POC Conf. Call 5-06-11
POC meeting, Webex Conference Call; Date: Tuesday May 10th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_5-03-11?
Issues arising from previous meetings:
Review of apical cell (PO:0030007) and its descendents
The problem:
Moss Ontology requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.
The existing term in the PO, "apical cell (PO:0004000)" referred to "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote". This term was obsoleted and replaced by embryonic apical cell (PO:0025284) for clarity.
A new term apical cell (PO:0030007) was created to be the general class for all apical cell types.
At the POC meeting on 4/28/11, we decided to name this term meristematic apical cell
meristematic apical cell (PO:0030007): New proposed def'n: A single meristematic cell at the tip of a plant structure where apical growth occurs.
is_a meristematic cell, sibling to initial cell
Proposed revised comment, for clarity: Meristematic apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex or protonema in bryophytes and some pteridophytes. Apical growth in these structures results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, (rather than from a population of meristematic cells located at the tip of an apical meristem). The meristematic apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped with two cutting faces (in non-vascular leaves or thalli) and may be established upon germination of a spore or upon the first cell division of an embryo or later.
Do we need a citation for this comment?
See: Apical cells
The issue:
At the POC_Conf._Call_4-28-11, there was an extensive discussion about whether to modify the definition of the existing 'apical cell' to refer to a general class encompassing the cell at the very tip of an angiosperm leaf or other any other structure.
The problem of adding a generic term for an "apical cell" is that it would cause confusion and it may not be biologically accurate.
The issue was raised that a scientist might isolate such a cell from the tip of a vascular leaf or root and be confused as to where the annotation should go. Is there actually a single cell at the tip of a vascular leaf or root? See the ppt below showing SAM and RAM tissues of angiosperms. There are references to stem cells in the central zone of the SAM, initial cells in the quiescent center of the RAM.
File:20-growth and development-02-A.pdf
See P.13: "The root apical meristem (RAM) is subterminal, but like the shoot apical meristem has a layered structure and a center of slowly dividing cells (the Quiescent Center (QC, shown in blue) surrounded by the initials for individual tissue (shown in green). (from Current Opinion in Genetics & Development 2003, 13:551–557)
The solution:
We can use the existing PO terms for cells at the leaf apex (PO:0020137) and leaf tip (PO:0025142),
For more precise work, we have the 'shoot apical meristem'(PO:0020148) and its part_of children (only some shown):
PO:0000224: central zone
PO:0009020: meristem L1
PO:0009021: meristem L2
PO:0009022: meristem L3
PO:0000225: peripheral zone
And the 'root apical meristem' (PO:0020147): and its part_of children (only some shown):
PO:0020149 : quiescent center (and its part_of child: root initial cell (PO:0000059))
PO:0030008 : root apical cell ????
PO:0006307 : root procambium
We decided to ensure clarity, we should append the names of the child terms with 'meristematic' in their names, except for embryonic apical cell.
We could use always_in and never_in taxon relations to help clarify which taxa these are from
New terms and definitions for apical cells
The definitions for the descendents of apical cell (listed below) were approved, pending approval of final definition of apical cell. See POC_Conf._Call_4-26-11#apical_cell for more details.
gametophytic apical cell (PO:0030014) > gametophytic meristematic apical cell
sporophytic apical cell (PO:0030015) > sporophytic meristematic apcial cell
thallus apical cell (PO:0030025) > thallus meristematic apical cell
root apical cell (PO:0030008) > root meristematic apical cell
shoot apical cell (PO:0030009) > etc.
gametophore apical cell (PO:0030019)
leaf apical cell (PO:0030011)
non-vascular leaf apical cell (PO:0030013)
vascular leaf apical cell (PO:0030012)
shoot axis apical cell (PO:0030010)
gametophore axis apical cell (PO:0030023)
vascular shoot axis apical cell (PO:0030024)
seta apical cell (PO:0030016)
embryonic apical cell (PO:0025284, replaces PO:0004000)
Also need to add a term for protonema meristematic apical cell.
rhizoids
Made a new term rhizoid (PO:0030078) is_a plant structure.
Proposed def.: A plant structure that is a uniseriate filament with positive geotropism and without chlorophyll that grows from an epidermis or protonema.
Comment: Serves to anchor the plant to the substrate, and may function in nutrient and water uptake. Includes epidermal rhizoids that grow from the epidermis of bryophytes and pteridophytes in the gametophytic phase or from the stems of some monocots, and protonemal rhizoids that branch from a protonema.
Changed rhizoid (PO:0030071) to epidermal rhizoid
Proposed def.: A rhizoid that develops from an epidermal rhizoid initial.
Comment: Found in bryophytes and pteridophytes growing from the epidermis of a gametophore or the lower surface of a thallus and in some monocots growing from the stem at the cotyledonary node. May be considered a type of trichome.
develops_from epidermal rhizoid initial
Do we want to create separate children for wurzelhalsrhizoid? Could just be a synonym of this term. An alternative name could be cotyldonary node rhizoid.
New term protonemal rhizoid (PO:0030079)
Proposed def.: A rhizoid that develops from a protonemal side branch rhizoid initial.
Comment: A protonemal rhizoid is a branch that arises from a protonema that grows into the substrate and lacks chlorophyll.
Changed the term rhizoid initial (PO:0030068) to epidermal rhizoid initial
Proposed def.: An epidermal initial cell that gives rise to a rhizoid.
Comment: Part of the epidermis of a thallus or gametophore of a bryophyte or pteridophyte in the gametophytic phase or the stem of a monocot in the sporophytic phase.
New term protonemal side branch rhizoid initial
Proposed def.: A protonemal side branch initial that gives rise to a protonemal rhizoid.
is_a protonemal side branch initial (PO:0030067, An initial cell that is produced by division of a sub-apical cell of a protonema.)
perianth calyptra (PO:0025299)
Proposed definition (accepted at the POC meeting on 4-28-11): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary.
Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.
Should we rename calytpra perianth?
synonyms: floral calyptra (exact) and floral operculum (related)
We already have "angiosperm calyptra" as a narrow synonym of corolla (PO:0009059). Says: In angiosperms, the petals may be fused into a calyptra, which is different than a calytra in mosses.
We may want to remove this synonym, as it is redundant with the new term PO:0025299.
Other Issues
*Review for OBO Foundry Acceptance
BS brought up the topic of review for OBO Foundry acceptance at the POC_Conf._Call_4-19-11. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks
List of Foundry Principles:[Accepted] with a brief summary of each:
The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.
The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.
The ontology possesses a unique identifier space within the OBO Foundry. The identifier uniquely and persistently identifies a definition, which itself unambiguous identifies some type of biological entity. The identifier is for the definition: it is NOT the name and it is NOT an identifier for the name.
The ontology provider has procedures for identifying distinct successive versions.
The ontology has a clearly specified and clearly delineated content. The ontology must be orthogonal to other ontologies already lodged within OBO.
The ontologies include textual definitions for all terms.
The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.
The ontology is well documented.
The ontology has a plurality of independent users.
The ontology will be developed collaboratively with other OBO Foundry members.
single locus of authority, tracker (SOP), responsive help desk
OBO is an open community and, by joining the initiative, the authors of an ontology commit to its maintenance in light of scientific advance and to working with other members to ensure the improvement of these principles over time
Upcoming meetings 2011:
Phenotype RCN Meeting: June 1-3rd, Boulder CO
PJ will attend
More details TBA
2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
-JE and JP will be attending
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
For more Workshop details: Semantic web.
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
Full-Day Workshops Schedule:
July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability
July 26 6.30pm-9pm Evening Workshop: Common Logic
July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium
- LC will attend and represent the PO. Invite other plant people?
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Early-bird registration ends May 13.
Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
