POC Conf. Call 10-26-10

POC meeting, Webex Conference Call; Date: TUESDAY Oct 26th, 2010 10am (PDT)

In attendance:

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

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab), Alejandra Gandolfo, (Cornell University), Justin Elser (OSU)

Collaborators: none

Acceptance of the minutes from the 10-20-10 meeting? no changes

Proposed fixes for terms without is_a parents

stylar ridge

There was some discussion of this item last week, and we decided more information was needed.

The following terms have no is_a parents and no definitions:

• stylar ridge of lower floret of pedicellate spikelet of ear (PO:0009024)

• stylar ridge of lower floret of sessile spikelet of ear (PO:0009076)

• stylar ridge of upper floret of pedicellate spikelet of ear (PO:0009079)

• stylar ridge of upper floret of sessile spikelet of ear (PO:0009092)

They already have part_of relationships to their corresponding spikelets

Each of them occurs in a different structure, and has slightly different development, but they are all characterized by the following description:

“The gynoecium development of the lower floret begins with the
 production of a ridge on the abaxial surface of the apical meristem of the 
floret, distal to the third stamen (which later degenerates). This is the
 stylar ridge.” (MaizeGDB:60893).

Definition from MaizsGDB cite Cheng & Pareddy, which is a book chapter in 'The Maize Handbook; by Freeling and Walbot (available at NYBG library, QL 34 .Z4 M245 1994).

PJ sent a reference from Le Roux and Kellogg (1999) which clearly described floret development in a number of Poaceae species. They use the term gynoecial ridge, rather than stylar ridge.

• We may want to rename these terms gynoecial ridge of ..., instead of stylar ridge, or at least use it as a synonym.

According to Le Roux and Kellogg: "The gynoecial ridge, as defined by Cheng and Pareddy (1994),is the stage at which the ovary begins to extend upwards around the nucellus, giving the appearance of an "egg" (the nucellus) in an "egg cup" (the ovary)."

They also say that in multiple grass species, "The gynoecial primordium elongates faster on the side of the inner lemma, producing a gynoecial ridge, surrounding an obvious nucellus (Figs. 15, 18, 21, 24).

This paper indicates that the stylar ridge is the early stage of gynoecium development and develops from the gynoecium primordium.

PJ suggested that we use the name 'gynoecium ridge' instead of gynoecial ridge, to be consistent with existing terms like gynoecium primordium. Will make gynoecial ridge an exact synonym.

• Suggest new parent terms gynoecial ridge (sensu Zea), and gynoecial ridge (sensu Poaceae)

New proposed definitions:

gynoecial ridge (sensu Poaceae): A gynoecium (sensu Poaceae) in the early stages of development, characterized as a ridge on the abaxial surface of the floret meristem that develops_from a gynoecium primordium. is_a gynoecium of (sensu Poaceae) Note: do we want to add term gynoecium primordium (sensu Poaceae) or leave out the formal develops from relation?

gynoecial ridge (sensu Zea): A gynoecial ridge (sensu Poaceae) that is a gynoecium of an ear floret in the early stages of development. is_a gynoecial ridge (sensu Poaceae) and is_a gynoecium of ear floret

BS suggested that we get away from the use of sensu terms (GO has gotten rid of them). We will need a top level term 'gynoecium ridge' that can be parent to the new terms 'Poaceae gynoecium ridge' and 'Zea gynoecium ridge'. However, this does not get rid of the taxon specific terms, and we will need to examine whether or not all of the taxon specific terms in the PO are necessary (do they actually have features that distinguish them from the more general parent?). BS also suggested that rather than renaming terms that has sensu in their name, we obsolete them and make new terms. Sent a paper by Kusnierczyk, 2008 on linking species to GO using NCBO taxon ontology, which we can use a a guide for how to deal with species specific concepts.

Chris also contributed an additional, related reference detailing the GO implementation based on Kusnierczyk's formalism : Deegan et al, 2010

We will test this strategy for the gynoecium ridge terms and see how it works out. Later, maybe extend it to other existing sensu terms.

Proposed definitions for children:

• gynoecial ridge of lower floret of pedicellate spikelet of ear: A gynoecial ridge (sensu Zea) that is a gynoecium of a lower floret of a pedicellate spikelet of ear in the early stages of development.

Comment: While the development of this stylar ridge is very similar to
 that of the upper florets, the development does not proceed beyond the 
early ridge stage.

• gynoecial ridge of lower floret of sessile spikelet of ear: A gynoecial ridge (sensu Zea) that is a gynoecium of a lower floret of sessile spikelet of ear in the early stages of development.

Comment: Continued overgrowth of the shoot apex (which becomes the
ovule primordium) by the ring of stylar tissue leads to the formation of
the stylar canal, which is detected as a slight protuberance on the mature
ovary.

• gynoecial ridge of upper floret of pedicellate spikelet of ear: A gynoecial ridge (sensu Zea) that is a gynoecium of an upper floret of pedicellate spikelet of ear in the early stages of development.

• gynoecial ridge of upper floret of sessile spikelet of ear: A gynoecial ridge (sensu Zea) that is a gynoecium of an upper floret of sessile spikelet of ear in the early stages of development.

All of these terms would have two is_a parents: gynoecial ridge (sensu Zea) and gynoecium of corresponding floret (PO:0006423-6426). The part_of relations to their corresponding floret (PO:000635-6453) are taken care of because their corresponding gynoecia already have part_of relationships to the florets.

These definitions were accepted, but have to be modified slightly to use Zea gynoecium ridge, instead of gynoecial ridge (sensu Zea).

We need to put a comment on these terms that they have multiple inheritance because we are dealing with an entity at a certain stage in its development. Need re-examine this once we know how we are going to deal with developmental stages for gynoecium.

Updated names and definitions for all terms will be posted on SourceForge tracker.

Emails were sent to Elizabeth Kellogg (UMSL) and Leszek Vincent (Missouri) asking for their feedback on these terms. They have not yet responded.

Link to page with image of gynoecial ridge ontology structure

Dehiscence zone

fruit dehiscence zone (PO:0004707) and anther dehiscence zone (PO:0005011) have no is_a parents. Suggest new term dehiscence zone. New term for mosses, capsule annulus, could also go here.

Current definitions:

fruit dehiscence zone (PO:0004707): A narrow band of cells that extends along the dehiscent fruit's dehiscence region which upon fruit maturation by drying, undergoes cell separation. This allows the valves to detach from the replum and for the seeds to be dispersed. [GR:pj, TAIR. Comment: Found in deshiscent fruit.

anther dehiscence zone (PO:0005011): A narrow band of cells that extends along the entire length of the anther. This site is observed as an indentation between the locules of each theca. Upon anther maturation, cell separation within the dehiscence zone allows the anther wall to break and for pollen to be released. [PMID:15319479]

Proposed definitions:

dehiscence zone: A portion of plant tissue that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure. dbxref: dehiscence (GO:0009900)

fruit dehiscence zone: A dehiscence zone that is part of a fruit. Comment: Upon fruit maturation by drying, undergoes cell separation, allowing the valves to detach from the replum and seeds to be dispersed.

anther dehiscence zone: A dehiscence zone that is part of an anther. Comment: Extends along the entire length of the anther and is observed as an indentation between the locules of each theca. Upon anther maturation, cell separation within the dehiscence zone allows the anther wall to break open and pollen to be released. [PMID:15319479]

capsule annulus (new term): A dehiscence zone that is part of a capsule, located at the base of an operculum. Synonym: capsule dehiscence zone Comment: Upon capsule maturation, cell separation in the annulus allows the operculum to separate from the capsule, aiding in spore dispersal.

Second part of the definition of capsule annulus (located at the base of an operculum) can move to comment. We will also need to add the terms capsule and operculum to the PSO, since they are included in the definition of capsule annulus.

Note: we also have the term abscission zone (PO:0000146): Zone at base of leaf, flower, fruit, or other plant part that contains an abscission (or separation) layer and a protective layer, both involved in the abscission of the plant part. [source: ISBN:047124529]. (is_a portion of plant tissue)

This definition should be reworded to parallel the definition of dehiscence zone. Will open SourceForge tracker for this definition.

Some discussion of whether or not there should be a common parent for abscission zone and dehiscence zone. Decided not to add it.

GO defines abscission and dehiscence separately:

abscission (GO:0009838): The controlled shedding of a body part. [source: ISBN:0140514031].

dehiscence (GO:0009900): The opening of an anther, fruit or other structure, which permits the escape of reproductive bodies contained within it. [source: ISBN:0879015322]

Based on these GO terms, suggest keeping abscission zone and deshiscence zone separate, and referencing GO terms in definition. Could add comments referring to abscission zone under dehiscence zone and vice versa.

New children for portion of plant tissue

The following terms have no is_a parents. Suggest making them children of portion of plant tissue, with the approprate part_of relations (most part_of relations already exist). Definitions have been modified slightly to fit genus differentia form.

Some of these terms may be classified as more specific types if tissue (e.g., parenchyma). Suggest making them children of portion of plant tissue for now, and looking at them later when we re-organize the children of portion of plant tissue.

protective layer (PO:0006212): The layer of cells in the abscission zone that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission. [ISBN:0122151704]

part_of abscision zone

Proposed new def: A portion of plant tissue composed of a layer of cells in the abscission zone that have lignin and suberin depositions and are found on the axial side of the break or exposed surface of abscission.

This definition is okay.

root cap (PO:00020123): A group of cells that covers the apical meristem of the root. [APWeb:Glossary]

part_of root

Proposed new def: A portion of plant tissue composed of a group of cells that covers the apical meristem of the root.

Some discussion of whether or not the root cap included the root apical meristem, in the end agreed that it did not. This definition is probably okay, but want to re-examine it.

elongation zone (PO:0020125): The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size. [GR:pj]

synonym "region of cell elongation" RELATED []:

synonym "region of radial enlargement" RELATED []:

part_of root

Proposed def: A portion of plant tissue that is part of the root and includes small, densely cytoplasmic cells that are dividing and expanding in size.

Comment from Dennis: Zone of elongation in roots at least refers to longitudinal expansion not radial. The new definition will not work. Also, those cells have enlarging vacuoles so the cytoplasm actually becomes less dense. Suggest waiting until Dennis and Alejandra are present to work on this definition.

Discussion of this term was tabled for future meeting.

central root cap (PO:0020130): The central part of a root cap in which the cells are arranged in longitudinal files. [GR:pj]

synonym "columella cells" RELATED []:

part_of PO:0020123 root cap

Proposed new def: A portion of plant tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.

lateral root cap (PO:0020131): The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704]

synonym "peripheral cells" RELATED []:

part_of PO:0020123 root cap

Proposed new def: A portion of plant tissue that is the part of a root cap and is parallel to the axis.

differentiation zone (PO:20135, alt_id PO:3002): The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function. [GR:pj]

synonym "maturation zone" RELATED []:

synonym "specialization zone" RELATED []:

part_of root

Proposed new def: A portion of plant tissue that is the part of a root and is located behind the elongation zone and contains cells that are differentiating into their final form and function.

quiescent center (PO:20149): Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap. [ISBN:0122151704]

part_of root

Proposed new def: A portion of plant tissue that is part of a root and contains hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap.

We reviewed a diagram of the different cell types in the root tip. RW will create separate tracker items for most of these terms, and work on the definitions, based on this diagram an other sources, and we will re-address these terms at another meeting.

Pollen tube

pollen tube (PO:0006345)

Current definition: A tubular cell extension formed by the germinating pollen grain; carries the male gametes into the ovule. [ISBN:0471245208, Esau]

Suggest making pollen tube is_a microgametophytic cell (new term), develops from tube cell (new term)

Proposed definitions:

microgametophytic cell (PO:0025027): A plant cell that is part of a male gametophyte. is_a plant cell, part_of male gametophyte (PO:0020091).

Do we want this term? Might not be appropriate for cells in microgametophytes of non-seed plants.

Children would include tube cell, generative cell, and vegetative cell.

tube cell: A microgametophytic cell that is part of a pollen grain that develops into a pollen tube. is_a microgametophytic cell (PO:0025027).

pollen tube (PO:0006345): A microgametophytic cell that develops from the tube cell and forms a tubular extension of the pollen grain. Comment: carries the male gametes to into or near the ovule.

We had limited time to discuss this item. Agreed that the term microgametophytic cell was probably not appropriate, terms should just be child of plant cell. Some discussion of whether or not there should be a general term for tube cell, that includes other cells like trichomes that have tubular extensions. Will discuss more later.

Other Items:

POC meeting to be held at NYBG in fall 2010. Date Nov 4-6th

Date: Thursday Nov 4th (LC and RW), all day on Friday, November 5th and Sat Morning, Nov 6th

• See Wiki page for more details.

Farshid Ahrestani of TraitNet cannot make it at 4 on Friday. We will invite TraitNet to join us at 11 and for lunch, instead of at 4.

Links to images through PlantSystematics.org

Tabled for future meeting.

• Goal is to add links between PO terms and images on PlantSystematics.org.

News:

• Ramona and Ale met with Kevin Nixon (who created and maintains PlantSystematics.org) after last week's conference call.

-He is willing to integrate PO IDs into PS.org database, so that when people are submitting images, they will get a hierarchical pull down list of PO terms to associate with their photos.

-Anyone can submit images, but they have to register first.

-Ramona sent him the current plant_ontology.obo flat file, and he will use this to create a series of tables that have the terms and their is_a and part_of hierarchies, so that recursive searches can be done in both directions (down the tree and up the tree).

-He was open to the idea of having html tags associated with the images to point to specific structures on parts of the image, but we will have to figure out the best way to implement this. Will this actually be any less work than having Ale make labeled images with arrows?

PS.org is set up so that users submit their search criteria, then this generates an SQL query, rather than having the queries generated directly. This prevents people from messing with the database. We can use Boolean operators for our queries, even though they aren't currently used on PS.org

• At the last meeting, Pankaj asked Alejandra and Ramona to prepare ~5 sample pages which would show the images and what other information that would be on the page.

See: PlantSystematics.org

• Ramona and Ale are working on templates pages to show what the search interface and search results pages should look like. Posted link on PlantSystematics.org collaborators page.

If we register PlantSystematics.org with the GO database directory, we could make those links automatic in Amigo. should send a message about this request to the GoHelpdesk

• Plant and Animal Genome XIX Conference- Workshop

January 15-19, 2011 PAG 2011

PAG 2011 workshop wiki page has been created: PAG_2011_Collaborators_Workshop

Upcoming meetings 2010-2011:

• Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

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

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

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

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010.

Lol and Ramona are planning on attending and setting up a PAG_2011_Collaborators_Workshop half day workshop and meeting with collaborators. We will present a computer demonstration,and poster and possibly a Phenote workshop. Alejandra cannot attend. PJ is not attending as he is teaching. DWS will attend also Justin Preece.

Abstract has been circulated, thanks for everyone's comments'

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

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

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

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

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

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

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology.

Ramona's abstract has been circulated, thanks for everyone's comments. RW and PJ will submit abstracts this week.