Babase Chado:

Chado and it's Integration with the Babase System

Document generated: 2017-05-10 09:35:26.

Copyright Notices

June 29, 2015

Revision History
Revision 0.1 June 29, 2015
Beta version
Revision 0.0 May 22, 2014
Initial document

Acknowledgments

We gratefully acknowledge the support of the National Science Foundation for the supporting the collection of the majority of the data stored in the database; in the past decade in particular we acknowledge support from IBN 9985910, IBN 0322613, IBN 0322781, BCS 0323553, BCS 0323596, DEB 0846286, DEB 0846532 and DEB 0919200. We are also very grateful for support from the National Institute of Aging (R01AG034513-01 and P01AG031719) and the Princeton Center for the Demography of Aging (P30AG024361). We also thank the Chicago Zoological Society, the Max Planck Institute for Demographic Research, the L.S.B. Leakey Foundation and the National Geographic Society for support at various times over the years. In addition, we thank the National Institute of Aging (R03-AG045459-01) for supporting recent work extending the database to incorporate genetic and genomic data.

Any opinions, findings, conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, the National Institute of Aging, the Princeton Center for the Demography of Aging, the Chicago Zoological Society, the Max Planck Institute for Demographic Research, the L.S.B. Leakey Foundation, the National Geographic Society, or any other organization which has supplied support for this work.

Table of Contents

1. Introduction
This Document
The Chado Approach
Other Resources
2. Some Chado Documentation
Table Overview
Entity-Relationship Diagrams
3. The Tables
Chado Tables
ANALYSISFEATURE (Analysis Feature Relationships)
ANALYSISFEATUREPROP (Analysis to Genomic Feature Relationship Proprieties)
ANALYSISPROP (Analysis Properties)
CV (Controlled Vocabularies)
CVTERM (Controlled Vocabulary Terms)
CVTERM_DBXREF (Controlled Vocabulary Term Ancillary External Database References)
CVTERM_RELATIONSHIP (Controlled Vocabulary Term Relationships)
CVTERMPATH (Controlled Vocabulary Term relationship Paths)
CVTERMPROP (Controlled Vocabulary Term Properties)
DB (External Databases)
DBXREF (External Database Object Cross-References)
FEATURE (Genomic Feature)
FEATURE_CVTERM (Feature Typing/Tagging)
FEATURE_DBXREF (Feature to External Database Object Cross-References)
FEATURE_GENOTYPE (Feature to Genotype Relationships)
FEATURE_RELATIONSHIP (Feature Inter-Relationships)
FEATURE_SYNONYM (Genomic Feature to Synonym Relationships)
FEATURELOC (Feature Locations)
FEATUREPROP (Feature Properties)
GENOTYPE (Genotypes)
ND_EXPERIMENT (Natural Diversity Experiment Result Set)
ND_EXPERIMENT_GENOTYPE (Natural Diversity Experiment Result Set to Genotype Relationships)
ND_EXPERIMENT_STOCK (Natural Diversity Experiment Result Set to Stock Relationships)
ND_EXPERIMENT_STOCKPROP (Natural Diversity Experiment Result Set to Stock Relationship Properties)
ND_EXPERIMENTPROP (Natural Diversity Experiment Result Set Properties)
ND_GEOLOCATION (Natural Diversity Geolocation)
ORGANISM
ORGANISM_DBXREF (Organism to External Database Object Cross-References)
PUB (Publication or Other Documentation of Provenance)
STOCK (Stocks)
STOCK_DBXREF (Stock to External Database Object Cross-References)
STOCK_DBXREFPROP (Stock External Database Entity Properties)
STOCK_CVTERM (Stock Typing/Tagging)
STOCK_RELATIONSHIP (Stock Inter-Relationships)
STOCKPROP (Stock Properties)
SYNONYM (Alternate Names)
Babase Chado Extensions
ANALYSIS (Analyses)
ANALYSIS_DBXREF (Analysis to External Database Object Cross-References)
ANALYSIS_CVTERM (Analysis Typing/Tagging)
ANALYSIS_RELATIONSHIP (Analysis Inter-Relationships)
ANALYSIS_ND_EXPERIMENT (Analysis to Natural Diversity Experiment Result Set Relationships)
ND_EXPERIMENT_FEATURE (Natural Diversity Experiment Result Set to Feature Relationships)
4. Chado Programs
Command Line Programs
abrp-genomics-update-testdir — update symlinks in the test portions of the /mnt/abrp_genomics hierarchy
chado-funcgen-dump — produce a zip file containing files of functional genomic analysis results from Babase/Chado; command line and web interfaces exist
chado-funcgen-load — load information regarding a file containing functional genomic analysis results, and, optionally, information on the stock analyzed, into Babase/Chado
chado-stock-load — load stock information into Babase/Chado
chado-vcf-load — load a VCF file into Babase/Chado
copy-to-abrp-genomics — copies and anonynomizes portions of Babase/Chado to the abrp-genomics public portal machine
receive-abrp-genomics-schema — receives a copy of portions of Babase/Chado and installs it into the database on the public portal machine
Web Interfaces
VCFDump (Download anonymized VCF files)
SQL Utilities
chado_analysis_delete — undo the loading of an analysis into the database
A. Indexes Added To Chado
Indexes On ANALYSIS
analysis_idx1b on ANALYSIS.Type_Id
analysis_bc1 on ANALYSIS.Name (Unique)
Indexes On FEATURE
feature_idx1b on FEATURE.Feature_Id, FEATURE.DBXref_Id
Indexes On FEATURE_RELATIONSHIP
feature_relationship_idx1b on FEATURE_RELATIONSHIP Object_Id, Subject_Id, Type_Id
Indexes On FEATURELOC
featureloc_idx1b on FEATURELOC Feature_Id, FMin, FMax

List of Figures

2.1. Key to the Chado Entity Relationship Diagrams
2.2. Chado Stock Module ER Diagram
2.3. Chado Sequence Module Entity Relationship Diagram
2.4. Chado Companalysis Module Entity Relationship Diagram
2.5. Meta-Data Portions of The Chado Natural Diversity Module ER Diagram
2.6. Stock Portions of The Chado Natural Diversity Module ER Diagram
2.7. Babase Extension Relating The Chado Natural Diversity And Analysis Modules ER Diagram
2.8. Protocol and Reagent Portions of The Chado Natural Diversity Module ER Diagram
2.9. Relationships Between The Chado Genetics Module, the Natural Diversity Module, And The Sequence module ER Diagram
2.10. Genomic Data Tracking Entity Relationship Diagram
2.11. Integrating Genomic Data Tracking With Chado ER Diagram

List of Tables

2.1. Some Chado Tables (Part I)
2.2. Some Chado Tables (Part II)
2.3. Some Chado Tables (Part III)

List of Examples

3.1. Using both FEATURELOC.Locgroup and FEATURELOC.Rank
4.1. Using Dollar Quoting to Get the Results of a Specific Analysis
4.2. Discovering how many lines have been processed
4.3. Deleting an Analysis by Analysis Id
4.4. Deleting an Analysis by Analysis Id
4.5. Deleting an Analysis by Query

Page generated: 2017-05-10T09:35:35-04:00.