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Changes for version 0.20000 - 2012-07-06

  • added Bio::Chado::NaturalDiversity::Reports, which has some canned reporting functions for working with natural diversity data (nmenda)
  • added greate_genotypeprops to Genetic::Genotype (nmenda)
  • added stock_phenotypes_rs, recursive_phenotypes_rs, stock_genotypes_rs, and stock_project_phenotypes to Stock::Stock (nmenda)


For describing cell lines
Augments sequence module with descriptions of computational analyses and features resulting from those analyses
A collection of bridge codes that have multiple dependancies so they don't happily go where is most obvious
model persons, institutes, groups, organizations, etc
Controlled vocabularies and ontologies
transcript or protein expression data
General purpose tables, including dbxrefs
Genotypes and mutant alleles
For describing molecular libraries
Alternative expression module, based on MAGE model
Non-sequence maps: genetic, radiation hybrid, cytogenetic, etc
Natural diversity module for dealing with populations, samples, genotypes, phenotypes and results of other assays.
Species data - does not include phylogeny
Entity-attribute-value phenotypic character descriptions
For representing phylogenetic trees; the trees represent the phylogeny of some some kind of sequence feature (mainly proteins) or actual organism taxonomy trees
The project table has been moved from general to its own module and has been expanded to provide properties, publications and contacts.
Bibliographic data on publications
Sequence and sequence features, their localization and properties
For tracking stock collections
developer-only maintenance script to sync this DBIx::Class object layer with the latest upstream version of Chado


A standard DBIx::Class layer for the Chado database schema.
featurelocs do not meet. symmetric
Model persons, institutes, groups, organizations, etc.
Model relationships between contacts
per-cv terms counts (excludes obsoletes)
per-cv terms counts (includes obsoletes)
The expression table is essentially a bridge table.
The environmental component of a phenotype description.
Parameters associated with image acquisition.
Extra assay properties that are not accounted for in assay.
Procedural notes on how data was prepared and processed.
Cross-reference experiment to accessions, images, etc
Linking table: experiments to the protocols they involve.
Linking nd_experiment(s) to publication(s)
Cross-reference experiment_stock to accessions, images, etc
Property/value associations for protocol.
Tag-value properties - follows standard chado model.
Global anchor for phylogenetic tree.
Standard Chado flexible property table for projects.
Linking table for associating projects and contacts.
Linking table for associating projects and publications.
Property or attribute of a feature_pub link.
Provenance for feature_relationshipprop.
Linking table between feature and synonym.
Library to be used by Bio::Chado::Schema test scripts.
utility functions shared by Bio::Chado::Schema objects


in lib/Bio/Chado/Schema/Result/Cv/
in lib/Bio/Chado/Schema/Result/Sequence/
in lib/Bio/Chado/Schema/Result/Stock/