POC Conf. Call 10-15-13

POC meeting, Skype Conference Call; Date: Tuesday Oct 15th, 2013 10:30am PDT/1:30pm EDT

In attendance: Laurel Cooper (OSU),Barry Smith (OBO), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Dennis W Stevenson (NYBG)

Absent:Justin Elser (OSU), Justin Preece (OSU),

OBO Foundry Review of Plant Ontology

It is official!: Updated OBO Foundry page

We are posting our responses on the wiki: Plant_Ontology_Response_to_OBO_Foundry_Review

Issue of the plant cell definition in PO

Should we refer to CL rather than GO for the definition of "plant cell"?

Currently: plant cell (PO:0009002): A cell which is a plant structure (PO:0009011). [source: GO:0005623, POC:curators]

Comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall.

• CL_0000000: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.

(comment associated with CL:cell "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)."

• GO:0005623: The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

• CARO_0000013: Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.xref refers to GO:0005623.

It would be best if the other ontologies would decide on which definition of cell was going to be used as the reference. It seems like it would make sense to have it come from CL

Ontologies referencing CL: OBI, TAO, ZFA, IDO, ZFA, BIOMODELS, SYN, FYPO, AEO, EHDAA2, ONSTR, VSO, BCGO, SYN, IDODEN, AEO, ONSTR, VSO,

Ontologies referencing GO: EFO, CL, FB-BT, NPO, SAO, NIFSTD, GO, CCO, BIOMODELS, FYPO, CARO, GO-EXT, GEXO, NEMO, NIGO, NIFCELL, REXO, RETO, TRON

Ontologies referencing CARO: AAO, TAO, ZFA, FB-BT, VHOG, HAO, XAO, AEO, EHDAA2, OPL, PORO, OBOE-SBC, VSAO, TRON, OBI-BCGO,

BS will talk to CL (Alex Diehl) about the reference to cell from GO.

Wrapping up the vascular leaf development stages:

Gonzalez et al 2012, Trends in Plant Science

vascular leaf differentiation stage (new PO:0025574)

• Revised def'n: vascular leaf differentiation stage (new PO:0025574): A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf epidermis (PO:0006016) and leaf vascular system (PO:0000036).

Need to also include the mesophyll tissues and other cell types. May be able to make it more general and encompass all the layers of the meristem (L1, L2, L3), that lead to the development of all the cells of the leaf

From BS: In the interest of users who are are searching by only a specific term, it is worthwhile to list the different cell types.

The ground tissues arise from one of the layers L1, L2, and L3 zone, (these need to be revised).

DWS: layers L1- give rise to the epidermal tissues, except for a few exceptions like yellow-margined Sansevieria; L2 gives rise to the vascular tissues and sub marginal meristems, L3 (if it is there) gives rise to ground tissues???

discussion: 17:30-27 to 27:30

vascular leaf expansion stage PO:0001052

old name and def'n: 2 leaf expansion stage (PO:0001052): Stage of leaf development which begins when cell differentiation and cell expansion occurs and finishes when the leaf reaches its full size.

Proposed revised name and def'n vascular leaf expansion stage (PO:0001052): A vascular leaf development stage (PO:0025570) during which vascular leaf size increases primarily through cell expansion.

Proposed comment: During this stage leaf shaping (GO:0010358) occurs which is defined as the developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

• Note: The majority of cell division occurs early in leaf development and cell expansion is the major agent of leaf expansion link or see above image.

Refer to the GO term: cell growth GO:0016049: The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. synonym: cell expansion.

Revised comment: During this stage, the process of cell growth (GO:0016049) occurs, defined as the process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present. synonym: cell expansion.

Suggested revisions to leaf shaping (GO:0010358); Proposed new name: multidimensional leaf expansion: The developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

vascular leaf post-expansion stage (PO:0001053):

old name and def'n: 3 leaf fully expanded stage (PO:0001053): Stage of leaf development when leaf is fully expanded.

Proposed new Name and def'n: vascular leaf post-expansion stage: A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and ends with the onset of the vascular leaf senescence stage (PO:0001054).

from 9-10-13: Perhaps change term to "vascular leaf mature stage", or maybe keep the "leaf fully expanded stage"???. Examples of leaves with indeterminate growth, ferns, viney leaves, some Mahogany plants, but they are the exceptions. Could add as a comment (get names from DWS).

The 'mature' vascular leaf (fully expanded and differentiated) can exist from a few weeks to a number of years, before starting to senescence.

vascular leaf senescence stage (PO:0001054)

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

Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf. Need to add the references to the GO terms.

Need to look at this more- abscission zone (PO:0000146) starts in the petioles (are part of the leaf), starts with cell senescence, should refer to 'point of attachment'. Don't need to specify where the abscission zone forms. Note all leaves abscise, end with death of the vascular leaf

Need to review leaf senescence- see plant cell resource

Links to Relevant References- vascular leaf development

• • Genetic Control of Leaf Development- Plant Cell teaching tools
  • Uchida et al (2010) Coordination of leaf development via regulation of KNOX1 genes. Journal of Plant Research 123: 7–14
  • Comparative plant development: the time of the leaf? Tsiantis & Hay, 2003 Nature Reviews Genetics
  • Li, Brutnell et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42: 1060–1067
  • Leaf adaxial–abaxial polarity specification and lamina outgrowth: evolution and development, Plant and Cell Physiology, 2012
  • Gleissberg 2002
  • FERNS Barbara A. Ambrose: The evolution, morphology, and development of fern leaves, Vasco et al 2013
  • Independent recruitment of a conserved developmental mechanism during leaf evolution
  • Gonzalez et al, Trends in Plant Science 2012

root apical meristem PO:0020147 and child terms

• Issue with child terms root apical meristem PO:0020147: should these be "gives rise to a xxxx root- not part of a xxxx root.?

• root apical meristem PO:0020147: A root meristem (PO:0006085) formed at the apex of a root (PO:0009005), including those originating from an lateral root apical meristem (PO:0006020).

• primary root apical meristem (PO:0006081): A root apical meristem (PO:0020147) that is part of a primary root (PO:0020127).

Should be: A root apical meristem (PO:0020147) gives rise to a primary root (PO:0020127).

• lateral root apical meristem (PO:0006020): A root apical meristem (PO:0020147) is part of a lateral root (PO:0020121).

Should be: A root apical meristem (PO:0020147) gives rise to a lateral root (PO:0020121).

• adventitious root apical meristem (PO:0006021): A root apical meristem (PO:0020147) that is part of an adventitious root.

Proposed def'n: A root apical meristem (PO:0020147) gives rise to a shoot-borne root (PO:0000042). Problem is that this is not actually a root meristem as it arises from the shoot axis and is not part of the root system.

Revised def'n: A gives rise to a shoot-borne root (PO:0000042). Added missing SF xref: OBO_SF2_PO: 163 part of relation to shoot-borne root (PO:0000042)

• shoot-borne root (PO:0000042): A post-embryonic root that develops from shoot tissue.

broad synonym: adventitious root

Revised def'n: A root (PO:0009005) that develops from shoot axis (PO:0025029) tissue, in the post-embryonic stage.

Upcoming meetings and Presentations 2013-2014:

• PAG 2014 January 11-15, 2014 - San Diego, CA, USA

• • Registration is now open: PAG 2014.

The deadline for Early Pre-Registration is November 1, 2013

Systems Biology and Ontologies Workshop

Link to: Googledoc

Confirmed speakers:

• Barbara Ambrose, NYBG
• Stefan Rensing, Marlburg Germany