Difference between revisions of "Notes on PGDSO revisions fall 2011"

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(Created page with '===[http://sourceforge.net/tracker/?func=detail&aid=3306250&group_id=76834&atid=835555 PGDSO terms without is_a parents]=== imbibition (PO:0007022) seedling growth (PO:0007131)…')
 
 
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===[http://sourceforge.net/tracker/?func=detail&aid=3306250&group_id=76834&atid=835555 PGDSO terms without is_a parents]===
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This is the working page for making notes on changes to the PGDSO as we go along.
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=Plan for revising the PGDSO, fall 2011=
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The current PGDSO is a mixture of processes and phases (although it was intended to be all stages/phases), and was designed with angiosperms in mind.
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We need to correct some specific problems with the PGDSO, and to make it applicable to all plants, as we have done withe PAO.
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=Open SourceForge trackers for the PGDSO=
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See [[Items_for_future_meetings#User_requests_still_open_on_Source_Forge.3B_PGDSO]] for a complete list.
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==[http://sourceforge.net/tracker/?func=detail&aid=3306250&group_id=76834&atid=835555 PGDSO terms without is_a parents]==
  
 
imbibition (PO:0007022)
 
imbibition (PO:0007022)
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shoot emergence (PO:0007130)
 
shoot emergence (PO:0007130)
  
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===Restructuring PGDSO for Occurents===
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==[https://sourceforge.net/tracker/?func=detail&aid=3131997&group_id=76834&atid=835555 'plant life' ('life of whole plant')]==
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(from agenda for 12-15-10, was never discussed)
 
  
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(see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/PGDSO_2011/plant_ontology_test.obo?view=log)
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Barry suggested that we need a term like "life of whole plant", of which all phases would form parts.
  
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Suggested New "working" Structure of the PGDSO:
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=Previous proposal=
  
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*The root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent").
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See [[POC_Conf._Call_12-15-10#Restructuring_PGDSO_for_Occurents]] for a description of a proposal that BS, LC and RW worked on in December.
  
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LC, BS and RW met on 11-30 to discuss this restructuring, and changed the upper level term from plant life cycle process to plant process, plus several other changes.
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Also see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/PGDSO_2011/plant_ontology_test.obo?view=log for a copy of the test ontology file and [[changes in new PGDSO version]] for a summary of changes that were made to the test file.
  
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The top level structure would have three branches, as below  
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In that proposal, the root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent"). The top level structure would have three branches, as below:
  
 
[[File:Life cycle process 2.jpg]]
 
[[File:Life cycle process 2.jpg]]
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None of the old term names or definitions have been changed yet, except to put (phase) on the end of some term names that did not have stage in their names.
 
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'''Key changes:'''
 
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* Most of the terms from PGDSO went under plant structure development phase, but a few went under plant structure development process.
 
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* In the case of seedling development (which went under plant structure development process) we added a new phase called seedling phase. Something like imbibition is not a phase, but a developmental process, so it went under plant structure development process.
 
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*Could add a germination phase that begins with imbibition and ends with emergence of the radicle.
 
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'''New: Barry has suggested we need a term like [https://sourceforge.net/tracker/?func=detail&aid=3131997&group_id=76834&atid=835555 'plant life' ('life of whole plant')] of which all phases would form parts'''
 
  
  
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'''From the 11-10-10 meeting:'''
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The proposal described here is simpler than December's (does not include biological processes, which could be in GO), but follow many of the same principals.
  
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-Add corresponding phases for each of the developmental processes.
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=New relations linking the PAO and the PGDSO=
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These still need to be discussed/worked on.
  
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For example: gametophytic phase corresponds to gametophyte development and leaf development phase could correspond to leaf development.
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===derives_from===
  
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Then it would be possible to move the developmental processes to GO, but keep the phases in PO.
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At the POC meeting on 7-19-11, we agreed to create a new relation in the PO called ''derives_by_manipulation_from'' (see [[POC_Conf._Call_7-19-11#derives_from_relations_in_PO:]]). This would be a special case of the RO relation ''derives_from''.
  
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-We reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms.
 
  
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Barry suggested that his goal was to have all PO terms in one of two branches:
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===participates_in and has_participant===
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* plant structures (plant anatomical entity = independent continuant)
 
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* plant processes (plant life cycle process = occurent)
 
  
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Lol and Ramona have been working on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit.
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See [[POC_Conf._Call_7-19-11#participates_in_relation]]
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*Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser.  
 
  
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Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.
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Chris asked: "will you add temporal relations to the stages?"
  
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-Stage term names need to be rewritten as nouns, for example: "whole plant in the phase where 1 leaf is visible
 
  
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-Complex terms could be rendered using post coordination; ie: 'on the fly' for users, but some may need to have actual PO IDs in order to accommodate annotations.
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===other===
  
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[[changes in new PGDSO version]]
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We may want to add temporal relations such as '''preceded_by''', '''precedes''' and '''follows''', or perhaps more precisely, '''immediately_preceded_by''', '''immediately_precedes'''. This would be comparable to the ''adjacent_to'' relation.

Latest revision as of 16:06, 12 September 2011

This is the working page for making notes on changes to the PGDSO as we go along.

Plan for revising the PGDSO, fall 2011

The current PGDSO is a mixture of processes and phases (although it was intended to be all stages/phases), and was designed with angiosperms in mind.

We need to correct some specific problems with the PGDSO, and to make it applicable to all plants, as we have done withe PAO.

Open SourceForge trackers for the PGDSO

See Items_for_future_meetings#User_requests_still_open_on_Source_Forge.3B_PGDSO for a complete list.

PGDSO terms without is_a parents

imbibition (PO:0007022)

seedling growth (PO:0007131)

shoot emergence (PO:0007130)

'plant life' ('life of whole plant')

Barry suggested that we need a term like "life of whole plant", of which all phases would form parts.

Previous proposal

See POC_Conf._Call_12-15-10#Restructuring_PGDSO_for_Occurents for a description of a proposal that BS, LC and RW worked on in December.

Also see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/PGDSO_2011/plant_ontology_test.obo?view=log for a copy of the test ontology file and changes in new PGDSO version for a summary of changes that were made to the test file.

In that proposal, the root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent"). The top level structure would have three branches, as below:

Life cycle process 2.jpg


The proposal described here is simpler than December's (does not include biological processes, which could be in GO), but follow many of the same principals.

New relations linking the PAO and the PGDSO

These still need to be discussed/worked on.

derives_from

At the POC meeting on 7-19-11, we agreed to create a new relation in the PO called derives_by_manipulation_from (see POC_Conf._Call_7-19-11#derives_from_relations_in_PO:). This would be a special case of the RO relation derives_from.


participates_in and has_participant

See POC_Conf._Call_7-19-11#participates_in_relation

Chris asked: "will you add temporal relations to the stages?"


other

We may want to add temporal relations such as preceded_by, precedes and follows, or perhaps more precisely, immediately_preceded_by, immediately_precedes. This would be comparable to the adjacent_to relation.

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