[Obo-cell-type] Annotations to cell types (using OBO-Cell)

[Chris Mungall]

On Jan 16, 2007, at 7:38 AM, Pankaj Jaiswal wrote:

> Sue, its a good idea to establish  Xrefs between CT and PO.

yep!

> Just a preliminary look at both the CT and PO for plant cell and  
> its instances.

You mean subtypes, not instances

:-)

Whilst I'm being picky, I recommend using either the unique ID-space  
(CL) or root node (cell) as a way of identifying an ontology - CT is  
a little confusing, it stands for too many other things

> Seems to be that there are more cell types listed in PO (almost  
> double). Also the free text definitions are not consistent with  
> those from PO. So I am not sure what is the source of the plant  
> cell types in CT.
>
> To avoid the inconsistencies, I suggest that the primary source of  
> all the plant cell types in CT should be PO and not the other way  
> round. If in case the CT needs new Plant cell types then a request  
> be forwarded to PO. CT managers can later using an automated way  
> collect/update it by pulling the plant cell type terms from PO.  
> Alternatively we can also generate a mapping file PO2CT and use it  
> for QC and consistency across both. Based on your suggestions I can  
> ask Shuly to generate a mapping and add the related ontology DBXref  
> to the PO terms.

sounds reasonable.

> BTW one more suggestion, is it possible to add the 'subset: plant'  
> or a namespace:plant to quickly identify which terms belong to the  
> plant cell types. The same is suggested for cell types from other  
> organisms as well.
>
> Any ideas?
>
> Pankaj
>
> Sue Rhee wrote:
>> Chris,
>> The Plant Ontology has a number of cell types under its Plant  
>> Structure branch and I think (though someone should confirm) that  
>> the Cell Type ontology's plant cell type terms have PO IDs as  
>> secondary IDs. Actually I think that this should be made  
>> bidirectional but am not sure if the PO terms have CT IDs as  
>> secondary IDs. In any case, there are 264 annotations to terms  
>> under plant cell, which are downloadable from the PO website  
>> (www.plantontology.org).
>> Sue
>> Chris Mungall wrote:
>>> Is anyone aware of downloadable annotations to CL IDs? I know  
>>> that  MGI provide cell type localisation info as qualifiers to  
>>> their GO  annotations; this will be available through AmiGO  
>>> sometime this year.
>>>
>>> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many  
>>> of  which are described as qualities borne by types of cell (eg   
>>> spermatocyte lacks asters)
>>>
>>> EVOC provides associations to dbEST libraries.
>>>
>>> Any others?
>>>
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> -- 
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
>
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683
>