Re: [Gmod-phendiver] Chado post-composition

[seth redmond]

Whilst working on the GMOD natural diversity module, we have repeatedly encountered problems where we need to post-compose cvterms into larger descriptions - this is particularly true where phenotypes are concerned. And rather than continue to provide ad-hoc solutions in various parts of chado, we feel it is worth revisiting post-composition across all of GMOD

Though there is a method for postcomp within chado (http://gmod.org/wiki/Chado_CV_Module#Post-coordinating_Terms), it is perhaps not the most obvious or user friendly way to go about thing and as such we'd be interested to know if anyone has put this into practice. In particular we'd like to know how postcomp is handled at ZFIN or Flybase - who, if their phenote configs are anything to go by, both allow post-composition in their phenotype descriptions.  

So, is anyone actually using this in anger? and if so, would they be interested in participating in it's further development?

thanks

-s



--
Seth Redmond
 Scientific Programmer, VectorBase
 Kafatos / Christophides Groups
 Div. Cell and Molecular Biology
 Imperial College, London
[hidden email]
--


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[Christian Pich]

Hi Seth,

I am not sure if someone already answered this but here is what I know
about post-composition at ZFIN:

We frequently post-compose terms here at ZFIN.
For our expression data we allow compositions of two regular terms of an
ontology in the following manner (not a complete list)
    - AO term with AO (e.g. amacrine cell of the retina)
    - AO term with a term from the spatial modifier (e.g. dorsal part of
the liver)
For phenotype data we use the (entity - quality - related entity) model
in which
an entity itself can be a post-composed (two-term) combination as for
the expression data.
Quality terms are taken from the PATO ontology and in case the quality
term is marked as a relational_slim another
post-composed (two-term combination) entity, here called related entity,
is added to the annotation.

Our expression data are stored in a table that contains the
post-composed term combination in two columns (super_term_id,
sub_term_id) with foreign
keys to the term table, which contains the individual term records.
Phenotype data reside in a separate table in which we have two columns
for the post-composed entity information (super and sub ids), a column
holding
the quality term id and another two columns holding the post-composed
related entity term ids.
With this DB schema we can easily create post-composed entities with
certain restrictions applying to the compositional union (e.g. sub terms
are optional).
This design does not support post-compositions that consist of more than
two basic terms.

I am not sure if that answers your question. Let me know if you have
more detailed questions.

Thanks,
Christian


--
------------------------------------------------------------------------
Christian Pich, Ph.D.
University of Oregon
Zebrafish Information Network
Phone: [phone]
Email: [hidden email]
Web: http://zfin.org
------------------------------------------------------------------------

>
>> *From: *seth redmond <[hidden email]
>> <mailto:[hidden email]>>
>> *Date: *June 3, 2011 11:06:18 AM PDT
>> *To: *gmod-phendiver <[hidden email]
>> <mailto:[hidden email]>>, GMOD-schema
>> <[hidden email]
>> <mailto:[hidden email]>>
>> *Cc: *<[hidden email] <mailto:[hidden email]>>, David Emmert
>> <[hidden email] <mailto:[hidden email]>>
>> *Subject: **re: Chado post-composition*
>>
>> Whilst working on the GMOD natural diversity module, we have
>> repeatedly encountered problems where we need to post-compose cvterms
>> into larger descriptions - this is particularly true where phenotypes
>> are concerned. And rather than continue to provide ad-hoc solutions
>> in various parts of chado, we feel it is worth revisiting
>> post-composition across all of GMOD
>>
>> Though there is a method for postcomp within chado
>> (http://gmod.org/wiki/Chado_CV_Module#Post-coordinating_Terms), it is
>> perhaps not the most obvious or user friendly way to go about thing
>> and as such we'd be interested to know if anyone has put this into
>> practice. In particular we'd like to know how postcomp is handled at
>> ZFIN or Flybase - who, if their phenote configs are anything to go
>> by, both allow post-composition in their phenotype descriptions.  
>>
>> So, is anyone actually using this in anger? and if so, would they be
>> interested in participating in it's further development?
>>
>> thanks
>>
>> -s
>>
>>
>>
>> --
>> Seth Redmond
>> Scientific Programmer, VectorBase
>> Kafatos / Christophides Groups
>> Div. Cell and Molecular Biology
>> Imperial College, London
>> [hidden email] <mailto:[hidden email]>
>> --
>>

--
------------------------------------------------------------------------
Christian Pich, Ph.D.
University of Oregon
Zebrafish Information Network
Phone: [phone]
Email: [hidden email]
Web: http://zfin.org
------------------------------------------------------------------------

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