Data mining

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Data Model

  1. About the WormBase data model - how data is stored and structured at WormBase
  2. AceDB classes - A comprehensive list of AceDB classes
  3. AceDB classes tutorial -Examples and descriptions of commonly accessed classes at WormBase
  4. GFF2 features - Descriptions of features contained in the WormBase GFF2 genome annotation files

WormMine

Link to documentation

SimpleMine

SimpleMine User's Guide: https://wiki.wormbase.org/index.php/UserGuide:SimpleMine

RNASeq Related Tools

SPELL: Clustering analyses for microarray, tiling array, and RNASeq expression. https://spell.wormbase.org/ Documentation: https://wiki.wormbase.org/index.php/SPELL

Expression Dataset Locator: https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi

RNAseq FPKM Download: https://wormbase.org/tools/rnaseq/fpkmmine.cgi

RNASeq FPKM Graphs: Graphs derived from ModENCODE can be located under the Expression Widget of Gene pages. Documentation: https://wiki.wormbase.org/index.php/UserGuide:RNASeqFPKMGraph


APIs

AcePerl, a Perl interface to AceDB/WormBase

  1. Mining AceDB/WormBase with AcePerl


Query Languages

  1. AQL tutorial - Using the AceDB query language, AQL -- DEPRECATED: moved to new site
  2. WQL tutorial - Using the WormBase query language, WQL -- DEPRECATED: moved to new site


Bio::DB::GFF

  1. Mining WormBase with Bio::DB::GFF - extract sequence annotations en masse using this Perl module

Miscellaneous

  1. Linking To WormBase
  2. Converting Coordinates between releases
  3. WormBase Identifiers - A quick guide to WormBase object identifiers
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