Hello Dave,
Thanks again for your help.I think I will take my chances and test
everything on a seperate copy of the database.In case of issues I
would need further technical clarifications..
thank you
Saurav
On Thu, 2 Dec 2004, Dave Matthews wrote:
> 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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