Difference between revisions of "POC Conf. Call 8-2-11"

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In attendance:  
 
In attendance:  
  
−
POC members:   
+
POC members:  Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)
  
−
Absent:
+
Absent: Pankaj Jaiswal (OSU), Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)
  
−
Collaborators:  
+
Collaborators: none
  
  
−
Acceptance of the minutes from the [[POC_Conf._Call_7-19-11]]?
+
Acceptance of the minutes from the [[POC_Conf._Call_7-19-11]]? ''There were no changes, additions, or deletions.''
  
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms] submitted by Austin Mast==
+
=Conference/Meetings updates:=
 +
==IBC 2011, Melbourne, Australia==
 +
The POC hosted the [[IBC_2011_Bio-Ontologies_Symposium]] on Thursday, July 28th.
  
−
Remaining:
+
The PO and our symposium (and the MaizeCyc database) were publicized in the [http://www.ibc2011.com/downloads/news/IBC%202011%20Congress%20News%20Thursday%2028%20July%20WEB.pdf conference newspaper].
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===
+
Both PJ and MAG had their research mentioned during the plenary lectures!
  
−
Last week, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.  
+
Throughout the meeting, RW and DWS spoke to a number of people from the plant systematics community who are interested in potential uses of the PO.
  
−
====Background:====
+
''PO will also look into collaboration with/tagging terms in JStor Plant Science. See page for [[Jstor_Herbarium_annotations]]''
  
−
Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:
+
''Talked to Rudi Appels about using PO terms for wheat gene expression data. See page for [[Wheat_Gene_Catalogue]]''
  
−
"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."
+
''Bruce Kirchoff would like to have a conference call with POC to discuss image annotation.''
  
 +
''Should follow up on the interest from the person in Melbourne setting up a Plant Phenomics center- PJ should know the name''
  
−
The main reference people cite for phyllodes is: '''D.R. Kaplan 1980''', Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.
+
==ICBO, 2011, Buffalo, NY==
 +
'''ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011  Buffalo, New York  [http://icbo.buffalo.edu ICBO]
  
−
Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."
+
-LC presented the Plant Ontology on Thursday, July 28th, 3:40pm in the session:  "Introduction to The OBO Foundry Initiative"
  
 +
Link:  [http://icbo.buffalo.edu/2011ProgramTemplate.pdf ICBO Program]
  
−
'''Some more contemporary uses of the term phyllode:'''
+
July 27 8.30am-4pm: LC co-organized the workshop [http://icbo.buffalo.edu/2011/WorkshopD.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability] and the OBO to OWL workshop,  along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
  
−
'''Gardner et al. 2005''' (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):
 
  
−
"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), '''the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles'''."
+
LC had many discussions with various groups about ontology interoperability,
  
−
and later in the paper:
+
* [http://icbo.buffalo.edu/ICBO-2011_Proceedings.pdf ICBO proceedings].  This includes all papers from the main conference, conference workshops, and other associated events.
  
−
"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.
+
Link to the slides: [http://icbo.buffalo.edu/2011/slides ICBO slides]
  
−
"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."
+
''CL has obsoleted all their plant cell terms. We should create a subset for them, and look over the plant cell terms and add any that are missing (see notes on last meeting's agenda)''
  
 +
''CM still thinks we should remove "plant" as prefix from term names, but we still feel it is right to keep it. We will be responsible for looking after the plant cell terms. Also, if we want to import terms from other ontologies (like cell from GO), it would cause conflicts if they have the same name.''
  
−
'''Leroy and Heuret 2007''' (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by '''a type of foliar organ''' called a phyllode." and "...the different transitional forms range from pinnate leaves to phyllodes..." 
+
''The presentation for OBO Foundry acceptance went well. No one brought up any objections to LC. OBO Foundry is working to schedule a meeting in Europe (probably England) in the fall. Ontologies will make a presentation similar to ICBO, followed by a review by the OBO Foundry committee.  Would be good (but not absolutely necessary) if someone form PO could go.''
  
−
'''See fig. 1 in this paper.''' They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.
+
''The letter for OBO Foundry acceptance is still under work. Some presenters at ICBO (not PO) misunderstood the principles of Collaboration and Locus of Authority. Have been clarified on the OBO Foundry page, so we can use the wording from there in the letter. Will take up after ASPB meeting''
  
 +
=MaizeGDB mappings for Annotations=
  
−
'''Yang et al. 2008''' (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.
+
*See also collaborator page: [[Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011]] for details from the 8-4-11 conference call.
  
 +
Mary Schaeffer of MaizeGDB is preparing a large number of annotations to our terms from a large microarray data set.  As part of that, she has prepared a mapping between the samples in the studies and our terms.  We need to look these over and make sure they make sense. 
  
−
'''Forster and Bonser 2009''', Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."
+
[[File:Maize_Atlas2011.pdf‎]]
  
 +
''How will PO users be able to access the comments in Mary's mapping file? There is not space for them in the annotation file. Each annotation links back to the contributor's page for the gene. Can they also link back to the rows of their mapping spread sheet? (RW: or does it make more sense for the link to be from the PO structure or growth stage term?''
  
−
RW did not find any contemporary papers that said that a phyllode is a petiole.
+
''BS: There is software available that will convert each row of a spreadsheet to a web page, making it easy to convert their mappings to links from PO.''
  
−
Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.
+
''Here is the link to their tissue pages: [http://www.maizegdb.org/cgi-bin/termdoclist.cgi?ref=9021423&type=32466 Maize Developmental Gene Atlas]''
  
−
'''Unifacial leaf''' as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311). Might be better to make a parent term '''ensiform leaf''' which has children phyllode and unifacial leaf.
+
''There is a page for each tissue, for example: [http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=2366347 anthers R1 B73], with links to the PO terms and photos''
  
−
====Proposed terms and definitions:====
+
''Use of column 16: Not completely clear what they want to use it for. Have to make sure it doesn't interfere with our plan to use it adding annotations for vascular/non-vascular leaves for similar.''
  
−
'''ensiform leaf''': A vascular leaf that has increased activity of the adaxial meristem early in development, leading to abscense of an abaxial surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)
+
''There are different ways to describe growth stages if they both map to the same PO term, then they should just be added a synonyms to the PO term, rather than going into column 16.''
  
−
Comment: Common in many monocots and some dicots. An ensiform leaf may be round in cross-section (unifacial) or it may be laminar, in which case lamina development is in a median plane  (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Ensiform leaves are often bifacial at the leaf base.
+
''There was also some question about the significance cutoff they are using, and how to convey that to users. Maybe MaizeGDB can create a page showing the methods they used. This question also came up for the Physco data. Not every experiment needs to use the same methods, but we need to have a page that explains what statistical tools were used for any experiment.''
  
−
synonym: unifacial leaf
 
  
 +
Action: We are working on setting up a [[Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011]] with Mary Schaffer to discuss the mappings and how the information can be presented.
  
−
'''phyllode:''' An adult ensiform leaf with a lamina that develops in a median plane  (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout the length of the leaf.
+
We should deal with these SF requests from them as well:
  
−
Comment: Common in legumes of the genus Acacia. Similar development occurs in some monocot leaves, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, transitional phyllode-type leaf). In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not. Phyllodes are generally xeromorphic.
+
==PAO terms for MaizeGDB==
  
−
is_a vascular leaf, is_a adult leaf (unless we add a term adult vascular leaf)
+
===[http://sourceforge.net/tracker/?func=detail&aid=3324058&group_id=76834&atid=835555 transition leaf - definition]===
  
 +
From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf.
  
−
'''phyllode-type transition leaf:''' A transitional vascular leaf in which the basal portion of the leaf has lamina development is a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.
+
For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf.  
  
−
Comment: Common in seedlings of legumes of the genus Acacia.
+
Provided by Erin Irish, who references this paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.
−
 
 
−
is_a transitional leaf, is_a vascular leaf
 
  
 +
'''Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf:''' Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenile and adult tissues, as in Brachypodium.
  
 +
Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.
  
−
 
+
''It is okay to add the comment. Fix grammar. Should say "stalk (stem)" for maize instead of "stem", because maize researchers use the term stalk.''
−
 
 
−
 
 
−
 
 
−
==Maize GDB==
 
−
 
 
−
===[http://sourceforge.net/tracker/?func=detail&aid=3324058&group_id=76834&atid=835555 transition leaf - definition]===
 
−
 
 
−
From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf. For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf. Provided by Erin Irish, who references t his paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.
 
−
 
 
−
'''Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf:''' Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenille and adult tissues, as in Brachypodium.
 
−
 
 
−
Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.
 
  
 
===[http://sourceforge.net/tracker/?func=detail&aid=3356716&group_id=76834&atid=835555 leaf base]===
 
===[http://sourceforge.net/tracker/?func=detail&aid=3356716&group_id=76834&atid=835555 leaf base]===
Line 106: Line 104:
  
 
I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.
 
I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.
 +
 +
''We should check with her during the conference call to make sure everything is clear about how to annotate the parts of the leaf.''
  
 
===[http://sourceforge.net/tracker/?func=detail&aid=3357921&group_id=76834&atid=835555 style, silk, Poaceae style]===
 
===[http://sourceforge.net/tracker/?func=detail&aid=3357921&group_id=76834&atid=835555 style, silk, Poaceae style]===
Line 124: Line 124:
 
28 terms in PAO with Zea in the name.
 
28 terms in PAO with Zea in the name.
  
−
Only on Poaceae terms in PGDSO, and it is on today's agenda to merge with another term.
+
Only one Poaceae term in PGDSO (PO:0007012 Poaceae inflorescence visible), and there is a [http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 Source Forge item] requesting that we merge it with another term.
 +
 
 +
''We need to be careful about merging terms to ensure that partonomy remains consistent and doesn't cause conflicts among taxa.''
 +
 
 +
''We should begin by looking at the terms in Mary's mapping spread sheet to see which ones need to be done first. We can at least begin by merging the terms needed for their current annotations.''
 +
 
 +
''RW will go over the spread sheet, and make some notes on the [[Eliminating Zea/Poaceae terms from PO]] page.  Can at least see what the ramifications are of making the specific changes she requested.''
 +
 
 +
''Comments from BS: problems with combinatorial explosion of terms if you try to add species-specific terms for every organism. Can be problems if you don't know what structures are homologous.  Should keep working on being a species-neutral reference ontology, but create synonyms and slims for organisms as needed.''
 +
 
 +
''RW: later: maybe conflict with Poaceae/Asteraceae floret was due to the old use of the part_of relation to mean either part_of or has_part. Now that we have clarified that part_of means only part_of, that might not be a problem.''
 +
 
 +
==PGDSO terms for MaizeGDB==
 +
We can discuss these items, if time allows.
 +
 
 +
See: [[Items_for_future_meetings#Maize_GDB]]
  
 
=Upcoming meetings 2011:=
 
=Upcoming meetings 2011:=
Line 140: Line 155:
  
  
−
* '''POC Meeting at New York Botanic Garden'''  Tentative dates, Sept 9th-11th, 2011
+
* '''POC Meeting at New York Botanic Garden'''  Tentative dates, Sept 10th-11th, 2011
  
 
DWS will look into booking the apartments at the NYBG for accommodations.
 
DWS will look into booking the apartments at the NYBG for accommodations.
  
−
''We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11.  DWS, PJ, BS, LC, and RW can make it. Need to find out if MAG can attend.''
+
''We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11.  DWS, PJ, BS, LC, MAG and RW can make it.''
 +
 
 +
RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.
 +
 
 +
''BS suggested that we should have a public lecture at the garden at some point. Perhaps it could be part of the public lecture series that is already held at the garden.''
 +
 
 +
''Maybe we could have some of the more plant-biology oriented parts of the meeting at the end, so Barry could leave earlier if necessary.''
 +
 
 +
''LC may stay in NYC until Monday, and host the presentation for Physco from the NYBG.''
 +
 
 +
''Probably start the first day talking about the PGDSO, then go from there.''
  
−
''RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.''
+
See: [[POC Meeting at NYBG; Sept 10th-11th, 2011]]
  
−
=Next meeting scheduled for Tuesday, Aug 16th, 2011 at 10am PDT/1pm EDT=
+
=Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT=

Latest revision as of 19:37, 8 March 2012

POC meeting, Webex Conference Call; Date: Tuesday Aug 2nd, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)

Absent: Pankaj Jaiswal (OSU), Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none


Acceptance of the minutes from the POC_Conf._Call_7-19-11? There were no changes, additions, or deletions.


Conference/Meetings updates:

IBC 2011, Melbourne, Australia

The POC hosted the IBC_2011_Bio-Ontologies_Symposium on Thursday, July 28th.

The PO and our symposium (and the MaizeCyc database) were publicized in the conference newspaper.

Both PJ and MAG had their research mentioned during the plenary lectures!

Throughout the meeting, RW and DWS spoke to a number of people from the plant systematics community who are interested in potential uses of the PO.

PO will also look into collaboration with/tagging terms in JStor Plant Science. See page for Jstor_Herbarium_annotations

Talked to Rudi Appels about using PO terms for wheat gene expression data. See page for Wheat_Gene_Catalogue

Bruce Kirchoff would like to have a conference call with POC to discuss image annotation.

Should follow up on the interest from the person in Melbourne setting up a Plant Phenomics center- PJ should know the name

ICBO, 2011, Buffalo, NY

ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York ICBO

-LC presented the Plant Ontology on Thursday, July 28th, 3:40pm in the session: "Introduction to The OBO Foundry Initiative"

Link: ICBO Program

July 27 8.30am-4pm: LC co-organized the workshop "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability and the OBO to OWL workshop, along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.


LC had many discussions with various groups about ontology interoperability,

  • ICBO proceedings. This includes all papers from the main conference, conference workshops, and other associated events.

Link to the slides: ICBO slides

CL has obsoleted all their plant cell terms. We should create a subset for them, and look over the plant cell terms and add any that are missing (see notes on last meeting's agenda)

CM still thinks we should remove "plant" as prefix from term names, but we still feel it is right to keep it. We will be responsible for looking after the plant cell terms. Also, if we want to import terms from other ontologies (like cell from GO), it would cause conflicts if they have the same name.

The presentation for OBO Foundry acceptance went well. No one brought up any objections to LC. OBO Foundry is working to schedule a meeting in Europe (probably England) in the fall. Ontologies will make a presentation similar to ICBO, followed by a review by the OBO Foundry committee. Would be good (but not absolutely necessary) if someone form PO could go.

The letter for OBO Foundry acceptance is still under work. Some presenters at ICBO (not PO) misunderstood the principles of Collaboration and Locus of Authority. Have been clarified on the OBO Foundry page, so we can use the wording from there in the letter. Will take up after ASPB meeting

MaizeGDB mappings for Annotations

Mary Schaeffer of MaizeGDB is preparing a large number of annotations to our terms from a large microarray data set. As part of that, she has prepared a mapping between the samples in the studies and our terms. We need to look these over and make sure they make sense.

File:Maize Atlas2011.pdf

How will PO users be able to access the comments in Mary's mapping file? There is not space for them in the annotation file. Each annotation links back to the contributor's page for the gene. Can they also link back to the rows of their mapping spread sheet? (RW: or does it make more sense for the link to be from the PO structure or growth stage term?

BS: There is software available that will convert each row of a spreadsheet to a web page, making it easy to convert their mappings to links from PO.

Here is the link to their tissue pages: Maize Developmental Gene Atlas

There is a page for each tissue, for example: anthers R1 B73, with links to the PO terms and photos

Use of column 16: Not completely clear what they want to use it for. Have to make sure it doesn't interfere with our plan to use it adding annotations for vascular/non-vascular leaves for similar.

There are different ways to describe growth stages if they both map to the same PO term, then they should just be added a synonyms to the PO term, rather than going into column 16.

There was also some question about the significance cutoff they are using, and how to convey that to users. Maybe MaizeGDB can create a page showing the methods they used. This question also came up for the Physco data. Not every experiment needs to use the same methods, but we need to have a page that explains what statistical tools were used for any experiment.


Action: We are working on setting up a Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011 with Mary Schaffer to discuss the mappings and how the information can be presented.

We should deal with these SF requests from them as well:

PAO terms for MaizeGDB

transition leaf - definition

From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf.

For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf.

Provided by Erin Irish, who references this paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.

Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf: Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenile and adult tissues, as in Brachypodium.

Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.

It is okay to add the comment. Fix grammar. Should say "stalk (stem)" for maize instead of "stem", because maize researchers use the term stalk.

leaf base

See tracker item for details.

I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.

We should check with her during the conference call to make sure everything is clear about how to annotate the parts of the leaf.

style, silk, Poaceae style

From Mary at MaizeGDB: Suggest that you merge these, keeping style, obsoleting silk and Poaceae style. Do the same for other floral parts that have a species spin on them, but are really the same as other more generic names for flower parts.

From PJ: Poaceae / Zea was necessary in some terms because often detail structures referred to parts of tassel/ear floret and it has conflict with floret compositeae besides the spatial aspects.


Rather than working on this piecemeal, we need to have an organized approach to eliminating the Poacaeae/Zea terms. Need to look at the structure from the top down and ensure part_of relations remain correct. Do we want to allocate time to this now or wait for next release?

See page for Eliminating Zea/Poaceae terms from PO

42 terms in PAO with Poaceae in the name.

28 terms in PAO with Zea in the name.

Only one Poaceae term in PGDSO (PO:0007012 Poaceae inflorescence visible), and there is a Source Forge item requesting that we merge it with another term.

We need to be careful about merging terms to ensure that partonomy remains consistent and doesn't cause conflicts among taxa.

We should begin by looking at the terms in Mary's mapping spread sheet to see which ones need to be done first. We can at least begin by merging the terms needed for their current annotations.

RW will go over the spread sheet, and make some notes on the Eliminating Zea/Poaceae terms from PO page. Can at least see what the ramifications are of making the specific changes she requested.

Comments from BS: problems with combinatorial explosion of terms if you try to add species-specific terms for every organism. Can be problems if you don't know what structures are homologous. Should keep working on being a species-neutral reference ontology, but create synonyms and slims for organisms as needed.

RW: later: maybe conflict with Poaceae/Asteraceae floret was due to the old use of the part_of relation to mean either part_of or has_part. Now that we have clarified that part_of means only part_of, that might not be a problem.

PGDSO terms for MaizeGDB

We can discuss these items, if time allows.

See: Items_for_future_meetings#Maize_GDB

Upcoming meetings 2011:

  • Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Gramene and Plant Ontology are hosting a Data Curation Workshop again, focusing on pathway curations.

LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Plant_Biology_2011_Outreach_Booth and we are invited to take part. We are hosting the website.


  • POC Meeting at New York Botanic Garden Tentative dates, Sept 10th-11th, 2011

DWS will look into booking the apartments at the NYBG for accommodations.

We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11. DWS, PJ, BS, LC, MAG and RW can make it.

RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.

BS suggested that we should have a public lecture at the garden at some point. Perhaps it could be part of the public lecture series that is already held at the garden.

Maybe we could have some of the more plant-biology oriented parts of the meeting at the end, so Barry could leave earlier if necessary.

LC may stay in NYC until Monday, and host the presentation for Physco from the NYBG.

Probably start the first day talking about the PGDSO, then go from there.

See: POC Meeting at NYBG; Sept 10th-11th, 2011

Next meeting scheduled for Tuesday, Aug 23rd, 2011 at 10am PDT/1pm EDT

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