making it easier for databases to use the PO

[Mary Polacco]

Shuly,

Thanks much.!!!:)))
 Synonyms would be great - not sure that we are talking about a large
quantity of terms - but  I can send them on to Jack who is mapping the
microarray library terms.

RE second issue (below)
I was just referring to the file on the CVS server for the Zea ontology.
This is different than than the POC and has different PO accession space. I
am encouraging users in the maize community to look to PO files (not the Zea
files) for the accessions ID and to contact me, or Leszek, if they have a
problem in the mapping.
 mary

On 1/25/05 10:56 AM, "Shuly Avraham" <shuly at cshl.edu> wrote:

> Mary,
> 
> I can also generate a file with the synonyms for each term, and email it
> to you if you need it now.
> 
> About the second issue, I am not sure I understand correctly, but the
> reason I am using Zea and not maize, is because that's the taxonomy
> number in the association file you provided. But, again, I am not sure I
> understood the problem right.
> 
> Shuly.
> 
> Mary Polacco wrote:
> 
>> Great.
>> Let me know when you do that - I will point the micro-array dudes there - I
>> have been in contact re the maize terms and have sent them my flat file,
>> attached in last email, with instructions to use AmiGO PO browser if they
>> couldn't find a term --  eg synonyms such as husk and kernel for a consensus
>> PO term -- or simply new terms not in my flat file.
>> 
>> Another issue about usage by databases - some folks  (or at least when they
>> are talking to me) think that they should be using the Zea ontology posting
>> for maize. Leszek and I will post a README in the CVS for the Zea ontology
>> indicating it is NOT the PO, but was used to develop the PO, and has maize
>> oriented definitions, etc etc.
>> 
>> m
>> 
>> On 1/25/05 10:38 AM, "Shuly Avraham" <shuly at cshl.edu> wrote:
>> 
>>  
>> 
>>> Hi Mary,
>>> 
>>> This kind of list is very easy to generate. If all you need is a flat
>>> list of terms organized alphabetically, I can generate the list and
>>> place the file on our (soon to come) FTP site.
>>> If there are other kinds of requsets or database queries, I can generate
>>> those as well.
>>> In addition, in the near future we will have a mysql database dump on
>>> the ftp site, so you can create a local copy of the database, and query
>>> it as you need.
>>> 
>>> Shuly.
>>> 
>>> Mary Polacco wrote:
>>> 
>>>    
>>> 
>>>> Hi all
>>>> 
>>>> Is there any reason not to post a list of the PO accessions and the terms,
>>>> alphabetically - ie no ontology structure?
>>>> 
>>>> It makes it easier for database folks such as myself both to retrofit, and
>>>> use the approved terms and their the accession IDs.
>>>> 
>>>> Attached is a list - from last fall, the CVS dump of terms with accessions
>>>> and ontology structure, that I used to help map to MaizeGDB. Missing terms,
>>>> eg synonyms for husk, I mapped using the PO AmiGO browser.  It should be
>>>> trivial for a regular update of this sort to be dumped from the AmiGO
>>>> database.
>>>> 
>>>> mary
>>>> 
>>>> 
>>>>      
>>>> 
>> 
>>  
>> 
>