POC Conf. Call 10-26-10

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

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 10-20-10 meeting?

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.

• Suggest a new parent term gynoecial ridge (sensu Zea),
• New proposed definition: A gynoecium of an ear floret in the early stages of development, characterized as a ridge on the abaxial surface of the floret meristem that develops_from a gyneocium primordium (of ear floret?).

For consistency's sake, we should also add the term gynoecial ridge (sensue Poaceae), which could be the parent of gyneocial ridge (sensu Zea), since other grass species besides maize have gynoecial ridges.

Proposed definitions for children:

• gynoecial ridge of lower floret of pedicellate spikelet of ear: A gynoecial ridge that is part 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 that is part 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 protruberance on the mature
ovary.

• gynoecial ridge of upper floret of pedicellate spikelet of ear: A gynoecial ridge that is part of a 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 that is part of a upper floret of sessile spikelet of ear in the early stages of development.

All of these terms would have an is_a parent: gynoecial ridge (sensu Zea) and part_of relations to their corresponding floret.

Emails were sent to Elizabeth Kellogg (UMSL) and Leszek Vincent (Missouri) asking for their feedback on these terms.

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.

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)

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.

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.

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.

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.

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.

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.

Links to images through PlantSystematics.org

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

With current technology, we can add html links to specific pages on PlantSystematics.org.

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

Separate Node Option: PlantSystematics can set up a sister node for Plant Ontology on their home page. This would create a separate browser/search page using PO terms and IDs. Ideally, we would integrate the PO ontology structure so that if someone searched for images for a parent term, all of the images associated with descendant terms would also show up. This search engine would locate terms that are uploaded by PO (Ale's image collection) as well as images in the main PlantSystematics database.

We could set it up so that the search results page also has a link to the corresponding term page on PO's Amigo browser, and maybe even includes some data from the PO on the search results (e.g. definition, parent term)

PJ: Better to have PO terms attached to the images and just have an additional drop down box for direct searches. Create mappings from the keywords to PO terms, add additional PO terms if necessary.

Ale will take care of uploading the images and making sure that their labels correspond to PO terms. Will need help from PJ's lab in setting up the PO node and using HTML labels to create links to specific areas of images

Image files are in series -- from lowest magnification to the highest. It would be good if we could set up the browser to allow users to scroll through multiple images of the same slide, so they wouldn't have to return to the search results each time.

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

Ramona and Ale are working on templates pages to show what the search interface and search results pages should look like. Will post them on the collaborators page when they are ready.

Other Items:

*Question from Daniel Lang <daniel.lang@biologie.uni-freiburg.de> (to Pankaj Sept 2009)

Looking for estimates of the number of cell types and the number of different tissue types in the gametophytic and sporophytic generations of the following angiosperms:

Arabidopsis lyrata, Arabidopsis thaliana, Carica papaya, Glycine max, Medicago truncatula, Populus trichocarpa, Ricinus communis, Vitis vinifera, Oryza sativa, Sorghum bicolor and Zea mays (current estimate: total 100 cell types) See details in 10-6 meeting

Has anyone responded to him? Dennis and Ramona should report back at this meeting.

• Setting up conference call with Bruce Kirchoff to discuss the Plant Ontology and the issues he raised at the Botany Meeting

See details of his comments in 10-6 meeting.

This was scheduled to be done after Sept 20th, so we should probably decide when we want to do it.

Laurel can set up a Doodle poll?? Who wants to take part?