ACEDB3 -> ACEDB4.1

Staffan Bergh staffan at biochem.kth.se
Mon Feb 5 02:19:42 EST 1996


Brian, you may already have had this answered by email, but as the news articles
in this group are now available as a searchable archive and the documantation is
lagging behind, I think it would be nice to have these comments available for
all:

In article <4etv4t$pl5 at canopus.cc.umanitoba.ca> Brian Fristensky <frist> writes:

>I am trying to upgrade from ACEDB3 to ACEDB4.1, but when I start
>ACEDB4.1, I get errors regarding my models. These models worked
>in ACEDB3. The errors seem to fall into 3 classes:
>
>###########################################################################
>
>1) Model error: non-tag ?Journal in column in model ?Paper
>
>//------------------------------------------------------------------
>?Paper   Reference Title UNIQUE ?Text
>                   Journal UNIQUE ?Journal XREF Paper
>                                  Unpublished

				   ^ here you have tags and ?Objects mixed in
column, which is not allowed. There will be one more error like this from the
Paper model, after Contained_in

>                   Volume UNIQUE Text Text
>                   [some stuff deleted ...]
>         Contained_in ?Paper XREF Contains
>                      Editor ?Author
>         Medline_ID  UNIQUE Int
> [some more stuff deleted ...]
>
>Journal does, in fact appear as a tag in tags.wrm.

The tags.wrm, systags.wrm and sysmodels.wrm files are now obsolete, ACE
constructs the list of tags from the models.wrm file.

>###########################################################################
>
>2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample
>//------------------------------------------------------------------
>?DNA_Sample Name Text
>            Experiment ?Experiment XREF DNA_Sample
>            Image   ?Image
>            Accession Text
>            DNA_Type UNIQUE Plasmid ?Plasmid XREF DNA_Sample
>                            Vector ?Vector XREF DNA_Sample
>                            Genomic ?Species Strain Text

					      ^ a tag after a ?Object is not
allowed, you have to use a constructed subtype

>###########################################################################
>3) Model error: In model ?Library, tag Paper XREF's to tag Library
>             in class ?Paper
>             can't find tag Library in model ?Paper

The model for ?Paper included does not have a Library tag

>
>Some class 3 errors are in models that are unchanged from the
>models.wrm as distributed with ACEDB3.

As Dave has already pointed out, there are some changes in the 'magic' tags
etc. Documentation on (at least some) of the magic stuff is at
	http://probe.nalusda.gov:8000/acedocs/index.html

>Has model syntax changed, or is ACEDB4.1 just more fastidious at
>detecting errors? 

ACEDB4.1 is much more picky. It now does error checking on the models ... Came
as a shock to me also when moving MycDB from 3 to 4!

Good Luck /staffan

Staffan Bergh
Biochemistry, KTH, S-100 44 Stockholm, Sweden

email: staffan at biochem.kth.se           + Don't let that horse eat that violin
phone: int+46 8 790 9230                +               cried Chagall's mother
fax: int+46 8 24 54 52                  + but he kept right on painting
                                        +             -- Lawrence Ferlinghetti

<A HREF="http://www.biochem.kth.se">Webmaster</A> and 
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