Difference between revisions of "POC Conf. Call 9-15-10"

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In attendance:  
 
In attendance:  
  
−
POC members:     
+
POC members:    Laurel Cooper, Alejandra Gandolfo, Justin Preece, Justin Elser, Ramona Walls, Pankaj Jaiswal.
  
−
Absent:  
+
Absent: Chris Mungal, Dennis Stevenson,  Barry Smith.
  
 
Collaborators: none
 
Collaborators: none
  
  
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Acceptance of the minutes from the 9-8-10 meeting?
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Acceptance of the minutes from the 9-8-10 meeting? No changes or additions.
 +
 
  
  
Line 16: Line 17:
  
  
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=== Responses, as of 9/8/2010:===
+
'''Items Arising from reviews, as of 9/14/2010:'''
 +
'''
 +
 
 +
From Paula Rudell, Kew Gardens'''
 +
 
 +
''' Flower;''' PO: 0009046 [A heterosporangiate strobilus, typically consisting of androecium, gynoecium, usually surrounded by a perianth and borne on an axis or receptacle. ]
 +
 +
New SF tracker for this term [https://sourceforge.net/tracker/?func=detail&aid=3062189&group_id=76834&atid=835555 flower]
 +
 
 +
Proposed Def'n: A determinate shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part. Comment: may have as part one or more petals, sepals or tepals.
 +
 
 +
This should be a 'child of shoot system', rather than part_of inflorescence (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence),
 +
 
 +
*Also note that we need to add a inflorescence has_part flower .
 +
 +
 
 +
''perhaps we should have a reproductive shoot system? (which is a term we don't have at the moment).''
 +
 
 +
''New proposed definition: A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part.''
 +
 
 +
''Comment: may have as part one or more petals, sepals or tepals. May contain pistillode or staminode or other aborted organs that don't show up in mature form.''
 +
 
 +
''Need to look at terms like lemma, palea, lodicule and nectary for next round of revisions.''
 +
 
 +
 
 +
 
 +
'''From Farshid Ahrestani (Columbia, TraitNet)'''
 +
Ramona responded to him that we agree that the terms he requested should be added to the ontology, but due to time constraints, we will not be adding any new terms to this release, but we will aim to add them before the next release.
 +
 
 +
*Will correct seed coat part_of plant tissue and add wood as synonym for secondary xylem for this release.
 +
 
 +
 
 +
''Seed coat is not part_of plant tissue, but is_a, which is correct, so no need to fix it.''
  
−
'''From Paula Rudall (Kew)'''
+
''Re. definition of secondary xylem: should add that it develops from vascular cambium, and add develops_from relation. Fix typo in comment (tress). SF tracker: [https://sourceforge.net/tracker/?func=detail&aid=3067090&group_id=76834&atid=835555 secondary xylem]''
  
−
1. Flower; PO: 0009046 [A heterosporangiate strobilus, typically consisting of androecium, gynoecium, usually surrounded by a perianth and borne on an axis or receptacle. ]
 
  
−
'''Does the definition make sense?'''
 
−
There is no mention of determinacy, which is an important defining feature of the flower. I would prefer "bisexual" to "heterosporangiate", but not all flowers are bisexual (or heterosprangiate).
 
−
The flower is notoriously difficult to define. Bateman et al. (2006: J Exp Bot 57: 3471-3503) discussed earlier definitions, and suggested the following: '. . . a determinate axis terminating in megasporangia that are surrounded by microsporangia and are collectively subtended by at least one sterile laminar organ'
 
  
−
'''Is it appropriate for all plants (not just angiosperms)?'''  
+
'''Rich Zobel (Root terms)'''
−
Not really, because the terms androecium and gynoecium are applied only to angiosperms. Flowers are not necessarily restricted to angiosperms.
 
  
 +
We have an open term request [https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms] from Rich Zobel from last November. We requested Rich's help with the review process, so  it makes sense to deal with the open tracker. 
  
−
''Those present felt that the current definition of flower was not acceptable (it is inaccurate), and that we needed to come up with a new working definition before the release.''
+
There are  a couple of upper level term that need to be added:  'basal root' (along with its child: 'non-pericyclic basal root')  Modification of [https://sourceforge.net/tracker/?func=detail&aid=3066305&group_id=76834&atid=835555 'shoot borne root (PO: 0000042)]  and taproot/primary root (PO:0000042).
  
−
''PROPOSED DEFINITION: A determinate shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part. Comment: may be have as part one or more petals, sepals or tepals.''
+
It should be possible to incorporate these changes into this release, (depending upon the amount of discussion generated).
 +
The essential issues are that there are 3 distinct types of roots: basal
 +
roots, shoot-borne roots, and taproot (primary root)
  
−
''Child of shoot system''
+
1.  new term [https://sourceforge.net/tracker/?func=detail&aid=3066301&group_id=76834&atid=835555 'basal root'].  I looked around in the literature and this is being used. 
 +
We will have to work on the definition though.  Seems pretty straightforward, also suggested a child term: 'non-pericyclic basal root') 
  
 +
2.  Change name of [https://sourceforge.net/tracker/?func=detail&aid=3066295&group_id=76834&atid=835555 primary root (PO:0000042) to 'taproot'].  This one I am not too sure about- is the primary root always a taproot?  What about in the grasses?
 +
I propose we leave this as is for now and keep taproot as a synonym.
  
−
''Also note that we need to add a inflorescence has_part flower (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence).''
+
Should it be 'tap root' or 'taproot'?  It is used both ways.
−
RW opened a SF tracker for this term [https://sourceforge.net/tracker/?func=detail&aid=3062189&group_id=76834&atid=835555 flower]
 
  
−
2. Collective phyllome structure; PO:0052023 [A collective plant structure that consists of two or more phyllomes originating from the same node or from one or more adjacent nodes with compressed internodes.]
+
3.[https://sourceforge.net/tracker/?func=detail&aid=3066305&group_id=76834&atid=835555 'shoot-borne root]-  addition of hyphen, problem with the synonym
 +
'adventitious'- too broad. seems pretty straightforward.
  
−
Does the definition make sense? It is not clear to me why the word collective occurs in both the term and the definition. It seems rather a strange term; at first I couldn't see what it would be used for, but when I found the discussion (e.g. the definition of the androecium as "A collective phyllome structure composed of two or more stamens") it made more sense. However, I'm not sure that this term needs to be defined separately.
+
LC opened individual SF trackers for each of these.
  
−
Is it appropriate for all plants (not just angiosperms)? yes
 
  
−
''We agreed to keep collective phyllome structure as it is for this release.''
 
  
 +
''We will add basal root as new term. New proposed definition: A root that develops from one of the of hypocotyl (which layer?) or "A root that arises from a part of the hypocotyl" ?.  Will deal with synonyms and child terms of basal root in next round of revisions.''
  
−
3. Central cell; PO: 0020090  [The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.]
+
''Decided to leave primary root named as is for now, keeping tap root as synonym, but will seek more outside input into what the best name should be. Will add comment: Is often the central axis of the root system.''
  
−
Does the definition make sense? Yes, but see below.
+
''Okay to add hyphen to shoot-borne root. Should add hyphens to other -borne terms in the ontology for consistency. We felt that adventitious root should not be a synonym, because some basal roots may be adventitious roots. Need to give adventitious roots further consideration, and maybe add as its own term for next round of revisions.''
  
−
Is it appropriate for all plants (not just angiosperms)? No; in a gymnosperm archegonium, the central cell is the cell that will divide to form the ventral canal cell and the egg cell (see Rudall 2006, Bioessays 28: 1067-1071).
+
''PJ: We also should discuss root terms with [http://www.biology.duke.edu/benfeylab/index.htm Phil Benfey (Duke)] and [http://gradeducation.lifesciences.cornell.edu/faculty/individual5367 Leon Kochian (Cornell)]. They are developing software for root type recognition. Should work to integrate PO with their software. Don't know if Rich is involved in discussions with them.''
  
−
''This will be an issue when we add terms for gymnosperms, so we will address it in the next release.''
 
  
  
−
'''From Elena Kramer (Harvard)'''
+
'''Naama Menda (tuber terms)'''
  
−
Does the definition of each term make sense?
+
Naama's response:
  
−
For collective tepal structure PO:0025021 - This seems like an odd  term that's never commonly used. I realize that the difficulty is finding a parallel collective concept for calyx and corolla. What if the first level under perianth was differentiated perianth and undifferentiated perianth. Then the first option would break down to calyx-->sepal and corolla-->petal while the second would just break down to tepal. I realize that structure is still not entirely parallel but at least it doesn't introduce terms that will never be used elsewhere.
+
NM:"I think the new hierarchy is better than the previous one (branch vs shoot). The child terms in the tuber node seem complete to me, at least from looking at the features that are being evaluated by the potato breeders community (mostly tuber skin, flesh, eyes)"
  
  
−
''The consensus was that the term undifferentiated perianth is not in use either, so it would better to keep collective tepal structure.''
+
NM: '''subterranean tuber axillary vegetative bud''' (PO:0025042): the term 'sprout' is often used by potato breeders. One example is the trait 'heat sprout rating' which measures new sprouts on the tuber. These range from 'swollen eyes' to 'chain tubers'. I'm not sure if 'tuber sprout' should be a synonym or a child term (develops from the axillary vegetative bud)"
 +
 +
The 'sprouts' are buds (eyes) that begin to grow. Since they actually develop from an existing axillary vegetative bud,  perhaps the term 'sprout' is more like a shoot than a bud?
 +
If so, they perhaps they  should be an axillary shoot (PO:0006343)?  Or maybe we need a new term 'subterranean tuber axillary shoot' ?
  
  
−
For hypanthium PO:0009065, I honestly wasn't sure what "cardinal" meant in the definition "A cup- or tube-shaped cardinal organ part". Does that refer to it being in the outer whorl?
+
''Can have swollen eye as synonym of tuber axillary bud. Sprout should be added a synonym of axillary shoot or better yet, add new term subterranean tuber axillary shoot.''
  
−
''We noted that both Kramer and Rudall appeared to misunderstand the genus/differentia form that uses the parent term in the definitions (comment on use of collective by Rudall and use of cardinal by Kramer). Perhaps we should add a glossary, FAQ link, or some other type of instructions to the web browser, to help novice users. There is some information available on the documentation page, but it inadequate, and it is not obvious when you are browsing the ontology.''
+
''Link to SF tracker for request for new term [https://sourceforge.net/tracker/index.php?func=detail&aid=3067097&group_id=76834&atid=835555 subterranean tuber axillary shoot]''
  
−
''The meaning of the term cardinal is described in the comment for cardinal organ part. Perhaps there should be a cross-reference to it in the child terms.''
 
  
 +
 +
NM: '''"tuber epidermis and tuber periderm''': 'potato skin' is a synonym for both terms. I see the clarification in the comment field, but I think it would be clearer to have a synonym of 'mature potato tuber skin' and 'young potato tuber skin'. Queries using 'potato skin' should still pick up both terms".
  
−
Is it appropriate for all plants (not just angiosperms)?
 
  
−
Since I only looked at floral terms, no, they are just appropriate 
+
''We agreed this is a good suggestion, and will fix.''
−
for angiosperms, although the micro/megasporophyll definitions would 
 
−
be comparable for gymnosperms.
 
  
−
Coverage:
 
−
Are the terms included under the node(s) you are reviewing (its descendent terms) sufficient?
 
  
−
Well, we work on petal spurs and they were missing under petal, so that would be a big problem for describing Aquilegia. Also, I wondered if there was some way to incorporate corolla tubes vs. free petals, inferior vs. superior ovaries, and the phenomenon of common primordia (that last one would only apply to the development ontology).
+
NM: "Are any plans to add tuber developmental and growth stages to PO? Currently this is the only portion I think is missing from the ontology. Data we have from potato breeders usually refers to fully mature tubers, but molecular biologist do look at gene expression during different growth stages". (''See below under Priorities for next round of revisions'')
  
−
''A spur is a part of a petal, so we could add a term for it under cardinal organ part. The other terms are phenotypic descriptors, and could be annotated using a combination of PO and PATO terms.''
 
  
  
−
'''From Farshid Ahrestani (Columbia, TraitNet)'''
+
'''Alejandra will follow up with Gar Rothwell'''
 +
 +
''Waiting for response from Gar Rothwell and Peter Linder.  MAG will copy responses to po-discuss.''
 +
 
  
−
There is a possibility that we (TraitNet and partners) may incorporate a slim-version of the 
 
−
PO for a Plant Functional Trait ontology that we are developing.
 
  
−
The following terms could be included in the ontology, depending on their relevance and importance:
 
  
−
Corm - Maybe as a synonym of stem.
+
=== Annotations that have no term associated with them===
  
−
Spine
+
-There are 10 terms that have been obsoleted from this version of the PO.
  
−
Podaria (which is synonym to Tubercle)
+
PO:0025003 compound plant organ 
  
−
Pneumatophore
+
PO:0025002 simple plant organ 
  
−
Stele
+
(These two were never in the live version, so they were actually destroyed, not obsoleted)
  
−
Diaspore
+
PO:0009014 dermal tissue
  
−
Cone
+
PO:0000057 inflorescence bud
  
−
Sorus
+
PO:0000058 vegetative bud
  
−
Shoot - Subclasses of the shoot are included, such as shoot apex and shoot axis
+
PO:0008034 leaf whorl
  
−
Tendril
+
PO:0008037 seedling
  
−
Wood - Although sapwood, late wood, early wood, heartwood present
+
PO:0009004 gametophyte
  
−
- Seed coat is present, but is part-of of Plant tissue. Is that correct?
+
PO:0009003 sporophyte
  
−
- Pollen Tube (and maybe others at that same level in the ontology) could do with a parent.
+
PO:0000056 floral bud
  
  
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''By slims, they are referring to something similar to a GO slim (based on conversations with Ramona), which they would develop using selected terms from the PO.''
+
'''Only the last 5 of them are problematic: leaf whorl, seedling, gametophyte, sporophyte and floral bud.''' 
  
−
''Shoot is a synonym of shoot system, and wood is a synonym of secondary xylem. Other terms can be added for the next release. Can fix seed coat part_of portion of plant tissue for this release.''
 
  
−
''Laurel will follow-up with Rich Zobel (Root terms) and Naama Menda (tuber terms), Alejandra will follow up with Gar Rothwell ''
+
'''PO:0008034 leaf whorl'''
  
 +
*Annotations: 15,802, from 'po_anatomy_gene_arabidopsis_tair.assoc'
  
 +
Source: TAIR
  
 +
These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022
  
 +
Response from TAIR (Tanya Berardini 8/16/10): -suggestion is fine, annotations should move if replacement term is in OBO stanza- it is.
  
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'''B.  Response emails'''
 
  
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After the meeting po-discuss@plantontology was set up and the members of po-internal were added to it.  This is the address that will be used in the letters to the reviewers.  Thanks to Chris Sullivan and Justin Elser for helping with this on short notice.
 
  
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Also, the feedback box on the beta browser will direct responses there
+
'''PO:0008037: seedling'''
  
 +
*16 annotations from 'po_anatomy_gene_arabidopsis_tair.assoc'
  
 +
Source: TAIR
  
 +
-Recommended to TAIR that they should be moved to seedling growth stage (PO:0007131) in PGDSO and also to whole plant (PO:0000003)in PSO.
  
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(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal).  I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?
+
Response from TAIR (Tanya Berardini 8/16/10):- suggestions are fine, annotations should move if replacement term is in OBO stanza
  
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We all agreed (last week) that these need to be reviewed and we need to deal with the spam problem as well.
+
''Laurel will add the ''consider'' relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.''
 +
  
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''No changes or actions taken.''
 
  
  
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=== Annotations that have no term associated with them===
+
'''PO:0009003: sporophyte''' 
  
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-Laurel and Ramona compiled a list of the 10 terms that have been obsoleted and how many annotations that are associated with them.  
+
* 1 annotation from: 'po_anatomy_gene_arabidopsis_tair.assoc'
  
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There were only 10 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte.  [[File:Obseleted_terms_(LC_8-10-10).pdf‎]]
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Source: TAIR
  
−
''In progress....''
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-Recommended to TAIR that they should be moved to sporophytic growth phase (PO:0028002) in PGDSO and also to whole plant (PO:0000003)in PSO.
  
−
Laurel sent a spreadsheet to TAIR and Gramene listing the annotations that were affected on 8/13/10, with our recommendations or suggestions on where they should be moved to.
+
Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotation should move if replacement term is in OBO stanza 
  
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'''A.  TAIR'''
+
''Laurel will add the ''consider'' relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.''
−
- 8/13/10 message sent to Donghui, Kate and Tanya:
 
  
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"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:
 
  
−
PO:0009003: sporophyte  1  (from: po_anatomy_gene_arabidopsis_tair.assoc)
 
  
−
PO:0000056: floral bud  54: (from:  po_anatomy_gene_arabidopsis_tair.assoc)
+
''Yes -- these annotations should also be attached to whole plant.''
  
−
PO:0008037:  seedling 16  (from po_anatomy_gene_arabidopsis_tair.assoc)
 
  
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The first three will need to be looked at to determine where to best put them.  We have put our recommendations or suggestions on the spreadsheet
+
*116 annotations from 'po_anatomy_gene_oryza_gramene.assoc' and 'po_anatomy_qtl_oryza_gramene.assoc'
 +
   
 +
Source: Gramene
  
 +
Suggested that the associations for genes be moved to PO:0000003 whole plant,  plus sporophytic growth phase (PO:0028002) for genes;
 +
 +
Seedling vigor QTLs are already associated with PO:0007131 seedling growth, suggested adding association to whole plant PO:0000003 as well, if appropriate
  
−
PO:0008034: leaf whorl  15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022
 
  
−
Spreadsheet: [[File:TAIR_dangling_annotations_(LC_8-13-10).pdf]]
 
  
  
−
'''
 
−
*Comments:'''
 
−
Response from Tanya Berardini@ TAIR 8/16/10:
 
  
−
"Hi Laurel,
+
'''PO:0009004 gametophyte'''
 +
* 1 annotation from 'po_anatomy_gene_oryza_gramene.assoc'
  
−
Thanks for the update and for the spreadsheet.  We should be able to handle the transition for the obsoleted terms pretty easily as we already have a mechanism set up for automated transfer of annotations from an obsolete term to a replacement term, if that replacement term is suggested in the OBO stanza. 
+
Source: Gramene
  
−
Comments:
+
Suggested that this association be moved to male gametophyte (PO:0020091) or female gametophyte (PO:00290092) or to gametophytic phase (PO:0028003) and/or to to whole plant PO:0000003
  
−
'''(1) sporophyte''' - suggestions are fine, annotations should move '''if replacement term is in OBO stanza'''  (see below:)
+
Note: It is already associated with the megagametophytic stage (PO:000721)''Note: This appears to be an error'' and pollen developmental stage (PO:0001007) in the PDGSO. 
  
−
'''(2) floral bud'''
+
''Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).''
  
−
Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful.  I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both.
 
  
−
'''(3) seedling''' - suggestions are fine, annotations should move if replacement term is in OBO stanza
+
'''PO:0000056: floral bud'''  
 +
* 54 annotations from:  po_anatomy_gene_arabidopsis_tair.assoc
  
−
'''(4) leaf whorl''' - suggestion is fine, annotations should move if replacement term is in OBO stanza
+
Source: TAIR
  
−
When do you anticipate the public release of the new version of the PO vocabularies?  We will monitor the annotations that we have to the terms that you highlighted to make sure that the appropriate transfers and updates occur.
+
'''Question from TAIR (Tanya Berardini@ TAIR 8/16/10)'''
  
−
Thank you for your help,
+
"Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful.  I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both."
  
−
Tanya"
+
This was discussed at the 9-8-10 meeting.  All those present felt it was preferable to keep the current structure for floral bud.
 +
For more detailed information and graphics, please see the [[http://wiki.plantontology.org:8080/index.php/Summary_of_changes_to_the_Plant_Ontology Summary of Changes]] page
 +
We were concerned about instituting a policy of changing the ontology, unless the change is biologically appropriate.
  
−
Laurel replied and provided more explanation and invited her to review that section and possibly attend the conference call.
+
Response: TB: "The PO suggestion "...to move the annotations to both axillary floral bud and terminal floral bud, if that is appropriate. " is not necessarily practical as this information is not always available and I would be reluctant to move the annotations to the child terms if I wasn't sure that these were correct."
  
  
  
−
'''B.  Gramene'''
+
In order to get a better understanding of the issue, Laurel went through the annotations associated with the term 'floral bud' and looked at each paper to see how they describe the plant tissue samples.  Most of them refer to "floral bud", "flower bud", or simply "buds". In a few cases they seem to be referring to the whole inflorescence.   
−
- 8/13/10 message sent to gramene@gramene.org contact email.  Ken replied and said that Pankaj was the best person to look at these.
 
  
−
[[File:Gramene_dangling_annotations_(LC_8-13-10).pdf‎]]
+
In light of this, we need to reopen the discussion of the bud structure and will reexamine these terms.
  
−
''
 
  
 +
''We had some discussion of bud terms. Since all floral buds are at the end of a shoot (since they are determinate) they should all be terminal buds, but then those terminal buds can arise either at the end of a shoot or in an axil. Pankaj and Lol will work on sketching new structures for bud terms that includes the categories reproductive bud and floral bud. Will re-open SF tracker so we can work on this more.''
  
−
'''C. Issues Arising:'''
+
==Annotation File formats==
  
−
'''*Changes to the annotation files:'''
+
We have had a question from Tanya Berardini@TAIR about whether or not we are planning to transition to the GAF 2.0 format or not.
  
−
- what is the mechanism for making these changes? Are we doing them here or is TAIR/Gramene going to send us new files? 
+
[http://geneontology.org/GO.format.annotation.shtml#gaf2 GAF 2.0]
  
 +
This will affect how they modify the above files
  
−
See comments from CM about replacing the terms: 
 
−
On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting     end_of_the_skype_highlighting begin_of_the_skype_highlighting    end_of_the_skype_highlighting wrote:
 
−
> We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)
 
  
−
>>CM: note that where the replacement is clear you can use replaced_by -  
+
Should we get one and test it first? Will it matter if there are some in GAF 1.0 and some in 2.0?
−
this means the replacement can happen automatically without a human  having to make a choice
 
  
−
- Is there a script for making the changes?  Does this apply to the annotation files or just the OBO files?
+
Maybe a goal for the next version?
  
  
−
'''*sporphytic phase and gametophytic phase '''
+
''Lol talked to Justin and Chris before meeting, and they say new format should work fine, so TAIR can send us the files in GAF 2.0''
  
−
> RW: in several cases (sporphytic phase for sporophyte, gametophytic phase for gametophyte, and seedling growth stage for seedling),
+
==Priorities for the Next Round of Revisions==
−
we cannot currently add the 'consider' term to the po_anatomy_test file because the consider terms are in a different file (po_temporal_test). Probably the easiest way to solve this would be to merge the two files before the live release.
 
  
 +
-Merging the plant structure and plant developmental stages ontologies
  
−
'''*Do we want to do the merge before the release?? it seems like this should have been done before sending out to the reviewers.''' 
+
-Adding Musa terms requested by Rosemary Shrestha
−
We do not want to delay the process any further-
 
−
What are other options?
 
  
−
CM: As an interim strategy you could embed the id in the comments using a standard syntax, then parse the tags out once you merge files.
+
-Root terms- Rich Zobel
  
−
What about a "bridge file"  We have discussed this in the past but have not implemented it.
+
-Legume terms submitted by Austin Mast
 
   
 
   
 +
-New terms requested by reviewers (from Ahrestani and Kramer)
 +
 +
-is_a parents for remaining terms (will require work on upper level structure for non-material entities)
 +
 +
-convert to intersection_of relations?
 +
 +
-work on PGDSO
 +
 +
-[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages], open on SF since 6/2009
 +
 +
-add links to more images
 +
 +
-Others??-
 +
PJ: Lol and Ramona will focus more on adding annotations (~50% of time)
 +
 +
 +
-What is the target date for the next release?
 +
 +
==Other Items:==
 +
 +
''Alejandra has the first set of images ready to load onto PlantSystematic.org. Alejandra, her technician, and Ramona (and anyone else who is interested) will try to meet by phone next week to go over the progress.''
 +
 +
 +
'''A.  Feedback page on Beta site fixed'''
 +
 +
Justin Elser fixed refer_to_url variable on the feedback page for the beta site.  It is now working from within the AmiGO browser.
 +
Now it will capture the url of the page the person is looking at.  Thanks Justin!
 +
 +
 +
'''B.  Announcement for Plant Sciences Bulletin:''' Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10
 +
 +
Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ end of September.
 +
 +
Ramona will follow up with Dennis after he gets back to see what the status of this is.
 +
 +
 +
 +
'''C. POC meeting to be held at NYBG in fall 2010. Date TBD.'''
 +
 +
Should we invite outside experts, scientists, students and postdocs?
 +
 +
'''Please fill out Doodle Poll''' re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg
 +
 +
'''We need to pick a date for this meeting ASAP so folks who are flying in can get tickets'''
 +
 +
 +
''Pankaj will check his calender to see if this is possible. Ramona will follow up with Dennis when he returns.''
 +
 +
==Upcoming meetings 2010-2011:==
 +
 +
* '''Latin American Congress of Botany'''
 +
[http://www.botanica-alb.org/X_Congreso/index.php LACB]. La Serena, Chile, October 4-10;
 +
 +
Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.
  
−
'''*floral bud'''
 
  
−
> > 2. Based on the response from TAIR (see above), we may want to reconsider obsoleting the term floral bud. Perhaps keeping this term for users is more important that getting rid of it to solve an ontological problem (term have multiple parentage).
 
  
 +
'''* Infectious Disease Ontology Workshop'''
  
−
CM: Multiple Inheritance isn't an ontological problem, it's an engineering problem for you, in that manually maintaining MI is tedious and error prone. You should move to towards using the reasoner to infer all these, but in the meantime your asserted links /must/ reflect the biology, which in many cases means asserting MI.
+
Dallas, Dec. 8th and 9th, 2010
  
−
''Those present at the meeting felt it was preferable to keep the current structure for floral bud. We were concerned about instituting a policy of changing the ontology here and there to fit the convenience of individual users, unless the change is biologically appropriate. Laurel will follow up with TAIR to see if they can work with the new structure for floral bud, and also to find out the status of their annotation files.''
+
Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. [http://www.bioontology.org/wiki/index.php/IDO_Workshop,_Dallas,_December_8-9,_2010 IDO Workshop December 2010]. Note that relations between the IDO and other ontologies is one of their provisional goals.
  
−
''Barry described using axioms for terms with multiple inheritance, rather than using asserted relations. Not certain how this translates in OboEdit -- perhaps through the use of intersection of relations. There was a question of whether or not annotations would be passed on (to parent terms) using axiomatic relations -- no one knew the answer.
+
Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.  
−
''
 
−
''Justin P. raised the issue that we should be mindful as to whether or not the utilities we use (like Amigo) will be able to support our future analysis needs (for example, implied relations do not show up in the Amigo browser).''
 
  
 +
For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html
  
−
'''D.  Resolution:'''
 
  
 +
'''*Plant and Animal Genome XIX Conference'''
  
−
''We still need to find out (maybe from Justin E. or Pankaj) what the procedure is for updating annotations before the release.''
+
January 15-19, 2011  [http://www.intl-pag.org/ PAG 2011]
  
−
'''A. Feedback Box:'''
+
Registration is open, abstract deadline Nov 1, 2010.
  
−
New link to [http://beta.plantontology.org:8080/db/feedback/send_feedback feedback box] on beta site- emails will go to '''po-discuss'''
+
''Lol and Ramona should plan on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Perhaps Dennis and Alejandra could also attend, and we could all meet there. PJ is not attending as he is teaching.''
  
−
*Laurel and Ramona are working on some changes to customize this with additional fields and boxes for more directed responses
 
  
 +
'''* International Botanical Congress (IBC2011)'''
  
−
Note: It would be better if the feedback box could fill in the relative link automatically from the page.  Is this possible??
+
July 23rd-30th 2011, Melbourne, Australia'''
−
"eg: Refer to URL:    http://www.plantontology.org/index.html "
 
  
−
''Apparently this got broken when it was moved to the new spot on the beta browser. JE is looking at getting it to capture the url of the current page being viewed.''
+
Registration is open- deadline for abstracts: 31 October 2010,  [http://www.ibc2011.com/Dates.htm Important dates]
  
  
−
''No new news on this to report.''
+
Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.  
  
 +
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.
  
 +
Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?
  
 +
Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and '''must submit abstracts by October 31st'''. Three additional speakers will be chosen from abstracts that are submitted.
  
  
 +
''Ramona and Pankaj will switch talks, so that Pankaj gives the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona gives the talk on the Plant Ontology.''
  
  
−
Announcement for Plant Sciences Bulletin: Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10
 
  
−
Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ mid September.
 
  
−
Ramona will follow up with Dennis and see what the status of this is.
+
===Next meeting scheduled for: ''' Weds, Sept 22nd, 10am PDT===

Latest revision as of 19:55, 20 September 2010

POC meeting, Webex Conference Call; Date: Sept 15th, 2010 10am (PDT)

In attendance:

POC members: Laurel Cooper, Alejandra Gandolfo, Justin Preece, Justin Elser, Ramona Walls, Pankaj Jaiswal.

Absent: Chris Mungal, Dennis Stevenson, Barry Smith.

Collaborators: none


Acceptance of the minutes from the 9-8-10 meeting? No changes or additions.


Status and Update of Progress: PO Release

Items Arising from reviews, as of 9/14/2010:

From Paula Rudell, Kew Gardens

Flower; PO: 0009046 [A heterosporangiate strobilus, typically consisting of androecium, gynoecium, usually surrounded by a perianth and borne on an axis or receptacle. ]

New SF tracker for this term flower

Proposed Def'n: A determinate shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part. Comment: may have as part one or more petals, sepals or tepals.

This should be a 'child of shoot system', rather than part_of inflorescence (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence),

  • Also note that we need to add a inflorescence has_part flower .


perhaps we should have a reproductive shoot system? (which is a term we don't have at the moment).

New proposed definition: A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part.

Comment: may have as part one or more petals, sepals or tepals. May contain pistillode or staminode or other aborted organs that don't show up in mature form.

Need to look at terms like lemma, palea, lodicule and nectary for next round of revisions.


From Farshid Ahrestani (Columbia, TraitNet) Ramona responded to him that we agree that the terms he requested should be added to the ontology, but due to time constraints, we will not be adding any new terms to this release, but we will aim to add them before the next release.

  • Will correct seed coat part_of plant tissue and add wood as synonym for secondary xylem for this release.


Seed coat is not part_of plant tissue, but is_a, which is correct, so no need to fix it.

Re. definition of secondary xylem: should add that it develops from vascular cambium, and add develops_from relation. Fix typo in comment (tress). SF tracker: secondary xylem


Rich Zobel (Root terms)

We have an open term request root terms from Rich Zobel from last November. We requested Rich's help with the review process, so it makes sense to deal with the open tracker.

There are a couple of upper level term that need to be added: 'basal root' (along with its child: 'non-pericyclic basal root') Modification of 'shoot borne root (PO: 0000042) and taproot/primary root (PO:0000042).

It should be possible to incorporate these changes into this release, (depending upon the amount of discussion generated). The essential issues are that there are 3 distinct types of roots: basal roots, shoot-borne roots, and taproot (primary root)

1. new term 'basal root'. I looked around in the literature and this is being used. We will have to work on the definition though. Seems pretty straightforward, also suggested a child term: 'non-pericyclic basal root')

2. Change name of primary root (PO:0000042) to 'taproot'. This one I am not too sure about- is the primary root always a taproot? What about in the grasses? I propose we leave this as is for now and keep taproot as a synonym.

Should it be 'tap root' or 'taproot'? It is used both ways.

3.'shoot-borne root- addition of hyphen, problem with the synonym 'adventitious'- too broad. seems pretty straightforward.

LC opened individual SF trackers for each of these.


We will add basal root as new term. New proposed definition: A root that develops from one of the of hypocotyl (which layer?) or "A root that arises from a part of the hypocotyl" ?. Will deal with synonyms and child terms of basal root in next round of revisions.

Decided to leave primary root named as is for now, keeping tap root as synonym, but will seek more outside input into what the best name should be. Will add comment: Is often the central axis of the root system.

Okay to add hyphen to shoot-borne root. Should add hyphens to other -borne terms in the ontology for consistency. We felt that adventitious root should not be a synonym, because some basal roots may be adventitious roots. Need to give adventitious roots further consideration, and maybe add as its own term for next round of revisions.

PJ: We also should discuss root terms with Phil Benfey (Duke) and Leon Kochian (Cornell). They are developing software for root type recognition. Should work to integrate PO with their software. Don't know if Rich is involved in discussions with them.


Naama Menda (tuber terms)

Naama's response:

NM:"I think the new hierarchy is better than the previous one (branch vs shoot). The child terms in the tuber node seem complete to me, at least from looking at the features that are being evaluated by the potato breeders community (mostly tuber skin, flesh, eyes)"


NM: subterranean tuber axillary vegetative bud (PO:0025042): the term 'sprout' is often used by potato breeders. One example is the trait 'heat sprout rating' which measures new sprouts on the tuber. These range from 'swollen eyes' to 'chain tubers'. I'm not sure if 'tuber sprout' should be a synonym or a child term (develops from the axillary vegetative bud)"

The 'sprouts' are buds (eyes) that begin to grow. Since they actually develop from an existing axillary vegetative bud, perhaps the term 'sprout' is more like a shoot than a bud? If so, they perhaps they should be an axillary shoot (PO:0006343)? Or maybe we need a new term 'subterranean tuber axillary shoot' ?


Can have swollen eye as synonym of tuber axillary bud. Sprout should be added a synonym of axillary shoot or better yet, add new term subterranean tuber axillary shoot.

Link to SF tracker for request for new term subterranean tuber axillary shoot


NM: "tuber epidermis and tuber periderm: 'potato skin' is a synonym for both terms. I see the clarification in the comment field, but I think it would be clearer to have a synonym of 'mature potato tuber skin' and 'young potato tuber skin'. Queries using 'potato skin' should still pick up both terms".


We agreed this is a good suggestion, and will fix.


NM: "Are any plans to add tuber developmental and growth stages to PO? Currently this is the only portion I think is missing from the ontology. Data we have from potato breeders usually refers to fully mature tubers, but molecular biologist do look at gene expression during different growth stages". (See below under Priorities for next round of revisions)


Alejandra will follow up with Gar Rothwell

Waiting for response from Gar Rothwell and Peter Linder. MAG will copy responses to po-discuss.



Annotations that have no term associated with them

-There are 10 terms that have been obsoleted from this version of the PO.

PO:0025003 compound plant organ

PO:0025002 simple plant organ

(These two were never in the live version, so they were actually destroyed, not obsoleted)

PO:0009014 dermal tissue

PO:0000057 inflorescence bud

PO:0000058 vegetative bud

PO:0008034 leaf whorl

PO:0008037 seedling

PO:0009004 gametophyte

PO:0009003 sporophyte

PO:0000056 floral bud


Only the last 5 of them are problematic: leaf whorl, seedling, gametophyte, sporophyte and floral bud.


PO:0008034 leaf whorl

  • Annotations: 15,802, from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022

Response from TAIR (Tanya Berardini 8/16/10): -suggestion is fine, annotations should move if replacement term is in OBO stanza- it is.


PO:0008037: seedling

  • 16 annotations from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to seedling growth stage (PO:0007131) in PGDSO and also to whole plant (PO:0000003)in PSO.

Response from TAIR (Tanya Berardini 8/16/10):- suggestions are fine, annotations should move if replacement term is in OBO stanza

Laurel will add the consider relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.



PO:0009003: sporophyte

  • 1 annotation from: 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to sporophytic growth phase (PO:0028002) in PGDSO and also to whole plant (PO:0000003)in PSO.

Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotation should move if replacement term is in OBO stanza

Laurel will add the consider relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.


Yes -- these annotations should also be attached to whole plant.


  • 116 annotations from 'po_anatomy_gene_oryza_gramene.assoc' and 'po_anatomy_qtl_oryza_gramene.assoc'

Source: Gramene

Suggested that the associations for genes be moved to PO:0000003 whole plant, plus sporophytic growth phase (PO:0028002) for genes;

Seedling vigor QTLs are already associated with PO:0007131 seedling growth, suggested adding association to whole plant PO:0000003 as well, if appropriate



PO:0009004 gametophyte

  • 1 annotation from 'po_anatomy_gene_oryza_gramene.assoc'

Source: Gramene

Suggested that this association be moved to male gametophyte (PO:0020091) or female gametophyte (PO:00290092) or to gametophytic phase (PO:0028003) and/or to to whole plant PO:0000003

Note: It is already associated with the megagametophytic stage (PO:000721)Note: This appears to be an error and pollen developmental stage (PO:0001007) in the PDGSO.

Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).


PO:0000056: floral bud

  • 54 annotations from: po_anatomy_gene_arabidopsis_tair.assoc

Source: TAIR

Question from TAIR (Tanya Berardini@ TAIR 8/16/10)

"Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful. I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both."

This was discussed at the 9-8-10 meeting. All those present felt it was preferable to keep the current structure for floral bud. For more detailed information and graphics, please see the [Summary of Changes] page We were concerned about instituting a policy of changing the ontology, unless the change is biologically appropriate.

Response: TB: "The PO suggestion "...to move the annotations to both axillary floral bud and terminal floral bud, if that is appropriate. " is not necessarily practical as this information is not always available and I would be reluctant to move the annotations to the child terms if I wasn't sure that these were correct."


In order to get a better understanding of the issue, Laurel went through the annotations associated with the term 'floral bud' and looked at each paper to see how they describe the plant tissue samples. Most of them refer to "floral bud", "flower bud", or simply "buds". In a few cases they seem to be referring to the whole inflorescence.

In light of this, we need to reopen the discussion of the bud structure and will reexamine these terms.


We had some discussion of bud terms. Since all floral buds are at the end of a shoot (since they are determinate) they should all be terminal buds, but then those terminal buds can arise either at the end of a shoot or in an axil. Pankaj and Lol will work on sketching new structures for bud terms that includes the categories reproductive bud and floral bud. Will re-open SF tracker so we can work on this more.

Annotation File formats

We have had a question from Tanya Berardini@TAIR about whether or not we are planning to transition to the GAF 2.0 format or not.

GAF 2.0

This will affect how they modify the above files


Should we get one and test it first? Will it matter if there are some in GAF 1.0 and some in 2.0?

Maybe a goal for the next version?


Lol talked to Justin and Chris before meeting, and they say new format should work fine, so TAIR can send us the files in GAF 2.0

Priorities for the Next Round of Revisions

-Merging the plant structure and plant developmental stages ontologies

-Adding Musa terms requested by Rosemary Shrestha

-Root terms- Rich Zobel

-Legume terms submitted by Austin Mast

-New terms requested by reviewers (from Ahrestani and Kramer)

-is_a parents for remaining terms (will require work on upper level structure for non-material entities)

-convert to intersection_of relations?

-work on PGDSO

-tuber growth and development stages, open on SF since 6/2009

-add links to more images

-Others??- PJ: Lol and Ramona will focus more on adding annotations (~50% of time)


-What is the target date for the next release?

Other Items:

Alejandra has the first set of images ready to load onto PlantSystematic.org. Alejandra, her technician, and Ramona (and anyone else who is interested) will try to meet by phone next week to go over the progress.


A. Feedback page on Beta site fixed

Justin Elser fixed refer_to_url variable on the feedback page for the beta site. It is now working from within the AmiGO browser. Now it will capture the url of the page the person is looking at. Thanks Justin!


B. Announcement for Plant Sciences Bulletin: Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10

Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ end of September.

Ramona will follow up with Dennis after he gets back to see what the status of this is.


C. POC meeting to be held at NYBG in fall 2010. Date TBD.

Should we invite outside experts, scientists, students and postdocs?

Please fill out Doodle Poll re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg

We need to pick a date for this meeting ASAP so folks who are flying in can get tickets


Pankaj will check his calender to see if this is possible. Ramona will follow up with Dennis when he returns.

Upcoming meetings 2010-2011:

  • Latin American Congress of Botany

LACB. La Serena, Chile, October 4-10;

Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.


* Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html


*Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010.

Lol and Ramona should plan on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Perhaps Dennis and Alejandra could also attend, and we could all meet there. PJ is not attending as he is teaching.


* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates


Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.


Ramona and Pankaj will switch talks, so that Pankaj gives the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona gives the talk on the Plant Ontology.



Next meeting scheduled for: Weds, Sept 22nd, 10am PDT
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