Release 19
See also:
Goals and Timeline for the next Release #19
Timeline for Release: Goal is mid December 2012
To-do list for Release #19
- 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
Priorities:
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]
New or expanded association files:
- wood genes TreeGenes and Fagaceae Genomics Web
- cotton- AgBase
- soybean- SoyBase
- potato
- rice
- grape
New Annotation Files
Strawberry
- Strawberry is on SVN: strawberry
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?
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
Complete old user requests/SF tracker items
Ongoing process....
See: Items_for_future_meetings
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?
