Difference between revisions of "Release 19"
| Line 84: | Line 84: | ||
* grape | * grape | ||
| + | =New Annotation Files= | ||
| + | |||
| + | ===Strawberry=== | ||
| + | |||
| + | * Strawberry is on SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry] | ||
| + | |||
| + | ===Potato Annotations=== | ||
| + | |||
| + | LC has been in contact with the group who published the [http://www.nature.com/nature/journal/v475/n7355/full/nature10158.html#/f4 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?'' | ||
==Complete old user requests/SF tracker items== | ==Complete old user requests/SF tracker items== | ||
Revision as of 18:18, 13 November 2012
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
Things that need to be addressed
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]
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.
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?
Complete old user requests/SF tracker items
Ongoing process....
priorities:
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?
