Chado Natural Diversity Module

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Under Construction

This page or section is under construction.

The Chado Natural Diversity Module is an extension to the Chado schema to better support natural diversity data.

Eventually this page will resemble the other Chado Module pages, with an overview followed by a detailed explanation of the tables, columns, and relationships in the module. However, while the module is under development, this page will have an alternative structure.

Introduction

Interactions with Other Chado Modules

Key Ontologies

Stock Relationship Ontology

Loading Data

There are, as yet, no standard flat file formats or loading scripts to load data into this module. Custom scripts will need to be written to insert your data in the database.

Web Front Ends

See Also

Email Threads

Use Cases

ER Diagram

A simplified schema diagram by N. Menda and R. Buels, from April. This is out of date in a few ways and will be updated shortly. Natdiv simplified SGN.png

Tables

This will be populated using the process outlined in Chado Tables to Wiki.

Table: nd_experiment

This is the core table for the natural diversity module, representing each individual assay that is undertaken (nb this is usually *not* an entire experiment). Each nd_experiment should give rise to a single genotype or phenotype and be described via 1 (or more) protocols. Collections of assays that relate to each other should be linked to the same record in the project table.
Experiment.type is a cvterm that will define which records are expected for other tables. Any CV may be used but it was designed with terms such as: [phenotype_assay, genotype_assay, field_collection, cross_experiment] in mind.

public.nd_experiment Structure
FK Name Type Description
nd_experiment_id serial PRIMARY KEY

nd_geolocation

nd_geolocation_id integer NOT NULL

cvterm

type_id integer NOT NULL

Tables referencing this one via Foreign Key Constraints:


Table: nd_experiment_contact

public.nd_experiment_contact Structure
FK Name Type Description
nd_experiment_contact_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer NOT NULL

contact

contact_id integer NOT NULL


Table: nd_experiment_dbxref

Cross-reference experiment to accessions, images, etc

public.nd_experiment_dbxref Structure
FK Name Type Description
nd_experiment_dbxref_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer NOT NULL

dbxref

dbxref_id integer NOT NULL


Table: nd_experiment_genotype

Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.

public.nd_experiment_genotype Structure
FK Name Type Description
nd_experiment_genotype_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer UNIQUE#1 NOT NULL

genotype

genotype_id integer UNIQUE#1 NOT NULL


Table: nd_experiment_phenotype

Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.

public.nd_experiment_phenotype Structure
FK Name Type Description
nd_experiment_phenotype_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer UNIQUE#1 NOT NULL

phenotype

phenotype_id integer UNIQUE#1 NOT NULL


Table: nd_experiment_project

public.nd_experiment_project Structure
FK Name Type Description
nd_experiment_project_id serial PRIMARY KEY

project

project_id integer NOT NULL

nd_experiment

nd_experiment_id integer NOT NULL


Table: nd_experiment_protocol

Linking table: experiments to the protocols they involve.

public.nd_experiment_protocol Structure
FK Name Type Description
nd_experiment_protocol_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer NOT NULL

nd_protocol

nd_protocol_id integer NOT NULL


Table: nd_experiment_pub

Linking nd_experiment(s) to publication(s)

public.nd_experiment_pub Structure
FK Name Type Description
nd_experiment_pub_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer UNIQUE#1 NOT NULL

pub

pub_id integer UNIQUE#1 NOT NULL


Table: nd_experiment_stock

Part of a stock or a clone of a stock that is used in an experiment

public.nd_experiment_stock Structure
FK Name Type Description
nd_experiment_stock_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer NOT NULL

stock

stock_id integer NOT NULL

stock used in the extraction or the corresponding stock for the clone

cvterm

type_id integer NOT NULL

Tables referencing this one via Foreign Key Constraints:



Table: nd_experiment_stock_dbxref

Cross-reference experiment_stock to accessions, images, etc

public.nd_experiment_stock_dbxref Structure
FK Name Type Description
nd_experiment_stock_dbxref_id serial PRIMARY KEY

nd_experiment_stock

nd_experiment_stock_id integer NOT NULL

dbxref

dbxref_id integer NOT NULL


Table: nd_experiment_stockprop

Property/value associations for experiment_stocks. This table can store the properties such as treatment

public.nd_experiment_stockprop Structure
FK Name Type Description
nd_experiment_stockprop_id serial PRIMARY KEY

nd_experiment_stock

nd_experiment_stock_id integer UNIQUE#1 NOT NULL

The experiment_stock to which the property applies.

cvterm

type_id integer UNIQUE#1 NOT NULL

The name of the property as a reference to a controlled vocabulary term.
value character varying(255)

The value of the property.
rank integer UNIQUE#1 NOT NULL

The rank of the property value, if the property has an array of values.


Table: nd_experimentprop

public.nd_experimentprop Structure
FK Name Type Description
nd_experimentprop_id serial PRIMARY KEY

nd_experiment

nd_experiment_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value character varying(255) NOT NULL
rank integer UNIQUE#1 NOT NULL


Table: nd_geolocation

The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.

public.nd_geolocation Structure
FK Name Type Description
nd_geolocation_id serial PRIMARY KEY
description character varying(255)

A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.
latitude real

The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.
longitude real

The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.
geodetic_datum character varying(32)

The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.
altitude real

The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.

Tables referencing this one via Foreign Key Constraints:



Table: nd_geolocationprop

Property/value associations for geolocations. This table can store the properties such as location and environment

public.nd_geolocationprop Structure
FK Name Type Description
nd_geolocationprop_id serial PRIMARY KEY

nd_geolocation

nd_geolocation_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL

The name of the property as a reference to a controlled vocabulary term.
value character varying(250)

The value of the property.
rank integer UNIQUE#1 NOT NULL

The rank of the property value, if the property has an array of values.


Table: nd_protocol

A protocol can be anything that is done as part of the experiment.

public.nd_protocol Structure
FK Name Type Description
nd_protocol_id serial PRIMARY KEY
name character varying(255) UNIQUE NOT NULL

The protocol name.

Tables referencing this one via Foreign Key Constraints:



Table: nd_protocol_reagent

public.nd_protocol_reagent Structure
FK Name Type Description
nd_protocol_reagent_id serial PRIMARY KEY

nd_protocol

nd_protocol_id integer NOT NULL

nd_reagent

reagent_id integer NOT NULL

cvterm

type_id integer NOT NULL


Table: nd_protocolprop

Property/value associations for protocol.

public.nd_protocolprop Structure
FK Name Type Description
nd_protocolprop_id serial PRIMARY KEY

nd_protocol

nd_protocol_id integer UNIQUE#1 NOT NULL

The protocol to which the property applies.

cvterm

type_id integer UNIQUE#1 NOT NULL

The name of the property as a reference to a controlled vocabulary term.
value character varying(255)

The value of the property.
rank integer UNIQUE#1 NOT NULL

The rank of the property value, if the property has an array of values.


Table: nd_reagent

A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.

public.nd_reagent Structure
FK Name Type Description
nd_reagent_id serial PRIMARY KEY
name character varying(80) NOT NULL

The name of the reagent. The name should be unique for a given type.

cvterm

type_id integer NOT NULL

The type of the reagent, for example linker oligomer, or forward primer.
feature_id integer

If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.

Tables referencing this one via Foreign Key Constraints:



Table: nd_reagent_relationship

Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.

public.nd_reagent_relationship Structure
FK Name Type Description
nd_reagent_relationship_id serial PRIMARY KEY

nd_reagent

subject_reagent_id integer NOT NULL

The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.

nd_reagent

object_reagent_id integer NOT NULL

The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.

cvterm

type_id integer NOT NULL

The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.


Table: nd_reagentprop

public.nd_reagentprop Structure
FK Name Type Description
nd_reagentprop_id serial PRIMARY KEY

nd_reagent

nd_reagent_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value character varying(255)
rank integer UNIQUE#1 NOT NULL