Re: [Gusdev-gusdev] Sequence Type controlled vocab

[Aaron J. M. <am...@pc...>]

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