Difference between revisions of "POC Conf. Call 2-14-12"

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In attendance:
 
In attendance:
  
−
POC members:
+
POC members: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)''
−
 
 
−
Absent:
 
  
 +
Absent: ''Pankaj Jaiswal (OSU),  Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab) ''
  
 
Collaborators: none
 
Collaborators: none
  
  
−
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12?
+
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12? ''none''
  
−
Back to [[POC Meetings Minutes]]
+
Back to [[POC Meetings Minutes]]
  
 
=News and Report from the Wood Ontology Meeting:=
 
=News and Report from the Wood Ontology Meeting:=
  
−
=Items carried over from last meeting:=
+
''This discussion was postponed until PJ was present.''
−
==Vascular tissues and cell types==
+
 
 +
We had a successful meeting last week at the NYBG with the group of wood experts we invited. 
 +
 
 +
* Link to the [[Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda]]
 +
 
 +
*Overall objective was to raise awareness and encourage the wood research community to get involved with the development and use of the Plant Ontology
 +
 
 +
'''Specific Goals with links to the pages:'''
 +
 
 +
To develop PO terms and definitions to describe:
 +
 
 +
1. Wood structures (PAE branch of PO) [[Goal_1._Anatomical_Entities]]
 +
 
 +
2. Stages of wood development (PSDS branch of PO) [[Goal_2._Plant_Structure_Development_Stages]]
 +
 
 +
3. Wood qualities and phenotypes (to go into TO and/or PATO) [[Goal_3._Wood_qualities_and_phenotypes]]
 +
 
 +
4. To obtain association data linked to the PO terms to be hosted in our database [[Developing_and_incorporating_new_annotations_for_woody_plants]]
 +
 
 +
* Links to flash presentations by all the participants:
 +
 
 +
[[Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda#2:00PM-2:45PM_Flash_talks_by_participants]]
 +
 
 +
*Link to wrap up and action items:  [[Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda#10:40AM-11:20PM_Wrap_up]]
 +
 
 +
==Questions Arising from the the Workshop==
 +
 
 +
* How is the best way to redirect users to terms that are in GO?  For example; casparian strip or pit membranes? 
 +
 
 +
Added a note to the AmiGO2 wish list [[POC_Technical_Issues_Page#AmiGo_2_Wishlist:]] for a means of redirection. 
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, mid vein]===
+
''One possibility is to have a PO slim in GO that could load with PO. This could cause problems with keeping the slim up to date. We could load the slim without GO annotations.''
 +
 
 +
''JP suggested that maybe we could incorporate a look-up service, so that when a search fails for PO terms, it automatically searches other ontologies.''
 +
 
 +
''BS suggested that we should keep track of people's searches on the PO web page, so we can add new terms that people are searching for.''
 +
 
 +
''There has been no activity on AmiGO revisions lately. In the interim, are we planning to upgrade to an intermediate version of AmiGO. It may not be worth it to have to modify AmiGO twice for PO.''
 +
 
 +
''The search function does not have to wait for AmiGO 2. The search takes you into AmiGO, but it is a separate chunk of code.''
 +
 
 +
* How are we going to deal with terms that contain adjectives; such as 'storied cambium', 'early wood', 'late wood' etc?  These are commonly used terms in this community and we need them.
 +
 
 +
''BS raised the concern that having terms with adjectives can cause problems with multiple inheritance -- two different ways of classifying wood leads to two different parents. Suggest that we put all the adjectives in a phenotype ontology to which we can refer.''
 +
 
 +
''However, there are instances where the terms need to be in the PO, particularly for adjectives that are used only for particular plant structures (like epigynous flower). On the other hand, some adjectives can be used for many different structures (like variegated), and terms like "variegated leaf" probably shouldn't go in the PO. Adjectives like "storied" are somewhere in between -- it can apply multiple tissue types, but not hundreds of them. We will need to examine these terms on a case by case basis.''
 +
 
 +
''BS, best practice: Terms like "septate" should go into PATO, and we include terms for fiber types and instruct people how to post compose terms as they need them. Some communities would eventually create compound terms like "septate phloem fiber", but they will not live in PO.''
 +
 
 +
''We will probably not be able to live up to this best practice, but at a minimum, when we do add terms with synonyms, we should introduce the synonym into PATO and add xrefs to them.''
 +
 
 +
''Note, latewood and earlywood should be one word.''
 +
 
 +
 
 +
* How do we want to approach the TO terms, since this is a complex area and officially outside the mandate of the PO? 
 +
 
 +
Where does this fit into our list of top priorities?? ''Discussion of this question was postponed.''
 +
 
 +
=Revisions of existing terms:=
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, mid vein]==
  
 
''These changes have already been made in the dev file.''  
 
''These changes have already been made in the dev file.''  
Line 33: Line 89:
  
 
synonym: leaf lamina vascular bundle
 
synonym: leaf lamina vascular bundle
 +
 +
''Changes are okay. We also need a term for petiole vascular bundle.''
  
 
* Proposed new term: '''primary leaf vein (PO:0025413)'''
 
* Proposed new term: '''primary leaf vein (PO:0025413)'''
  
−
proposed def'n: A leaf (lamina) vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
+
proposed def'n: A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
  
−
Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.
+
Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the leaf midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.
 +
 
 +
''okay''
  
  
 
*'''midvein (PO:0020139)'''
 
*'''midvein (PO:0020139)'''
  
−
'''revised def.:''' A primary (leaf) vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
+
'''revised def.:''' A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
  
 
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).
 
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).
Line 50: Line 110:
  
  
−
''We already have terms for secondary, tertiary, quaternary, and higher order veins. Do we want to make their naming consistent with the changes suggested above for primary leaf vein?''
+
''Rename "leaf midvein".''
 +
 
 +
''We already have terms for secondary, tertiary, quaternary, and higher order veins. Do we want to make their naming consistent with the changes suggested above for primary leaf vein? --Yes!''
  
 
==[https://sourceforge.net/tracker/?func=detail&aid=3481640&group_id=76834&atid=835555 PO terms for lateral meristems]==
 
==[https://sourceforge.net/tracker/?func=detail&aid=3481640&group_id=76834&atid=835555 PO terms for lateral meristems]==
Line 67: Line 129:
  
 
comment: Participates in lateral growth (request has been made for lateral growth in GO) of a plant organ, primarily shoot axes (PO:0025029) and roots (PO:0009005). Contrast with apical meristem (PO:0020144).
 
comment: Participates in lateral growth (request has been made for lateral growth in GO) of a plant organ, primarily shoot axes (PO:0025029) and roots (PO:0009005). Contrast with apical meristem (PO:0020144).
 +
 +
''New proposed def.: A portion of meristem (PO:0009013) tissue located parallel to the sides of a plant axis (PO:0025004), the cells of which undergo periclinal and anticlinal (tangential?) division.''
 +
 +
''New comment: Participates in lateral growth (request has been made for lateral growth in GO) of a  shoot axis (PO:0025029) or root (PO:0009005), leading to an increase in the cross-sectional area. Contrast with apical meristem (PO:0020144) or intercalary meristem (PO:0006073).''
 +
 +
''Add lateral meristem part_of plant axis.''
 +
 +
''May want to add periclinal, anticlinal cell division to GO (or maybe just add periclinal and anticlinal to PATO).''
 +
 +
''Definition of intercalary meristem need a little work too, to distinguish it from lateral meristem.''
  
  
Line 77: Line 149:
 
''Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it was defined.''
 
''Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it was defined.''
  
 +
 +
''New proposed def.: A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.''
 +
 +
''Also need to add term for cambial zone, is a cardinal organ part.''
  
  
Line 86: Line 162:
  
 
''Got rid of relation vascular cambium part_of vascular bundle.''
 
''Got rid of relation vascular cambium part_of vascular bundle.''
 +
 +
''No one likes "gives off" or "girth".''
 +
 +
''New proposed comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).''
  
  
 
'''cork cambium/phellogen (PO:0005599)'''
 
'''cork cambium/phellogen (PO:0005599)'''
  
−
'''revised def'n:''' A cambium (PO:0005597) that is part of a shoot axis periderm (PO:0005048) and produces phellem (PO:0004003) and phelloderm (PO:0005050).
+
'''revised def'n:''' A cambium (PO:0005597) that is part of a periderm (PO:0005046) and produces phellem (PO:0004003) and phelloderm (PO:0005050).
  
 
comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.
 
comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.
 +
 +
''Definition okay. Phellogen should change from related synonym to exact synonym.''
  
  
 
'''primary thickening meristem (PO:0005039)'''
 
'''primary thickening meristem (PO:0005039)'''
  
−
Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.  
+
Esau defines it as originating in the apical meristem, but [http://www.jstor.org/stable/4354165 Rudall's review] shows that in some species, it is discontinuous with the SAM.  
  
 
'''revised def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).
 
'''revised def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).
  
 
comment: Contributes to primary thickening of a stem (PO:0009047), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
 
comment: Contributes to primary thickening of a stem (PO:0009047), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
 +
 +
''DWS was skeptical about whether or not the PTM is actually discontinuous with the SAM in some species, but we will leave the comment in for now, since it is described in Rudall's review.''
 +
 +
''Need to add synonyms PTM, meristematic cap, and collar meristem.''
 +
 +
''Definition okay.''
  
  
 
'''secondary thickening meristem (new term)'''
 
'''secondary thickening meristem (new term)'''
  
−
'''proposed def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).
+
'''proposed def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) that is not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).
  
 
comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.
 
comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.
  
 +
''There are also secondary thickening meristems in roots of some monocots (Cheadle 1937, JSTOR:2471543), so this should be lateral meristem, rather than a shoot lateral meristem.''
  
  
Line 123: Line 212:
  
 
Suggest that we also add root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium. Set up root cambium and shoot lateral meristem as XPs, so we don't have multiple inheritance.
 
Suggest that we also add root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium. Set up root cambium and shoot lateral meristem as XPs, so we don't have multiple inheritance.
 +
 +
''DWS will check if there are secondary thickening meristems in some kinds of monocots. In that case, we should leave the general term for root lateral meristem.''
 +
 +
''New proposed def., root lateral meristem: A lateral meristem that is part of a root.''
 +
 +
''This will be an XP of is_a lateral meristem and part_of root. We will make new terms for root vascular cambium and root cork cambium that are subtypes of vascular cambium and cork cambium, respectively, and will be inferred children of root lateral meristem.''
  
  
Line 131: Line 226:
 
There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.  
 
There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.  
  
−
Shoot lateral meristem should be set up as an xp, so subtypes and be inferred, just like root lateral meristem. Same for root meristem and shoot meristem.
+
''Shoot lateral meristem should be set up as an xp, so subtypes and be inferred, just like root lateral meristem. Will create new terms for shoot vascular cambium and shoot cork cambium, as per root terms.''
 +
 
  
 
'''inflorescence lateral meristem (PO:0009105)'''
 
'''inflorescence lateral meristem (PO:0009105)'''
Line 138: Line 234:
  
 
This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.
 
This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.
 +
 +
''revised def: An inflorescence meristem that gives rise to an inflorescence branch.''
  
  
Line 144: Line 242:
 
This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).
 
This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).
  
−
'''revised def'n:''' An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.
+
'''revised def.:''' An inflorescence branch meristem that gives rise to a branch of an ear inflorescence.
 +
 
 +
''okay''
  
 
==Primary and secondary growth, etc.==
 
==Primary and secondary growth, etc.==
Line 203: Line 303:
  
 
==vascular and related cell types==
 
==vascular and related cell types==
−
===Current parent: axial cell===
+
''Postponed for a future meeting.''
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481651&group_id=76834&atid=835555 axial cell]====
 
−
'''axial cell (PO:0000081):''' A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]
 
−
 
 
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
 
−
 
 
−
The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).
 
−
 
 
−
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system (see [[Items for future meetings#other wood terms]])
 
−
 
 
−
===New proposed hierarchy (children of plant cell):===
 
−
 
 
−
plant cell
 
−
 
 
−
>sieve element (new term)
 
−
 
 
−
>>sieve tube member (syn.: sieve tube element)
 
−
 
 
−
>>sieve cell (new term)
 
−
 
 
−
>tracheary element
 
−
 
 
−
>>tracheid
 
−
 
 
−
>>vessel member
 
−
 
 
−
>ground tissue cell (PO:0025030)
 
−
 
 
−
>>sclerenchyma cell (PO:0000077)
 
−
 
 
−
>>>sclerid (new term)
 
−
 
 
−
>>>fiber cell (new term)
 
−
 
 
−
>>>>phloem fiber cell
 
−
 
 
−
>>>>xylem fiber cell
 
−
 
 
−
===New definitions - [https://sourceforge.net/tracker/?func=detail&aid=3481654&group_id=76834&atid=835555 sieve elements]===
 
−
Definitions from Esau's Anatomy of Seed Plants
 
−
 
 
−
'''sieve element (new term)'''
 
−
 
 
−
From Esau (glossary): The cell in the phloem tissue concerned mainly with longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.
 
−
 
 
−
Also from Esau (in text): Their principal morphological characteristics are sieve areas (modified pits) in their walls and the absence of nuclei in mature protoplasts.
 
−
 
 
−
'''proposed def.:''' A plant cell that is part of a portion of phloem tissue, has sieve areas (modified pits) in its walls, and lacks a nucleus in its mature protoplast.
 
−
 
 
−
Comment: Sieve cells function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.
 
−
 
 
−
part_of phloem, participates_in sporophyte stage
 
−
 
 
−
 
 
−
'''sieve cell (new term)'''
 
−
 
 
−
proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.
 
−
 
 
−
Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas. 
 
−
 
 
−
 
 
−
'''sieve tube member (PO:0000289)'''
 
−
 
 
−
'''current def.:''' One of the series of cells that make up a sieve tube; it shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores).
 
−
 
 
−
comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.
 
−
 
 
−
 
 
−
'''proposed def.:''' A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
 
−
 
 
−
Comment: Sieve tube members have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.
 
−
 
 
−
syn.: sieve tube element, sieve tube segment
 
−
 
 
−
part_of sieve tube (new term)
 
−
 
 
−
 
 
−
'''See below for companion cells and other parenchyma cells found in vascular tissue.'''
 
−
 
 
−
====New term for sieve tube====
 
−
 
 
−
'''sieve tube, proposed definition:''' A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.
 
−
 
 
−
Comment: A sieve plate (GO:0097218) is part of a sieve tube member.
 
−
 
 
−
====New terms for GO====
 
−
These subcellular components have been added to GO:
 
−
 
 
−
*GO:0097217 sieve area
 
−
*GO:0097218 sieve plate
 
−
*GO:0097219 compound sieve plate
 
−
*GO:0097220 simple sieve plate
 
−
 
 
−
'''sieve area:''' A cell wall part that is a pit-like area in a plant-type cell wall of a sieve element and has as parts pores lined with callose and occupied by strands of protoplasmic material that interconnect the protoplasts of contiguous sieve elements.
 
−
 
 
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505); part_of sieve element (PO:xxxx) - may have to go in comment
 
−
 
 
−
 
 
−
'''sieve plate:''' A cell wall part that is the part of a wall of a sieve tube member that bears one or more highly specialized sieve areas.
 
−
 
 
−
comment: Typical of angiosperms.
 
−
 
 
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505), has_part sieve area (GO:xxxx); part_of sieve tube member (PO:xxxx).
 
−
 
 
−
Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.
 
−
 
 
−
 
 
−
'''compound sieve plate:''' A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.
 
−
 
 
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
 
−
 
 
−
is_a sieve plate
 
−
 
 
−
 
 
−
'''simple sieve plate:''' A sieve plate that has as part a single specialized sieve area.
 
−
 
 
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3481658&group_id=76834&atid=835555 New definitions - tracheary elements]===
 
−
 
 
−
''These edits are done in the obo file.''
 
−
 
 
−
'''xylem element (PO:0000273):''' A cell making up xylem tissue.
 
−
 
 
−
Currently, this is parent of tracheary element and xylem fiber. I suggest we '''obsolete''' it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber.
 
−
 
 
−
 
 
−
'''tracheary element (PO:0000290)'''
 
−
 
 
−
current def.: General term for any water conducting cell, tracheid or vessel member.
 
−
 
 
−
Currently is part_of primary xylem and part_of secondary xylem.
 
−
 
 
−
proposed def.: A plant cell (PO:0009002O) that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.
 
−
 
 
−
comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells (PO:0025407) by the presence of bordered pits, although there are intermediate forms called fiber tracheids (PO:0000355).
 
−
 
 
−
participates_in sporophyte stage, part_of xylem, disjoint from hydroid
 
−
 
 
−
 
 
−
'''tracheid (PO:0000301)'''
 
−
 
 
−
current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.
 
−
 
 
−
proposed def.: A tracheary element (PO:0000290) that has no perforations in its cell wall.
 
−
 
 
−
comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members (PO:0002003) it has openings in the cell wall called perforations, organized into perforation plates (term has been requested in GO).
 
−
 
 
−
 
 
−
'''vessel member (PO:0002003)'''
 
−
 
 
−
current def.: One of the cellular components of a vessel, a dead cell with the wall between adjacent members being variously perforated and the walls that persist variously thickened.
 
−
 
 
−
proposed def.: A tracheary element (PO:0000290) that is part of a vessel (PO:0025417) and has as parts perforation plates.
 
−
 
 
−
Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (term has been requested in GO). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.
 
−
 
 
−
syn.: vessel element, vessel segment
 
−
 
 
−
part_of vessel (new term)
 
−
 
 
−
 
 
−
'''vessel (PO:0025417)'''
 
−
 
 
−
proposed def.: A portion of xylem (PO:0005352) tissue that has as parts a tube-like series of vessel members (PO:0002003), the common walls of which have perforations.
 
−
 
 
−
 
 
−
'''perforation plate''' (for GO)
 
−
 
 
−
proposed def.: A cell wall part that is the part of a wall of a vessel member and bears one or more openings (perforations).
 
−
 
 
−
comment: Part of a vessel member (PO:0002003). May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.
 
−
 
 
−
Reference ISBN:0471245194 (Esau's Anatomy of Seed Plants).
 
−
 
 
−
===New definitions - ground tissue cells===
 
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481660&group_id=76834&atid=835555 sclerenchyma cells]====
 
−
''These edits are done in the obo file.''
 
−
 
 
−
'''sclerenchyma cell (PO:0000077)'''
 
−
 
 
−
current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.
 
−
 
 
−
proposed def.: A ground tissue cell (PO:0025030) with thickened secondary cell walls that are lignified.
 
−
 
 
−
comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from tracheary elements (PO:0000290) or sclerified parenchyma cells (PO:0000074). Distinguishable from collenchyma cells (PO:0000075) because collenchyma cells alive at maturity. Collenchyma cells provides flexibility while sclerenchyma cells provide hardness.
 
−
 
 
−
Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.
 
−
 
 
−
 
 
−
'''sclerid (PO:0025418)'''
 
−
 
 
−
proposed def.: A sclerenchyma cell (PO:0000077) that has thick secondary walls with many pits.
 
−
 
 
−
comment: Usually not very elongated.
 
−
 
 
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481662&group_id=76834&atid=835555 parenchyma cells in phloem tissue]====
 
−
''These edits are done in the obo file.''
 
−
 
 
−
'''companion cell (PO:0000071)'''
 
−
 
 
−
'''current definition:''' A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.
 
−
 
 
−
'''proposed definition:''' A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube member (PO:0000289) and arises from the same initial cell (PO:0004011) as the sieve-tube member.
 
−
 
 
−
comment: Found in angiosperms. Compare to albuminous cells (PO:0025412), which are found in gymnosperms.
 
−
 
 
−
Currently part_of primary phloem '''and''' part_of secondary phloem, which can't be true. Should change to part_of phloem.
 
−
 
 
−
Suggest that we add relation companion cell adjacent_to sieve tube member.
 
−
 
 
−
'''Need to check definition of phloem mother cell. Does it only differentiate into secondary phloem, or can it be for primary phloem too?'''
 
−
 
 
−
 
 
−
'''albuminous cell (new term)'''
 
−
 
 
−
'''proposed def.:''' A parenchyma cell (PO:0000074) that is morphologically and physiologically associated with a sieve cell (PO:0025415) but does is not derived from the same initial cell (PO:0004011) as the sieve cell.
 
−
 
 
−
comment: May be found in the ray system (PO:0025411) and sometimes the axial system (PO:0025410) of gymnosperms. Compare to companion cells (PO:0000071), which are found in angiosperms.
 
−
 
 
−
is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.
 
−
 
 
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481665&group_id=76834&atid=835555 fiber cells]====
 
−
''These edits are done in the obo file.''
 
−
 
 
−
'''fiber cell (new term, PO:0025407)'''
 
−
 
 
−
proposed def.: An elongated, tapering schlerenchyma cell (PO:0000077) with a more or less thick secondary cell wall.
 
−
 
 
−
comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from tracheary elements (PO:0000290).
 
−
 
 
−
 
 
−
'''phloem fiber cell (PO:0004519)''' (was called phloem fiber)
 
−
 
 
−
current def.: A fiber in phloem.
 
−
 
 
−
proposed def.: A fiber cell (PO:0025407) that is part of a portion of phloem (PO:0005417) tissue.
 
−
 
 
−
Made part_of phloem, instead of part_of secondary phloem.
 
−
 
 
−
 
 
−
'''xylem fiber cell (PO:0000274)''' (was called xylem fiber)
 
−
 
 
−
current def.: A fiber in xylem.
 
−
 
 
−
proposed def.: A fiber cell (PO:0025407) that is part of a portion of xylem (PO:0005352) tissue.
 
−
 
 
−
comment: It may be difficult to distinguish xylem fiber cells from tracheary elements (PO:0000290).
 
−
 
 
−
Made part_of xylem, instead of part_of secondary xylem.
 
−
 
 
−
 
 
−
'''libriform fiber cell (PO:0004520)'''
 
−
 
 
−
current def.: A xylem fiber commonly with thick walls and simple pits.
 
−
 
 
−
proposed def.: A xylem fiber cell (PO:0000274) with simple pits.
 
−
 
 
−
Comment: Libriform fiber cells have unbordered pits while fiber tracheids (PO:0000355) have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fiber cells and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Libriform fiber cells have a slit-like aperture toward the cell lumen, but no pit cavity.
 
−
 
 
−
 
 
−
'''fiber tracheid (PO:0000355)'''
 
−
 
 
−
current def.: A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.
 
−
 
 
−
proposed definition: A xylem fiber cell (PO:0000274) with bordered pits with pit cavities.
 
−
 
 
−
comment: Commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fiber cells (PO:0004520) and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.
 
−
 
 
−
 
 
−
'''septate fiber (PO:0004521)'''
 
−
 
 
−
current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.
 
−
 
 
−
Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.
 
−
 
 
−
'''proposed definition, septate fiber tracheid:''' A fiber tracheid (PO:0000355) that has as parts one or more thin internal partitions or septa.
 
−
 
 
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
 
−
 
 
−
'''proposed definition, septate libriform fiber cell:''' A libriform fiber cell (PO:0004520) that has as parts one or more thin internal partitions or septa.
 
−
 
 
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
 
−
 
 
−
'''proposed definition, septate phloem fiber cell:''' A phloem fiber cell (PO:0004519) that has as parts one or more thin internal partitions or septa.
 
−
 
 
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
 
−
 
 
−
====other kinds of fiber cells?====
 
−
 
 
−
'''gelatinous fiber cell (new term, PO:0025422):''' A xylem fiber cell (PO:0000274) in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.
 
−
 
 
−
comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.
 
−
 
 
−
ref: Fahn
 
−
 
 
−
synonym: mucilaginous fiber cell
 
  
 
=Upcoming meetings and Presentations 2012:=
 
=Upcoming meetings and Presentations 2012:=

Latest revision as of 19:45, 8 March 2012

POC meeting, Webex Conference Call; Date: Tuesday Feb 14th, 2012 10am (PST)

In attendance:

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

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

Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12? none

Back to POC Meetings Minutes

News and Report from the Wood Ontology Meeting:

This discussion was postponed until PJ was present.

We had a successful meeting last week at the NYBG with the group of wood experts we invited.

  • Overall objective was to raise awareness and encourage the wood research community to get involved with the development and use of the Plant Ontology

Specific Goals with links to the pages:

To develop PO terms and definitions to describe:

1. Wood structures (PAE branch of PO) Goal_1._Anatomical_Entities

2. Stages of wood development (PSDS branch of PO) Goal_2._Plant_Structure_Development_Stages

3. Wood qualities and phenotypes (to go into TO and/or PATO) Goal_3._Wood_qualities_and_phenotypes

4. To obtain association data linked to the PO terms to be hosted in our database Developing_and_incorporating_new_annotations_for_woody_plants

  • Links to flash presentations by all the participants:

Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda#2:00PM-2:45PM_Flash_talks_by_participants

Questions Arising from the the Workshop

  • How is the best way to redirect users to terms that are in GO? For example; casparian strip or pit membranes?

Added a note to the AmiGO2 wish list POC_Technical_Issues_Page#AmiGo_2_Wishlist: for a means of redirection.

One possibility is to have a PO slim in GO that could load with PO. This could cause problems with keeping the slim up to date. We could load the slim without GO annotations.

JP suggested that maybe we could incorporate a look-up service, so that when a search fails for PO terms, it automatically searches other ontologies.

BS suggested that we should keep track of people's searches on the PO web page, so we can add new terms that people are searching for.

There has been no activity on AmiGO revisions lately. In the interim, are we planning to upgrade to an intermediate version of AmiGO. It may not be worth it to have to modify AmiGO twice for PO.

The search function does not have to wait for AmiGO 2. The search takes you into AmiGO, but it is a separate chunk of code.

  • How are we going to deal with terms that contain adjectives; such as 'storied cambium', 'early wood', 'late wood' etc? These are commonly used terms in this community and we need them.

BS raised the concern that having terms with adjectives can cause problems with multiple inheritance -- two different ways of classifying wood leads to two different parents. Suggest that we put all the adjectives in a phenotype ontology to which we can refer.

However, there are instances where the terms need to be in the PO, particularly for adjectives that are used only for particular plant structures (like epigynous flower). On the other hand, some adjectives can be used for many different structures (like variegated), and terms like "variegated leaf" probably shouldn't go in the PO. Adjectives like "storied" are somewhere in between -- it can apply multiple tissue types, but not hundreds of them. We will need to examine these terms on a case by case basis.

BS, best practice: Terms like "septate" should go into PATO, and we include terms for fiber types and instruct people how to post compose terms as they need them. Some communities would eventually create compound terms like "septate phloem fiber", but they will not live in PO.

We will probably not be able to live up to this best practice, but at a minimum, when we do add terms with synonyms, we should introduce the synonym into PATO and add xrefs to them.

Note, latewood and earlywood should be one word.


  • How do we want to approach the TO terms, since this is a complex area and officially outside the mandate of the PO?

Where does this fit into our list of top priorities?? Discussion of this question was postponed.

Revisions of existing terms:

leaf vein, primary vein, mid vein

These changes have already been made in the dev file.

  • leaf vein (PO:0020138)

Suggest: rename "leaf lamina vein" (not changed yet)

revised def'n, leaf (lamina) vein (PO:0020138): A vascular bundle (PO:0005020) that is part of a leaf lamina vascular system (PO:0000048).

part_of leaf lamina vascular system

synonym: leaf lamina vascular bundle

Changes are okay. We also need a term for petiole vascular bundle.

  • Proposed new term: primary leaf vein (PO:0025413)

proposed def'n: A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).

Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the leaf midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.

okay


  • midvein (PO:0020139)

revised def.: A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).

Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).

broad synonyms: mid rib, midrib, mid-rib; exact synonym: vascular leaf midvein; related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128


Rename "leaf midvein".

We already have terms for secondary, tertiary, quaternary, and higher order veins. Do we want to make their naming consistent with the changes suggested above for primary leaf vein? --Yes!

PO terms for lateral meristems

These edits have been done in the dev obo file, except as noted below.

See Items_for_future_meetings#Primary_and_secondary_growth.2C_etc. for more details on terms that will be requested in GO.

The PO has a general term for lateral meristem, of which cambium is a subtype:

Lateral meristem1.jpg

lateral meristem (PO:0020145)

revised def'n: A portion of meristem (PO:0009013) tissue located parallel to the circumference of a plant organ (PO:0009008).

comment: Participates in lateral growth (request has been made for lateral growth in GO) of a plant organ, primarily shoot axes (PO:0025029) and roots (PO:0009005). Contrast with apical meristem (PO:0020144).

New proposed def.: A portion of meristem (PO:0009013) tissue located parallel to the sides of a plant axis (PO:0025004), the cells of which undergo periclinal and anticlinal (tangential?) division.

New comment: Participates in lateral growth (request has been made for lateral growth in GO) of a shoot axis (PO:0025029) or root (PO:0009005), leading to an increase in the cross-sectional area. Contrast with apical meristem (PO:0020144) or intercalary meristem (PO:0006073).

Add lateral meristem part_of plant axis.

May want to add periclinal, anticlinal cell division to GO (or maybe just add periclinal and anticlinal to PATO).

Definition of intercalary meristem need a little work too, to distinguish it from lateral meristem.


cambium (PO:0005597)

revised def'n: A lateral meristem (PO:0020145) that is part of a plant axis (PO:0025004) and has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files. (Ref.: Esau)

comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).

Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it was defined.


New proposed def.: A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.

Also need to add term for cambial zone, is a cardinal organ part.


vascular cambium (PO:0005598)

revised def'n: A cambium (PO:0005597) that is located between and gives rise to secondary xylem (PO:0005848) and secondary phloem (PO:0005043).

comment: Vascular cambium gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis (PO:0025004).

Got rid of relation vascular cambium part_of vascular bundle.

No one likes "gives off" or "girth".

New proposed comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).


cork cambium/phellogen (PO:0005599)

revised def'n: A cambium (PO:0005597) that is part of a periderm (PO:0005046) and produces phellem (PO:0004003) and phelloderm (PO:0005050).

comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.

Definition okay. Phellogen should change from related synonym to exact synonym.


primary thickening meristem (PO:0005039)

Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.

revised def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).

comment: Contributes to primary thickening of a stem (PO:0009047), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.

DWS was skeptical about whether or not the PTM is actually discontinuous with the SAM in some species, but we will leave the comment in for now, since it is described in Rudall's review.

Need to add synonyms PTM, meristematic cap, and collar meristem.

Definition okay.


secondary thickening meristem (new term)

proposed def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) that is not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).

comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.

There are also secondary thickening meristems in roots of some monocots (Cheadle 1937, JSTOR:2471543), so this should be lateral meristem, rather than a shoot lateral meristem.


Other types of lateral meristems: (have not done these edits yet)

*root lateral meristem (PO:0006308)

This is just a lateral meristem in the root, which is only the cambium (vascular cambium and phellogen). Therefore, it makes more sense to call it a root cambium.

proposed new name and def'n: root cambium: A cambium that is part of a root.

This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.

Suggest that we also add root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium. Set up root cambium and shoot lateral meristem as XPs, so we don't have multiple inheritance.

DWS will check if there are secondary thickening meristems in some kinds of monocots. In that case, we should leave the general term for root lateral meristem.

New proposed def., root lateral meristem: A lateral meristem that is part of a root.

This will be an XP of is_a lateral meristem and part_of root. We will make new terms for root vascular cambium and root cork cambium that are subtypes of vascular cambium and cork cambium, respectively, and will be inferred children of root lateral meristem.


  • PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel meristem (PO:0009107), plus their subtypes.

Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches develop from apical meristems, not a lateral meristem.

There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.

Shoot lateral meristem should be set up as an xp, so subtypes and be inferred, just like root lateral meristem. Will create new terms for shoot vascular cambium and shoot cork cambium, as per root terms.


inflorescence lateral meristem (PO:0009105)

current def'n: The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.

This should be called inflorescence branch meristem, and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.

revised def: An inflorescence meristem that gives rise to an inflorescence branch.


ear lateral meristem (PO:0009110)

This should be called ear inflorescence branch meristem, and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).

revised def.: An inflorescence branch meristem that gives rise to a branch of an ear inflorescence.

okay

Primary and secondary growth, etc.

request has been made to GO.

These terms are for GO, not PO. Definitions are here for reference.

proposed terms for GO

primary growth (new term):

proposed definition: Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)

comment: Has its inception in the apical meristems (PO:0020144) and continues in their derivative meristems - protoderm (PO:0006210) and procambium (PO:0025275) - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.

is_a growth (GO:0040007)


secondary versus lateral growth

GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290

Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by Rudall et al. in Botanical Review (JSTOR:4354165).

I suggest that GO add a general term for lateral growth (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.


lateral growth (GO:new term): Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).

Comment: Includes thickening of plant axes (PO:0025004) due to the activity of a cambium (PO:0005597), known as secondary growth and found in most gymnosperms and dicotyledons, a primary thickening meristem (PO:0005039) as found in many monocotyledons, some ferns and some cycads, or secondary thickening meristem, (PO:0025414) as found in some monocotyledons.


proposed new def., secondary growth (GO:0080117): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)

Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium or phellogen (PO:0005599). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.

Add exact synonym "cambial secondary growth", which is makes the meaning clearer.


secondary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:0025414).

comment: Occurs in shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.

References: Fahn 1990, ISBN:0080374903; Rudall 1991, JSTOR:4354165


primary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)

comment: Occurs in shoot axes and rarely in roots in many monocotyledons.

Ref: JSTOR:4354165, Rudall 1991; and Esau ISBN:0471245208


diffuse secondary thickening (GO:new term): Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fiber cells of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.

comment: Occurs in the stems (PO:0009047) of some Arecaceae (palms).

Ref.: Fahn 1990, ISBN:0080374903

vascular and related cell types

Postponed for a future meeting.

Upcoming meetings and Presentations 2012:

Phenotype RCN meeting, February 23rd-25th, 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.

The projects of the Plant Working Group that we started in CO will be worked on during the next meeting, in the fall.

RW will attend, the RCN is covering her air travel.

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

LC submitted an abstract for consideration for a short talk

The PO and Gramene will most likely be co-hosting a workshop. Details TBA....

Katherine Esau Research Symposium

Integrating Plant Structure with Function, Development and Evolution

Thursday, March 29, 2012

1002 Giedt Hall, UC Davis

We will keep a track of this symposium and request if we can be invited for a short presentation. Esau's work has helped us build the ontology to a greater extent.


5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• Notification date: February 3, 2012

PJ is planning to attend, may do a talk. LC is planning to attend.

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:


RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

  • Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

Link to meeting page: ASPB2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Joint workshop is planned with PO, Gramene and TAIR

Registration scheduled to open first week in January.

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

Relevant dates

  • Paper submission deadline extended to...Feb. date?
  • Feb. 28th, 2012: Notification of paper acceptance
  • March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
  • April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
  • June 30th 2012: Deadline for all camera-ready copies for the proceedings

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

RW will circulate a draft of a manuscript for a plant disease extension of the Infectious Disease Ontology. Must be submitted by Jan. 31, 2012.

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.


BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts

Next meeting scheduled for Tuesday, Feb. 21st, 2012 at 10am PST/1pm EST

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