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Ace-MODS urgent help!!

Dave Matthews matthews at greengenes.cit.cornell.edu
Fri Dec 3 03:25:32 EST 2004


Hi Saurav,

Yes, this modification is well tested and quite stable.  But you're right,
you need some documentation to use it.  What's available is sketchy and
dispersed.  

First, you don't have to make any changes in your models.wrm or your .ace
data.  What you do is create a rule in wspec/markup.pl that is used by
AceBrowser to parse the data and create the href link if there is a match
to the rule.  

This example,
http://www.graingenes.org/cgi-bin/ace/tree/graingenes?name=BE403741&class=Sequence
has several links to external databases.  Let's look just at the DB_info
line.

The ACEDB data for this is:

Sequence : "BE403741"
DB_info External_DB "GenBank" "BE403741"

AceBrowser has added the href links "[DDBJ|EMBL|GenBank]" according to the
rule in wspec/markup.pl.

The model for class Sequence is:

?Sequence ...
          DB_info External_DB Text Text

The rule in markup.pl is:

##########################################
# Connection to external DB for Sequence #
##########################################
{'root'=> {'cl'=>'Sequence'},
 'branch' => [{ty=>tg,va=>'DB_info'},
              {ty=>tg,va=>'External_DB'},
              {ty=>tx,va=>'GenBank'},
              {ty=>tx}],
 'urls' => [{'name'=>'EMBL', 'URL'=>'http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[embl-acc:$keys[0]]'},'GenBankAC',{'name'=>'DDBJ', 'URL'=>'http://getentry.ddbj.nig.ac.jp/cgi-bin/get_entry.pl?$keys[0]'}],
},
#

Documentation on writing these rules is given in
http://www.acedb.org/Cornell/ace95/nalwww.html#appendix3.  Briefly,
"cl" means class, "ty" means type, "tg" means tag, "va" means value, and
"tx" means text.  The value of that final ty=>tx field will be substituted
in for the variable $keys[0].  

In this rule, 'GenBankAC' is the name for an URL that is defined in another
file, externalURLs, which is located in the AceBrowser configuration 
directory.  The GenBankAC line in this file should currently say:
GenBankAC:GenBank:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=$keys[0]

Writing these rules is actually easier than it looks, and there are a
lot of examples in the distributed markup.pl file.

> 2) is the release stable and has it been tested??If not what type of
> support can I expect in case of urgent malfunctioning if I decide to
> incorporate the new set of scripts into my database.

I would counsel some caution, e.g. setting it up on a test machine first.
Hugh himself has been able to install it on two other servers but I don't 
know if anyone has done it using only the instructions provided.

best,
- Dave

> From saurav at algodon.tamu.edu  Thu Dec  2 13:40:52 2004
> 
> Hello Dave,
> 
> Thank you for your reply.
> I have some queries reagrding the Ace-Mods
> 
> 1) what changes needs to
> be done in the
> .ace files slurped by AceDB and to the corresponding class in the 
> wspec/models.wrm .In short what modifications(tag addition for external
> Url linking) need to be done to the
> concerned class defination in the models.wrm to make the whole thing work.
> 
> 2) is the release stable and has it been tested??If not what type of
> support can I expect in case of urgent malfunctioning if I decide to
> incorporate the new set of scripts into my database.
> 
> 
> 
> 3)If possible can you please send me just the class definition and one
> data
> object of the .ace file of the graingenes database for reference where
> you have implemented this feature..
> 
> 4) Is there any sort of comprehensive documentation..which I guess is not
> necessary for me  if you can send me just an example as requested in 3
> ,but anyway
> necessary for any one who would really like to be completely sure  
>  Thank you for your help in advance..I would be really thankful of you can
> help me out of this.
> 
> regards
> Saurav

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