[Gmod-schema] Re: Documentation stored in chado

[Sue R. <rh...@ac...>]

Sounds good. There is a many-to-many relationship between cvterm and
doc_application and between cvterm and doc_documentation, right?

Sue

On Thu, 18 Sep 2003, Scott Cain wrote:

> Hello,
>
> At the curators breakout session of the GMOD meeting held September 2003,
> the participants suggested that the standard operating procedures (SOP) be
> reorganized to a tree view (ontology) and additionally to annotate what
> software modules are available, with for example, what their strengths and
> weaknesses are for a given task.  Since this potentially is a fairly complex
> set of data that may benefit from more than one representation (ie, sort by
> data object function, sort by locally available software, html table, unordered
> html list, plain text, pod, text searches), it makes sense to put this data
> into the database schema, in a documentation module with a suggested table
> prefix of 'doc_'.  This module presumably will be quite simple requiring
> probably only two tables, doc_documentation and doc_application.  Here are
> suggested CREATE statements:
>
>   CREATE TABLE doc_documentation (
>     doc_id serial not null,
>     doctype_id int,
>     foreign key (doctype_id) references cvterm (cvterm_id) on delete set null,
>     app_id int,
>     foreign key (app_id) references doc_application (app_id) on delete set null,
>     doc text not null
>   );
>
>   CREATE TABLE doc_application (
>     app_id serial not null,
>     name varchar(100) not null,
>     apptype_id int,
>     foreign key (apptype_id) references cvterm (cvterm_id) on delete set null,
>     notes text,
>     is_installed boolean not null default 'false'
>   );
>
> This schema could be used to store documentation for any GMOD application,
> though I don't think requiring it is a good idea.  At a minimum, there
> should be SOP related documentation and site specific (ie, turnkey)
> user documentation (obviously, these may overlap to some extent).  For the
> format of the documentation, I would suggest that we require a standard, and
> that the standard be POD, as it is very easy to write POD and convert it to
> other useful formats like plain text, html and man page format.  One down
> side of POD is that link resolution can be tricky when converting to html.
> We should decide on suggestions for MOD maintainers for whether to store docs
> in chado, as well as providing an insert tool.
>
> Scott
>
> PS: this document has been committed to the new 'gmod' module in
> gmod/doc/doc_notes.pod
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                         ca...@cs...
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
>

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Sue Rhee                         	rh...@ac...
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
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