Difference between revisions of "Data mining"

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(New page: == Data Model == # About the WormBase data model - ''how data is stored and structured at WormBase'' # AceDB classes - ''A comprehensiv...)
 
 
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== Data Model ==
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== Data Model ==
  
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# [[About_the_WormBase_data_model|About the WormBase data model]] - ''how data is stored and structured at WormBase''
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#[[About the WormBase data model|About the WormBase data model]] - ''how data is stored and structured at WormBase''  
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# [[AceDB_classes|AceDB classes]] - ''A comprehensive list of AceDB classes''
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#[[AceDB classes|AceDB classes]] - ''A comprehensive list of AceDB classes''  
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# [[AceDB_classes_tutorial|AceDB classes tutorial]] -''Examples and descriptions of commonly accessed classes at WormBase''
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#[[AceDB classes tutorial|AceDB classes tutorial]] -''Examples and descriptions of commonly accessed classes at WormBase''  
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# [[GFF2_features|GFF2 features]] - ''Descriptions of features contained in the WormBase GFF2 genome annotation files''
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#[[GFF2 features|GFF2 features]] - ''Descriptions of features contained in the WormBase GFF2 genome annotation files''
  
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== Query Languages ==
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== WormMine ==
  
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# [[Data_mining:AQL_tutorial|AQL tutorial]] - ''Using the AceDB query language, AQL''
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[[ WormMine | Link to documentation]]
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# [[Data_mining:WQL_tutorial|WQL tutorial]] - ''Using the WormBase query language, WQL''
 
  
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== WormMart ==
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== SimpleMine  ==
  
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# [[Data_mining:WormMart|WormMart]]
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SimpleMine User's Guide: https://wiki.wormbase.org/index.php/UserGuide:SimpleMine
  
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== APIs ==
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== RNASeq Related Tools ==
  
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=== AcePerl, a Perl interface to AceDB/WormBase ===
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SPELL: Clustering analyses for microarray, tiling array, and RNASeq expression. https://spell.wormbase.org/ Documentation: https://wiki.wormbase.org/index.php/SPELL
  
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# [[Mining_AceDB/WormBase_with_AcePerl|Mining AceDB/WormBase with AcePerl]]
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Expression Dataset Locator: https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi
  
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=== Bio::DB::GFF ===
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RNAseq FPKM Download: https://wormbase.org/tools/rnaseq/fpkmmine.cgi
  
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# [[Mining_WormBase_with_Bio::DB::GFF|Mining WormBase with Bio::DB::GFF]] - ''extract sequence annotations en masse using this Perl module''
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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
  
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== Miscellaneous ==
 
  
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# [[Linking_To_WormBase|Linking To WormBase]]
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== APIs  ==
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# [[Converting_Coordinates_between_releases|Converting Coordinates between releases]]
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=== AcePerl, a Perl interface to AceDB/WormBase  ===
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#[[Mining AceDB/WormBase with AcePerl|Mining AceDB/WormBase with AcePerl]]
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== Query Languages  ==
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#[[Data mining:AQL tutorial|AQL tutorial]] - ''Using the AceDB query language, AQL''  -- DEPRECATED: moved to new site
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#[[Data mining:WQL tutorial|WQL tutorial]] - ''Using the WormBase query language, WQL'' -- DEPRECATED: moved to new site
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 +
 
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=== Bio::DB::GFF  ===
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#[[Mining WormBase with Bio::DB::GFF|Mining WormBase with Bio::DB::GFF]] - ''extract sequence annotations en masse using this Perl module''
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== Miscellaneous  ==
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#[[Linking To WormBase|Linking To WormBase]]  
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#[[Converting Coordinates between releases|Converting Coordinates between releases]]
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#[[WormBase Identifiers]] - ''A quick guide to WormBase object identifiers''
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[[Category:User Guide]]

Latest revision as of 01:36, 1 April 2022

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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