POC Conf. Call 12-4-12

POC meeting, Webex Conference Call; Date: Tuesday Dec 4th, 2012 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Barry Smith (University at Buffalo, NY),Dennis W Stevenson (NYBG), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU)

Absent: Marie Alejandra Gandolfo (Cornell), Ramona Walls (NYBG), Chris Mungall (LBLL)

Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=70433597&rKey=3b3b150b132a73b2

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=70433597&rKey=c3752f536419495d

Plans for Upcoming Release #19

Timeline for Release: Goal is mid December 2012 Release_19

Priorities for inclusion in the Release:

- Revisions to PSDS:

- Fruit development stages

- New datasets: grape, cotton, rice

LC: will send MAG and YY a list of the new PAE terms that we need translations for.

Goal is to complete the edits and annotation sets by Friday Dec 7th, then load the database over the weekend onto beta. That will give us the following week to troubleshoot issues and hopefully have it completed by Dec 14th.

Proposed New Evidence Code for High Throughput Data

Inferred from preferential Expression Pattern

PJ has suggested that we should create a new evidence code, that would reflect a higher cut-off.

In the RNA-seq or microarray datasets, we have thousands of genes identified, so it becomes less meaningful. In a m/a study you can make a comparison to other tissues, and say "The gene is expressed in one tissue vs another, ie it is preferentially expressed in XYZ plant structure."

IEP can be for any gene any time. This would depend upon the specified cut-offs for each study.

e.g. A gene is expressed in a shoot or a root, but the gene is preferentially expressed in the root.

BS: Need to have some kind of relativity, we are limited in the scope of the annotation format. Then you would need to have two annotations and you could say the second annotation is inferred from the fact that the expression is elevated relative to the first one. There is a general desire that the annotations could contain more contextual information, currently each annotation is an atom. Need to create the machinery and show what it brings you.

Need to be able to show the statistical significance, suggest two or three alternatives to IEP (or children of IEP). They would have a second annotation?

e.g. In Sam's rice salt study, 75% of the rice genes are expressed

After the call:

Perhaps we should be actually using and contributing to the Evidence code ontology: http://purl.bioontology.org/ontology/ECO

For example, they already have a term: RNA-seq evidence (ECO:0000295)

Wrapping up some open trackers:

lamina intramarginal vein

New term added by request:

leaf lamina intramarginal vein (new PO:0025520): A leaf lamina vein (PO:0020138) that is just inside the leaf lamina margin (PO:0025009) and extends from the leaf base (PO:0020040) to the leaf tip (PO:0025142).

Comment: The leaf lamina intramarginal vein is much thinner than the leaf midvein (PO:0020139; syn: midrib), and is of constant thickness.

Note: I think it is better to use leaf tip (the apical most portion of a leaf) rather than leaf apex (it is not precisely defined how far toward the base from the tip a leaf apex extends)

character index

Additional photos here: http://www.flickr.com/photos/xylopia/4659513712/

Question: do these occur in other phyllomes such as petals? If so we should also create a phyllome lamina intramarginal vein.

Should use leaf lamina base rather than leaf base and leaf apex, rather than leaf tip.

K second mitotic division stage (PO:0001015)

Revised definition and comment, added new synonyms:

Revised definition: A pollen development stage (PO:0001007) during which the generative cell (PO:0020097) undergoes mitotic division to form two male gametes, the pollen sperm cells (PO:0025121).

Added two new synonyms, as requested: - tricellular stage (broad) - tricellular pollen development stage (exact)

Revised comment: In taxa with mature two-celled pollen (PO:0025281), the second mitotic division takes place after pollen germination (GO:0009846), in germinating pollen tube cell (PO:0025195).

Notes: The whole pollen development stage class requires work, as some of these terms (such as this one) describe processes, rather than stages, but we will add the synonyms for now and do further revisions for the next release.

This term overlaps with: generative cell mitosis (GO:0055047): The process in which the generative cell divides by mitosis to form two haploid cells. These will subsequently differentiate into sperm cells.

plant gametangium (PO:0025124)

Current def'n: A plant organ that produces and contains one or more gametes that are located in it and is part of a whole plant in the gametophytic phase.

Note: in some green algae such as Ulva, the gametangia are single cells (Raven et al, (1992) Biology of plants, 5th ed.) so can this still be a plant organ? Also the gametes are not always contained in the gametangium.

Raven definition: "A cell or organ in which gametes are formed." In this case we would have to make it a plant structure.

The only other way to deal with this is create two child terms for the two types of plant gametangia: multicellular plant gametangium (is a plant organ) and unicellular plant gametangium (is_a plant cell).

Revised name and def'n: multicellular plant gametangium (PO:0025124): A plant organ (PO:0009008) that produces one or more gametes (PO:0025006) and is part of a whole plant (PO:0000003) in the gametophyte development stage (PO:0028003).

unicellular plant gametangium (new PO:ID): A plant cell (PO:0009002) that produces one or more gametes (PO:0025006) and is part of a whole plant (PO:0000003) in the gametophyte development stage (PO:0028003).

archegonium

Currently: archegonium (PO:0025126): A plant gametangium that produces an archegonium egg cell that is located in it.

proposed revised def'n: archegonium (PO:0025126): A multicellular plant gametangium (PO:0025124) that develops from an archegonium initial cell (PO:0025510) and has as parts a venter (PO:0030038) and an archegonium neck (PO:0030039).

proposed comment: At maturity, the archegonium contains an archegonium egg cell (PO:0025122). In mosses, the archegonium also has part an archegonium stalk (PO:0030036).

Comments from: POC_Conf._Call_11-20-12

DWS: The archegonium is a multicellular female gametangium; has a number of components: the neck, the archegonium neck; neck canal cells, a ventral canal cell as well as the archegonium egg cell. It is essential to include these in definition, it will eliminate the circularity- common to all bryophytes, gymnosperms and ferns.

archegonium egg cell

Currently: archegonium egg cell (PO:0025122): A plant egg cell that is produced by and located in an archegonium.

proposed revised def'n: archegonium egg cell (PO:0025122): A plant egg cell (PO:0020094) that develops from the archegonium central cell (PO:0025509) and is contained in the archegonium (PO:0025126).

Comment: The archegonium central cell divides asymmetrically to form a smaller archegonium neck canal cell (PO:0030065) and a larger archegonium egg cell (PO:0025122) in gymnosperms.

PJ: We should not say: 'produced by', it is better to say that the archegonium egg cell develops_from a specific cell type in the archegonium,

The archegonium egg cell develops_from the archegonium central cell, it has a common origin with the central canal cell.

Note from Skype discussion: In ferns they do not use the term 'central cell'- ventral canal cell.

archegonium initial cell

Currently, archegonium initial cell (PO:0025510): An initial cell that is part of an archegonium megagametophyte (PO:0025282) and divides to give rise to an archegonium (PO:0025126).

should have a part_of relation to archegonium megagametophyte (PO:0025282); probabaly need to reword this def'n as well.

• archegonium central cell (PO:0025509): A plant cell (PO:0009002) that is the distal cell arising from the first division of an archegonial initial cell (PO:0025510) in a gymnosperm.

Comment: The archegonium central cell is larger than the other cell that arises from the initial division of the archegonium initial cell. Divides asymmetrically to form a smaller archegonium neck canal cell (PO:0030065) and a larger archegonium egg cell (PO:0025122) in gymnosperms.

Part_of children of archegonium: We currently have:

• archegonium stalk (PO:0030036): A stalk that the basal part of an archegonium. Comment: Raises the venter above the rest of the gametophyte.

revised def'n: A stalk that is the basal part of an archegonium which raises the venter above the rest of the gametophyte.

• archegonium neck (PO:0030039): A cardinal organ part that is the elongated apical part of an archegonium. Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

• venter (PO:0030038): A cardinal organ part that is the enlarged basal part of an archegonium and has an archegonium egg cell located in it.

• archegonium neck canal (PO:0030066): A canal in the center of an archegonium neck. Comment: Forms after the archegonium neck canal cells disintegrate.

• archegonium neck canal cell (PO:0030065): A plant cell that is one of the axial row of cells in an immature archegonium neck. Comment: As the archegonium matures, the archegonium neck canal cells disintegrate to form the archegonium neck canal.

central cell (PO:0020090): The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.

http://books.google.com/books?id=L8DHHSO2RFsC&dq=ventral+canal+cell&source=gbs_navlinks_s

Plant Structure Dev Stage terms:

items will be moved here from Items_for_future_meetings page

Upcoming meetings and Presentations 2012-2013:

PAG 2013, San Diego, CA; January 12th - 16th, 2013

We will be running a workshop focusing on:

Applications of Ontologies for Plant and Animal Genomics

• Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6

Speakers: Eva Huala, Reinhard Simon, Elizabeth Arnaud, Chris Mungall, and Pankal will present the cROP Vision

JP will be presenting a SIA Computer Demo:

Date and Time: Sunday, January 13, 2013; 5:20 PM, California room

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.

possible venue for cROP white paper?

website and registration are now open: Biocuration 2013

PRO-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

Goals:

1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
2. To identify potentially fruitful applications which such enhanced coordination might bring
3. To enhance the Protein Ontology treatment of plant-related proteins
4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
5. To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]

Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)

BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University