Difference between revisions of "Chado Doc Project"
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* [[Chado Contact Module|Contact]] - needs introduction and examples | * [[Chado Contact Module|Contact]] - needs introduction and examples | ||
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* [[Chado Expression Module|Expression]] - needs introduction and examples | * [[Chado Expression Module|Expression]] - needs introduction and examples | ||
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* [[Chado Genetic Module|Genetic]] - needs introduction and examples | * [[Chado Genetic Module|Genetic]] - needs introduction and examples | ||
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* [[Chado Library Module|Library]] - needs review | * [[Chado Library Module|Library]] - needs review | ||
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* [[Chado Organism Module|Organism]] - needs introduction and examples | * [[Chado Organism Module|Organism]] - needs introduction and examples | ||
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* [[Chado Publication Module|Publication]] - needs introduction and examples | * [[Chado Publication Module|Publication]] - needs introduction and examples | ||
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* [[Chado Stock Module|Stock]] - needs introduction and examples | * [[Chado Stock Module|Stock]] - needs introduction and examples | ||
Revision as of 19:07, 8 May 2007
Contents
Introduction
One remaining significant task in this effort to organized GMOD’s documentation is to further document Chado. You’ve noticed that there is some good documentation on Chado in the Wiki now, this is material that has been drawn from a number of different files, re-organized, and edited. Much of this material is theoretical and introductory. We shouldn't minimize it’s importance, in fact it’s essential. What we need now is material that is very practical and specific.
There are 2 basic tasks:
- Document all the Best Practices.
- Review all the dedicated module pages
There are about 25 Best Practices topics currently and 17 module pages. This topics and pages have been divided into 8 groups, and the intention is to gather similar topics and pages into one group.
Why This is Important
A bit of cheerleading: In another job I recently did a little project where I studied a number of open source schemas that handle sequence data and data related to sequence (e.g. Atlas, Biowarehouse, aMaze, Chado, GUS). There is no doubt that Chado stands head & shoulders above its comrades in terms of its expressiveness, logic and coherence, and extensibility. It is truly a work of conceptual art. It is also not the easiest schema to use, compared to its comrades. Let us complete this work that needs to be done on Chado so that the largest number of people can benefit from it. Bosborne 11:24, 8 May 2007 (EDT)
Work Packages
Please choose one and enter your name.
Package 1
Contributor:
- Audit - needs review
- Companalysis - needs review
- Chado_Best_Practices#Genomic_Rearrangements
- Chado_Best_Practices#Inversions
- Chado_Best_Practices#Translocations
- Chado_Best_Practices#Deletions
- Chado_Best_Practices#Posttranslational_Modifications
Package 2
Contributor:
- Contact - needs introduction and examples
- Controlled Vocabulary (cv) - needs review
- General - needs review
- Chado_Best_Practices#Canonical_Gene_Model
- Chado_Best_Practices#Querying_for_Canonical_Genes
- Chado_Best_Practices#Noncoding_Genes
- Chado_Best_Practices#Copy_Number_Variations
- Chado_Best_Practices#Single_Nucleotide_Polymorphisms_.28SNPs.29
- Chado_Best_Practices#Extensions
- Chado_Best_Practices#Similiarities_to_Alignments
Package 3
Contributor:
- Expression - needs introduction and examples
- Mage - needs review
- Chado_Best_Practices#Feature_Localization
- Chado_Best_Practices#Feature_Localization_to_Contigs_in_Assembly
- Chado_Best_Practices#Redundant_Localizations_to_Different_Assembly_Levels
- Chado_Best_Practices#Redundant_Storage_of_Coordinates_on_Different_Assembly_Levels
- Chado_Best_Practices#N-level_Assemblies
Package 4
Contributor:
- Chado_Best_Practices#Immature_or_Primary_RNA
- Chado_Best_Practices#Genotypes
- Chado_Best_Practices#Phenotypes
Package 5
Contributor:
- Chado_Best_Practices#Operon
- Chado_Best_Practices#Protein_Complexes
- Chado_Best_Practices#Trans-spliced_Gene
Package 6
Contributor:
- Chado_Best_Practices#Transposons
- Chado_Best_Practices#Gene_with_Implicit_Features_Manifested
- Chado_Best_Practices#Unlocalized_Gene
- Chado_Best_Practices#Cleavage
Package 7
Contributor:
- Publication - needs introduction and examples
- Sequence - needs review
- Chado_Best_Practices#Sequence_Alignments
- Chado_Best_Practices#Results_from_BLAST
- Chado_Best_Practices#Multiple_Sequence_Alignments
Package 8
Contributor:
