Release 20

Goals and Timeline for the next Release #20

Timeline for Release: Goal is April 2013

• Summary_of_Changes_to_Release_20

See also:

• New_terms_and_obsolete_terms_Release_20

Continue major revision of PSDS

Focus on the revisions on:

PO:0007033 : whole plant development stage

> PO:0028002 : sporophyte development stage

>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)

>>> PO:0007047 : 3 inflorescence detectable stage [29131]

>>>PO:0007016 : 4 flowering [28057]

>>>PO:0007042 : 5 fruit formation [31009]

>>>PO:0007010 : 6 ripening [37642]

>> PO:0007134 : sporophyte vegetative stage [60370]: (Some still have the numbers preceding them, others don't)

>>>PO:0007057 : 0 seed germination stage [29568]

>>>PO:0007112 : 1 main shoot growth stage [47411]

>>>PO:0007131 : seedling development stage [26673]

PO:0009012 : plant structure development stage:

> PO:0007615 : flower development stage [48067]

>PO:0001083 : inflorescence development stage [48067]

PO:0025339 : plant organ development stage [46618]

>PO:0001050 : leaf development stage [45968]

>PO:0007520 : root development stage [25208]

PO:0025338 : collective plant structure development stage [49645]

>PO:0007615 : flower development stage [48067]

To-do list for Release #20

- Update the webpages- which ones are top priority? See below

- move files to live tag, update /trunk/ontology/OBO_format/Readme.txt

- file naming and which variations of the file to create for each release - check with cjm

- update translations synonyms- send to Ale and YY

Plant Ontology Web Site and Browser Update:

• need to update the download page and the citations pages!!

Please see Plant_Ontology_Web_Site_Update:_2012 for more details

• Items on the tracker:

PO:IDs in definitions working as links, fixes to web page headers

• Browser update- what is the status of this?

Annotation Guidelines

Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

Tabled for the next release:

Continue revisions and adding new terms for wood ontology

Most terms are in the PAE branch or for GO.

Can continue to add annotations as we go along, as well.

Potato Annotations

LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.

From Dr. Richard Finker (Wageningen, The Netherlands):

"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."

This will go in the next release, do they have expression data- RNA Seq?

Wood Annotations

TreeGenes and Fagaceae Genomics Web