information.
Bio::Tools::EUtilities::Query::GlobalQuery
Container class for egquery data.
Bio::Tools::EUtilities::Summary
Class for handling data output (XML) from esummary.
Bio::Tools::EUtilities::Summary::DocSum
Data object for document summary data from esummary.
Bio::Tools::EUtilities::Summary::Item
Simple layered object for DocSum item data.
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).

Other files