Difference between revisions of "July 2012 Release"

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=Goals and Timeline for the next Release #18=
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The latest release of the Plant Ontology, version #18, is available on our [http://www.plantontology.org/amigo/go.cgi Ontology Browser].
Timeline:   End of June to early-July- '''before''' BSA meeting- goal is so have it out by the 4th.
 
  
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This full database release features 22 new terms in the Plant Anatomical Entity branch of the Plant Ontology, of which 15 involve different types of primordia. 
  
==To-do list==
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No new terms have been added to the Plant Structure Development Stage branch of the Ontology, although all terms now include the word "stage" in their name.
-new multi-tissue structures and CPS still say LC:test, change to POC:curators
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Two significant new terms have been added to help categorize the problematic plant structures such as fruit and seed, and their parts. 
  
-fix definition hilum groove, open tracker
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* '''multi-tissue plant structure''' (PO:0025496) has been added as a direct sub-class of plant structure (PO:0009011) and is the new parent term for fruit (PO:0009001), seed (PO:0009010), and plant organ (PO:0009008).
  
-need icon for located_in, update on wiki page
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* '''cardinal part of multi-tissue plant structure''' (PO:0025498)- This term includes cardinal parts of plant organs such as leaf lamina (PO:0020039) or receptacle (PO:0009064), as well as parts of other multi-tissue plant structures, such as fruit distal end (PO:0008001) or arilloid (PO:0019022).
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A new term, '''collective plant structure''' (PO:0025497), was created to describe collections of plant structures and to serve as parent term to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269). Note that collective plant organ structure (PO:0025007) was formerly named "collective plant structure" (the same name as the new upper-level term), but was renamed for clarity.
  
-fix annotations on flower primordium
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This release also features updated Japanese and Spanish translations of the term names.
 
 
=Summary of Changes=
 
  
 
For more information about the release, please visit our wikipage with a [[Summary of Changes to PO July 2012]].
 
For more information about the release, please visit our wikipage with a [[Summary of Changes to PO July 2012]].
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You can also view a list of [[New terms and obsolete terms July 2012 Release]]
 
You can also view a list of [[New terms and obsolete terms July 2012 Release]]
  
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For more information and to view a summary of the release statistics, please visit: [http://archive.plantontology.org/docs/release_notes/releasenotes18.html Plant Ontology Release #18 July 2012].
  
  
==Continue major revision of PSDS==
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==Updated Pages on PO site==
Focus on the revisions on:
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The PO [http://plantontology.org/amigo_user_guide/index.html AmiGO user's guide] has been updated with current screen shots and links.
 
 
'''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 [http://dendrome.ucdavis.edu/treegenes/ TreeGenes] and [http://www.fagaceae.org/ Fagaceae Genomics Web]
 
 
 
* cotton- [http://www.agbase.msstate.edu/ AgBase]
 
 
 
* soybean- [http://soybase.org/ SoyBase]
 
 
 
* potato
 
 
 
* rice
 
 
 
* grape
 
 
 
==Plant Ontology Web Site and Browser Update:==
 
 
 
Please see [[Plant_Ontology_Web_Site_Update:_2012]] for more details
 
 
 
*Items on the [http://palea.cgrb.oregonstate.edu/trac/report/1 tracker]:
 
 
 
PO:IDs in definitions working as links, fixes to web page headers
 
 
 
*Browser update- what is the status of this?
 
 
 
==Update Tutorials on PO site==
 
 
 
==Complete old user requests/SF tracker items==
 
Ongoing process....
 
  
priorities:
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A slide show with an [http://plantontology.org/docs/presentations/demo/poc-demo-1.html introduction to the PO] has been updated.

Latest revision as of 00:41, 18 April 2014

The latest release of the Plant Ontology, version #18, is available on our Ontology Browser.

This full database release features 22 new terms in the Plant Anatomical Entity branch of the Plant Ontology, of which 15 involve different types of primordia.

No new terms have been added to the Plant Structure Development Stage branch of the Ontology, although all terms now include the word "stage" in their name.

Two significant new terms have been added to help categorize the problematic plant structures such as fruit and seed, and their parts.

  • multi-tissue plant structure (PO:0025496) has been added as a direct sub-class of plant structure (PO:0009011) and is the new parent term for fruit (PO:0009001), seed (PO:0009010), and plant organ (PO:0009008).
  • cardinal part of multi-tissue plant structure (PO:0025498)- This term includes cardinal parts of plant organs such as leaf lamina (PO:0020039) or receptacle (PO:0009064), as well as parts of other multi-tissue plant structures, such as fruit distal end (PO:0008001) or arilloid (PO:0019022).

A new term, collective plant structure (PO:0025497), was created to describe collections of plant structures and to serve as parent term to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269). Note that collective plant organ structure (PO:0025007) was formerly named "collective plant structure" (the same name as the new upper-level term), but was renamed for clarity.

This release also features updated Japanese and Spanish translations of the term names.

For more information about the release, please visit our wikipage with a Summary of Changes to PO July 2012.

You can also view a list of New terms and obsolete terms July 2012 Release

For more information and to view a summary of the release statistics, please visit: Plant Ontology Release #18 July 2012.


Updated Pages on PO site

The PO AmiGO user's guide has been updated with current screen shots and links.

A slide show with an introduction to the PO has been updated.