Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Angel P. <an...@ma...>]

Aaron,

I can't agree more with your points. Please keep up the good suggestions.

I thought a while back, GUS developers had agreed to replace CBIL's 
ad-hoc sequence ontology terms and gene models (not ad-hoc, but derived 
from EpoDB?) with SO as the major ontology for defining them. Makes 
sense to just extend the use of SO within GUS for all sequence 
categorizations.

The drawback I can see is the added layer of logic that developers must 
now know. For instance the WDK queries *may* become more complex, 
sequence annotation tools must now type sequences on defined terms, 
possibly a hierarchy of them. But since we are ditching the annot tool 
project that is not a concern. WDK queries writers would need to know 
the semantics of the current attribute model anyway, so it is not a 
stratch for them to learn sematics of SO and apply them. Also that new 
knowledge will be applicable to more than just a WDK query, so that is a 
win.

Two other advantages: 1) since it is widely accepted, most annotation 
tools should eventually provide native support for SO, and 2) we would 
more easily be able to share our gene models across GUS sites and othe 
non-GUS sites.


Angel

Aaron J. Mackey wrote:

> First, I would encourage you to look at SOFA, the subset of SO useful 
> for sequence annotation (which is presumably what you're doing, right?)
>
> I would argue that these extra "attributes" you don't find explictly 
> listed in SO are actually redundant to specific datatypes found in SO, 
> i.e. these are encapsulated in the definition of each term.
>
> On Feb 3, 2005, at 7:54 AM, Steve Fischer wrote:
>
>> Polymer Type   - no
>>  - DNA  - no
>>  - RNA - no
>
>
> an mRNA is RNA, not DNA; a chromosome is DNA, not RNA (unless its a 
> viral genome, etc).
>
>> Strandedness - no
>> - single  - no
>> - double  - no
>
>
> ditto; strandness is inherent to the definition of a type
>
>> Sequencing process   - derived_from
>> - Genomic - no
>> - EST  -  SO:0000345
>> - predicted - no
>> - transcribed - no
>> - what else?
>
>
> all of these are there, you just have to look for them in more 
> biologically meaningful terms than what you have here.  and 
> "derived_from" is not a SO term, it's a relationship type.
>
>> Source - no
>> - nucleus  - no
>> - mitochondria - no
>> - plastid  - no
>> - plasmid  - no
>> - episome  - no
>
>
> ditto.
>
> SO is/was designed to recapitulate biology (as best as possible), not 
> the awkward attribute simplifications you seem to want to use (for 
> instance, it seems in your scheme that I could have a sequence type 
> that was DNA, mRNA, double stranded, predicted and episomal all at 
> once).  With SO, you find the specific name for the thing you have ...
>
> To put it in a more generic context: with SO you have "integer", 
> "unsigned integer", "long integer", "unsigned long integer", "signed 
> integer", etc., related in a hierarchy of isa/derived_from/part_of 
> relationships; you don't have "signed" and "unsigned", "long" and 
> "short", etc. as singular terms.  Now if you wanted to overlay a 
> second ontology of term relationships (e.g. the "signedness" 
> ontology), you could relate terms by these "attributes", and have the 
> best of both worlds.
>
> -Aaron
>
> -- 
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  am...@pc...
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
>
>
>
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-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
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Philadelphia, PA 19104-6160

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