Re: [Obo-anatomy] [Obo-cell-type] who uses the CL for annotation?

[Melissa H. <mha...@uo...>]

Hi Chris,

Excellent job putting it all together.  You even make implementation by
biologists look easy :)

One addition I'd like to see is more biological description of the problem
at the very beginning.  This will be advantageous for folks entering the
site without the benefit of the listserve discussions.  I'd be happy to
contribute a paragraph, or you could adapt some of what's already been
written.

One other thing is to make it even more clear that the difference between
the light-weight implementation and the heavy-weight one is whether or not
the SCA editor works in OBO 1.2 format and can use the intersection tags. 
For ZFIN, we can't move to 1.2 format just yet and this is what is holding
us back.

This is a terrific resource and I am looking forward to hearing feedback
from the other MODs regarding this approach.

Cheers,
Melissa

>
> I've add a page to the NCBO CL wiki showing in detail how the
> approach Melissa describes is compatible with using CL as a reference
> ontology, and showing how the oboedit reasoner can be used to keep
> ZFA and CL consistent. The same methodology applies to any species-
> centric ontology to species-neutral reference ontology combination.
>
> http://www.bioontology.org/wiki/index.php/CL:Aligning_species-
> specific_anatomy_ontologies_with_CL
>
> Feel free to edit or request clarifications - it's a first draft.
>
> Linked to from:
> http://www.bioontology.org/wiki/index.php/CL:Main_Page
>
> Cheers
> Chris
>
> On Aug 23, 2006, at 1:10 PM, Melissa Haendel wrote:
>
>> Hi all,
>> I just wanted to give you an update as to how we've decided to
>> implement
>> the cell ontology at ZFIN.  We will be creating a cell type slim for
>> zebrafish, and then adding these terms to the zebrafish anatomy
>> ontology.  They will retain their CL IDs as dbxrefs, but will also be
>> assigned zebrafish (ZFA) IDs.  This allows us to map cell types to
>> tissues such that queries on tissues will bring back annotations to
>> cells.  It solves problem number 3 below, because in essence what is
>> being done is to create a zebrafish cell type with an is_a
>> relationship
>> to the cell type in the CL.  This is ontologically correct because we
>> are specifying a xzebrafish cell type.  This will also help prevent
>> over-proliferation of the CL with organism specific terms.
>>
>> As a corollary, ZFIN will not be incorporating the GO cellular
>> component
>> ontology.  This part of anatomy will have to be post-composed during
>> annotation.
>>
>> Thanks,
>> Melissa
>>
>>
>>
>> Melissa Haendel wrote:
>>> Hi everyone,
>>> I am wondering if anyone out there has begun using the CL for making
>>> annotations.  I have some questions as to how this can be
>>> implemented.
>>>
>>> 1. Has anyone mapped the cell types to an anatomy ontology? I know
>>> mouse
>>> has done this, is the mapping being used?
>>> 2. If so, do you support queries for cell type children of an
>>> anatomical
>>> structure?
>>> 3. It has been suggested that this type of mapping is of questionable
>>> ontological validity. Basically, for example, that stating that
>>> thyrotrope (CL:0000476) is part_of adenohypophysis (ZFA:0001282) is
>>> incorrect, because every instance of a thyrotrope is not part of a
>>> zebrafish adenohypophysis. However, it seems to me that if one cannot
>>> make this kind of mapping between the anatomy and cell ontologies
>>> than
>>> there really isn't much cause to use the cell ontology.   We need
>>> to be
>>> able to support queries for cells within tissues.  The alternative
>>> is to
>>> create species specific cell terms for each mapping, but I think
>>> we want
>>> to avoid this type of term proliferation as much as possible, or else
>>> each organism might as well have their own cell ontology.  Perhaps we
>>> need a new relationship type to describe the mapping between cells
>>> and
>>> tissues.
>>>
>>> Any thoughts?
>>> Thanks, Melissa
>>>
>>>
>>>
>>
>> --
>>
>> Melissa Haendel, Ph.D.
>>
>>
>>
>> ZFIN Scientific Curator
>>
>> Zebrafish Information Network
>>
>> 5291 University of Oregon
>>
>> Eugene, OR 97403-5291
>>
>> Phone: (541) 346-5108
>>
>>
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