Difference between revisions of "POC Conf. Call 9-10-13"

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Content of the review has been moved to a [https://docs.google.com/document/d/1ExBEb0qFi1sh4rTjvwqMsWdSR35zzrw0Znab7pzAXSk/edit?usp=sharing gdoc]
 
Content of the review has been moved to a [https://docs.google.com/document/d/1ExBEb0qFi1sh4rTjvwqMsWdSR35zzrw0Znab7pzAXSk/edit?usp=sharing gdoc]
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=Principle 7: Use of Relations=
 
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*Some improvement desirable
 
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For the most part, the PO uses RO relations. The relation that is PO specific is provided with adequate documentation in the form of a definition and comment. Some relations are, however, defined in the PO that are within RO or BFO scope and yet do not have appropriate cross-references/Mireoted URIs. These include ‘has_participant’, ‘located_in’ and ‘participates_in’. This should be addressed, and full inclusion of such properties will facilitate the use of their logical properties for error checking.
 
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Specific points:
 
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* '''derives_by_manipulation_from''' is described as a subproperty of derives_from, whereby there has been a human processing step. This appears to be some kind of shortcut but isn’t yet logically defined as such. We would urge PO to work with OBI to leverage the work they have done in defining organismally derived entities, whereby such entities are the outcome of a ‘material processing’ process, has_specified_output the processed entity, and are derived_from the parent anatomical entity (for example see ‘urine specimen’).
 
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* '''Plant developmental stage classes do not yet have precedes relations for temporal ordering.'''  ''Implemented in Version #20''
 
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*  '''Consider using the stage relations (for example, existence_starts_during) from Uberon''' and similar to the zebrafish anatomy ontology, to relate organism developmental stages to the organismal entities at those stages. For example, ‘plant embryo’ could be defined as ‘whole plant' and (existence_ends_with some 'embryo stage') and (existence_starts_with some 'embryo stage') rather than use of the participates relation.
 
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==Principle 8: Documentation==
 
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*Pass
 
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* Extrinsic: The ontology is well documented with an extensive website and several publications.
 
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* Intrinsic: The ontology has high quality text definitions for every term.
 
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*Specific points:
 
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* There is some conflation in the use of annotation properties. A lot of information is placed in the comments field, including examples of usage, subclass assertions, and stage or taxon specific considerations. You may wish to break these out into more specific annotation properties. See IAO-core metadata and/or Uberon for some options, and please feedback to IAO if you desire a standard annotation property that isn’t yet available.
 
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* In some cases, '''definitions are attributed to “POC:curators'''”. We’d urge you to consider use of specific persons or sources for attribution, and as the Foundry moves towards the use of ORCID IDs, to include these as part of your attribution strategy.
 
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*  While we applaud the '''reference of tracker items directly in the ontology, these items can be included as URLs''' such that the link is easily made directly from the ontology, for example see ‘leptome’ to “OBO_SF_PO:3295055”.
 
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* Similarly with the '''PO_REFs- please make these URLs or imports''' so that they can be easily located. It is likely that a new standardized annotation property for this purpose should be created and used across the Foundry.
 
  
 
=NSF PI meeting Sept 4th-6th in DC=
 
=NSF PI meeting Sept 4th-6th in DC=

Revision as of 17:00, 12 September 2013

POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Brian Atkinson (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Barry Smith, Marie Alejandra Gandolfo (Cornell)

Absent: none

- please see the Items_for_future_meetings page, will be moved here before the meeting

multi-tissue plant structure development stage (PO:new)

  • Needs a parent term: multi-tissue plant structure development stage (PO:new), then the definitions can be re-written, currently a direct child of plant structure development stage (PO:0009012). This would also be the parent for seed development and plant organ development (see below)

Accepted, will post proposed definition on SF tracker

leaf development stage (PO:0001050)

  • See Google Doc for revisions in progress.
  • Need to look into non-vascular leaf development and see if it applies there as well, or if we will need separate terms for vascular and non-vascular leaves.
  • leaf development stage (PO:0001050): A phyllome development stage (PO:0025579) that has as a primary participant a leaf (PO:0025034).

Current structure: All these will be renamed "vascular leaf...."

Leaf dev stages.jpg

vascular leaf development stage and child terms

Proposed new term and definition:

  • vascular leaf development stage (new PO:0025570): A leaf development stage (PO:0001050) that begins with the onset of vascular leaf initiation stage (PO:0007040) and ends with the termination of the vascular leaf senescence stage (PO:0001054).

Add comment on how every stage can end in accidental death. Also mention something death being the conical end point

  • non-vascular leaf development stage (new PO:id): A leaf development stage (PO:0001050) that begins with the onset of non-vascular leaf initiation stage and ends with the termination of the non-vascular leaf senescence stage.

see also: moss phyllides, moss info and Background_info_on_Physco_biology_and_culture.

New/revised child terms under vascular leaf development stage (PO:0025570)

  • Note: Use "during which" rather than "when" and "ends with the beginning of the..."
  • Each definition should have a consistent format (ie. begin with the termination/ends with the initiation).
  • Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.
  • vascular leaf initiation stage (PO:0007040): A vascular leaf development stage (PO:0025570) when localized cells of the peripheral zone (PO:0000225) in the shoot apical meristem (PO:0020148) transition from indeterminate growth to determinate growth and ends with the beginning of the vascular leaf expansion stage (PO:0001052). Comment: Cells in the primordium are not yet differentiated.

DWS: Should omit transition from indeterminate growth -> determinate growth. The peripheral meristem is always in the shoot apical meristem.

The cells in the SAM transition from anticlinal divisions to periclinal divisions, leading to a leaf primordium or bump. Usually in L2 or L3, rarely in L1.

Later mitosis ceases leaving the marginal or submarginal meristems and the leaf expansion stage is mainly cell expansion

Leaf development in Monocots need to be looked at as they have a basal intercalary meristem.


What are "localized cells"? The cell divisions are localized

Create a 'vascular leaf primordium development stage', followed by a stage called 'vascular leaf surface polarity determination stage (synonym "pre-expansion stage)'


  • vascular leaf expansion stage (PO:0001052): A vascular leaf development stage (PO:0025570) that begins with cell differentiation and cell expansion forming the leaf lamina (PO:0020039) and ends with the onset of the leaf fully expanded stage (PO:0001053).
    • new comment: The majority of leaf expansion is due to cell enlargement. The leaves of some plants may not have a conspicuous midrib or rachis.
  • vascular leaf post-expansion stage (PO:0001053): A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and cell expansion has ceased and ends with the onset of the vascular leaf senescence stage (PO:0001054).

Perhaps change term to vascular leaf mature stage

  • vascular leaf senescence stage (PO:0001054): A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.

Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf.

Leaf dev new.png


Note: Will have the new preceded_by relation added to order them

Children of vascular leaf initiation stage (PO:0007040)


Comment: The leaf primordium is not yet distinguishable.

Children of vascular leaf expansion stage (PO:0001052)- revised names and definitions:

this terms should move up to be a child of vascular leaf dev stage

need to review this in terms of leaflet discussion

check "ligule (PO:0020105) primordium"- PO:id should be after the term



OBO Foundry Review of Plant Ontology

Content of the review has been moved to a gdoc

NSF PI meeting Sept 4th-6th in DC

  • PJ and DWS attended

Any news?

Upcoming meetings and Presentations 2013-2014:

No one from PO is planning to attend

  • PAG 2014 January 11-15, 2014 - San Diego, CA, USA
    • PJ has been contacted by PAG organizers; Suggest slightly new focus "Plant Ontologies and Systems Biology"
    • Ideas for speakers- someone from GO and others?>>
    • Registration is now open: PAG 2014. Early reg'n till Nov. 1st

Next meeting scheduled for Tuesday, Sept 24th, 2013 at 10am Pacific/1pm Eastern

-MAG has requested the meeting be moved to 10:30am Pacific/1:30 pm Eastern- would that works for the others in the group?

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