cv subsets

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cv subsets

Stephen Ficklin-2

Hi All,

 

This question is related to another discussion earlier this month about the cvprop table and adding elements of the OBO file into Chado.  I’m currently working on a PHP OBO parser to load ontologies into Chado.  This parser will be part of Tripal.  

 

What would be the best way to store subsets of an ontology  (e.g. plant GO slims)?  The options I can think of are:

 

1) add a new CV for the subset and duplicate the terms… but this will make it hard to trace parent/child relationships for terms not in the subset.

2) suggest a new table ‘cvsubset’ or something… but I have to wait for the next release of Chado for it to be generally available.

3) use the cvtermprop table to link a term to a subset… sounds like the best bet for now.

4) don’t add subsets

 

Does the current Perl loader handle subsets?

 

Thanks,

Stephen


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Re: cv subsets

Naama Menda
In my opinion cvtermprop is the easiest and most flexible solutio. Just add prop name 'is slim X' or something like that, then your software could filter whatever it needs to filter.

The current perl loader does not handle slims, but it could easily be changed to do so.

-Naama

 
Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
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On Mon, Nov 29, 2010 at 4:37 PM, Stephen Ficklin <[hidden email]> wrote:

Hi All,

 

This question is related to another discussion earlier this month about the cvprop table and adding elements of the OBO file into Chado.  I’m currently working on a PHP OBO parser to load ontologies into Chado.  This parser will be part of Tripal.  

 

What would be the best way to store subsets of an ontology  (e.g. plant GO slims)?  The options I can think of are:

 

1) add a new CV for the subset and duplicate the terms… but this will make it hard to trace parent/child relationships for terms not in the subset.

2) suggest a new table ‘cvsubset’ or something… but I have to wait for the next release of Chado for it to be generally available.

3) use the cvtermprop table to link a term to a subset… sounds like the best bet for now.

4) don’t add subsets

 

Does the current Perl loader handle subsets?

 

Thanks,

Stephen


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http://p.sf.net/sfu/intelisp-dev2dev
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