Follow up meeting: Sept 15, 2011

formatting for column 16 is correct.

Sent: Tue 9/13/2011 12:24 PM To: Walls, Ramona Cc: cooperl@science.oregonstate.edu Subject: Re: merged maize terms with annotations

HI Laurel, Ah, you meant yesterday then. Sorry - I was away from email most of the week after Thurs pm.

I am free this week save for today, and 11:30-1 central time on Fri. When's the best time for you? I can set up the conf call pretty quickly. Wed, tomorrow sometime? Based on where you were moving, I used the more general terms, but do plan to check to make sure. My plan is to add double annotations for items also in column 16. A question, I am not sure was formatting column 16 correctly in last send - does it matter? You list on the po how to page an example:

    part_of(PO:0009025)

Re changes at MaizeGDB re terms,yes, it would help if I had a tab-delimited file of all the PO terms at some point, where 'obsolete' was added, as you do now, for those that are no longer used. This way I will be sure to catch them all.

Let me know best times - I will get to this data tomorrow and start sending up in chunks.

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Original Message-----

From: Schaeffer, Mary L. [1] Sent: Tue 9/13/2011 6:03 PM To: Walls, Ramona Subject: Re: changes to PO terms

Hi Ramona, I made comments (mostly OK's) and tried to answer questions at the tracker place. I will try and find a current reference for the separation of tasseling and ear development but provided the 1992 tech report I was using. It is not clear to me what I can do to help with the last term, below: Inflorescence visible. The posted solutions seem fine.

I have yet to look at the wiki.

-mary

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Tue, 6 Sep 2011 13:36:16 -0500 Subject: changes to PO terms

Hi Mary,

I have finished merging all of the Zea/Poaceae terms into their parent terms. I have detailed all of the changes on our wiki page at: http://wiki.plantontology.org:8080/index.php/Eliminating_Zea/Poaceae_terms_from_PO

If you have time, you can look over that page and let me know if you agree or disagree with the changes. Beware, it is a lot of information!

I would also like to ask you to take a look at a few Source Forge tracker items. I made some changes to terms other than merging/eliminating them, including new names or definitions, and it would be great to get feedback from someone who is a maize expert.

Could you please look at the following tracker items, and post a comment on them if you think there are any problems:

Poaceae hull: http://sourceforge.net/tracker/index.php?func=detail&aid=3132525&group_id=76834&atid=835555

lemma/palea: https://sourceforge.net/tracker/?func=detail&aid=3400245&group_id=76834&atid=835555

glume: https://sourceforge.net/tracker/?group_id=76834&atid=835555

floret: http://sourceforge.net/tracker/?func=detail&aid=3397632&group_id=76834&atid=835555

I also posted our responses on your tracker items for:

IL.03 full inflorescence length reached: http://sourceforge.net/tracker/?func=detail&aid=3357762&group_id=76834&atid=835555

LP.18 eighteen leaves visible: https://sourceforge.net/tracker/?func=detail&aid=3357766&group_id=76834&atid=835555

inflorescence visible - rework the tree, add a term: http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 inflorescence visible - rework the tree, add a term

There are some questions for you on these, if you can look at them.

Thanks in advance,

Ramona

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8-30-11 Hi Laurel,

Links to GeneModel will have same URL structure/link unless the models go away or change, and then it will be by synonym or something. They seem not to be changing too much between versions from the early reports - mostly coordinates.

http://www.maizegdb.org/cgi-bin/displaygenemodelrecord.cgi?id=GRMZM2G172795

What would be the best way to provide the maize tissue links ? One way: Use column 8 for example and supply in this form:

             MGDB_tissue:2366347

The URL would be the standard one for MaizeGDB – just by ID Else, for quicker lining with view of image and journal:

     http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347

Another way:

 In the reference field , column 6, add the tissue ID (which links to the reference in the above link) - this is logically more consistent with GO notions I would think.

A question about NULL values, may I use the term 'NULL'? Or do you require that there be a blank? Sorry about not sending files yesterday – got busy, but now it looks like a good idea to have waited a tad.

-mary

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List of merged terms

term (# annotations) > term merged into (= target term)

PO:0006337 inflorescence bract of ear (26) > PO:0009054 inflorescence bract

PO:0006472 Zea stamen (1) > PO:0006441 Poaceae stamen (7) > PO:0009029 stamen

PO:0006473 Zea anther (363) > PO:0006442 Poaceae anther (6) > PO:0009066 anther

PO:0006487 Zea stigma (56) > PO:0006468 Poaceae stigma (0) > PO:0009073 stigma

PO:0006488 silk (56) > PO:0006469 Poaceae style (100) > PO:0009074 style

PO:0006445 Poaceae anther wall (2) > PO:0000002 anther wall

PO:0006455 Poaceae carpel (3) > PO:0009030 carpel

PO:0006446 Poaceae endothecium (1) > PO:0020002 anther wall endothecium

PO:0006318 Poaceae floret (71) > PO:0009082 floret

PO:0006329 Poaceae floret meristem (1) > flower meristem PO:0000229

PO:0006384 Poaceae gynoecium (3) > PO:0009062 gynoecium

PO:0006465 Poaceae integument (3) > PO:0020021 integument

PO:0006508 Poaceae integument epidermis (1) > PO:0006043 integument epidermis

PO:0006464 Poaceae megaspore (1) > PO:0020019 megaspore

PO:0006463 Poaceae megasporocyte (2) > PO:0000431 megasporocyte

PO:0006444 Poaceae microsporangium (2) > PO:0025202 microsporangium

PO:0006452 Poaceae microspore (22) > PO:0020048 microspore

PO:0006451 Poaceae microsporocyte (1) > PO:0020047 microsporocyte

PO:0006462 Poaceae nucellus (2) > PO:0020020 nucellus

PO:0006456 Poaceae ovary (1) > PO:0009072 ovary

PO:0006457 Poaceae ovule (5) > PO:0020003 ovule

PO:0006497 Poaceae stigma epidermis (3) > PO:0006061 stigma epidermis

PO:0006449 Poaceae stomium (1) > PO:0020101 stomium

PO:0006450 Poaceae tapetum (3) > PO:0009071 anther wall tapetum

PO:0006337 inflorescence bract of ear (26) > PO:0009054 inflorescence bract