[BioSQL-l] RE: [Bioperl-l] Biosql documentation request

[Brian Osborne]

Hilmar,

I went ahead and installed postgres as well as the biosql schema when I
found out that Cygwin would install postgres. Kudos to you: the installation
of postgres, postgres initialization, and biosql database creation took
about 10 minutes and I've never used postgres before. I was basically
following the INSTALL instructions. The new biosql.html has been commited.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
Sent: Friday, June 04, 2004 2:16 PM
To: Brian Osborne
Cc: Hilmar Lapp; BioPerl; Biosql
Subject: Re: [Bioperl-l] Biosql documentation request

It pretty much is the latest. Amazing, isn't it? The schema is *very*
stable.

There are a few additions in the Oracle version which aren't really
officially blessed yet (meaning, they're not in the MySQL/Pg versions
but will be soon), and none of which breaks backwards compatibility.

I'll try and see whether I can get postgres_autodoc installed over the
weekend.

Or maybe somebody on the biosql list has this setup already?

        -hilmar

On Jun 4, 2004, at 4:38 AM, Brian Osborne wrote:

> Hilmar,
>
> Neither does the ERD show nullability. The ERD is good but some useful
> information is missing, yes.
>
> The ERD is dated 6/4/2003, is this the latest version? Pardon my
> ignorance.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: Friday, June 04, 2004 2:20 AM
> To: Brian Osborne
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Biosql documentation request
>
> Brian, if I understand the output correctly it only documents the
> schema elements. Do you feel that the ERD (doc/biosql-ERD.pdf) does not
> fulfill this purpose well enough?
>
> The ERD diagram actually doesn't show the unique key constraints, so
> that would be a difference indeed.
>
>         -hilmar
>
> On Thursday, June 3, 2004, at 05:56  AM, Brian Osborne wrote:
>
>> Bioperl-l,
>>
>> Dave Howorth has provided a detailed critique of the bioperl-db/biosql
>> documentation which I'm working through. One thing that he noticed was
>> that
>> the Biosql file doc/biosql.html was out-of-date. This file was created
>> by
>> running a script called postgres_autodoc.pl on a Postgres instance of
>> the
>> biosql schema. Can anyone provide me with a current version of this
>> file? I
>> run biosql on Mysql myself and I haven't found a script or utility
>> equivalent to postgres_autodoc.pl. postgres_autodoc.pl is available at
>> http://www.rbt.ca/autodoc/.
>>
>> Brian O.
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
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--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

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