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Chado Publication Module

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Introduction

The Publication module describes references to sources of knowledge. Usually these are published articles but can also include conferences, Web pages, and so on.

Tables

Table: pub

A documented provenance artefact - publications, documents, personal communication.

pub Structure
F-Key Name Type Description
pub_id serial PRIMARY KEY
title text

Descriptive general heading.
volumetitle text

Title of part if one of a series.
volume character varying(255)
series_name character varying(255)

Full name of (journal) series.
issue character varying(255)
pyear character varying(255)
pages character varying(255)

Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.
miniref character varying(255)
uniquename text UNIQUE NOT NULL

cvterm

type_id integer NOT NULL

The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv. See FBcv for publication descriptor, or FBcv.obo
is_obsolete boolean DEFAULT false
publisher character varying(255)
pubplace character varying(255)

Tables referencing this one via Foreign Key Constraints:


Table: pub_dbxref

Handle links to repositories, e.g. Pubmed, Biosis, zoorec, OCLC, Medline, ISSN, coden...

pub_dbxref Structure
F-Key Name Type Description
pub_dbxref_id serial PRIMARY KEY

pub

pub_id integer UNIQUE#1 NOT NULL

dbxref

dbxref_id integer UNIQUE#1 NOT NULL
is_current boolean NOT NULL DEFAULT true


Table: pub_relationship

Handle relationships between publications, e.g. when one publication makes others obsolete, when one publication contains errata with respect to other publication(s), or when one publication also appears in another pub.

pub_relationship Structure
F-Key Name Type Description
pub_relationship_id serial PRIMARY KEY

pub

subject_id integer UNIQUE#1 NOT NULL

pub

object_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL


Table: pubauthor

An author for a publication. Note the denormalisation (hence lack of _ in table name) - this is deliberate as it is in general too hard to assign IDs to authors.

pubauthor Structure
F-Key Name Type Description
pubauthor_id serial PRIMARY KEY

pub

pub_id integer UNIQUE#1 NOT NULL
rank integer UNIQUE#1 NOT NULL

Order of author in author list for this pub - order is important.
editor boolean DEFAULT false

Indicates whether the author is an editor for linked publication. Note: this is a boolean field but does not follow the normal chado convention for naming booleans.
surname character varying(100) NOT NULL
givennames character varying(100)

First name, initials
suffix character varying(100)

Jr., Sr., etc


Table: pubprop

Property-value pairs for a pub. Follows standard chado pattern.

pubprop Structure
F-Key Name Type Description
pubprop_id serial PRIMARY KEY

pub

pub_id integer UNIQUE#1 NOT NULL

cvterm

type_id integer UNIQUE#1 NOT NULL
value text NOT NULL
rank integer UNIQUE#1