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, so
LC: the problem is that this new type of Evidence Code will cast doubt as to the validity of the existing data.
PJ: One way to address this would be to make a second annotation, so they would all have the IEP, but a second annotation would go on the limited number.
The statistical cutoff should be captured somewhere. The data like that from Westerns and Northerns have been individually confirmed, while the large scale data is on a whole-genome scale, and should have the new EC. This will ahve to be presented to the GO community.
Suggest we work on this for the next round. PJ will add the rice annotations with IEP only and will add an additional annotation with the new EC.
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)
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. Yes, most likely, but will wait and add if we need it.
Should use leaf lamina base rather than leaf base and leaf apex, rather than leaf tip. Add synonyms: leaf lamina tip to leaf tip, leaf lamina apex to leaf apex.
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.
Would be better to add: tricellular pollen stage (broad)
PJ: When mitosis occurs it forms the two sperm nuclei, there is not division of the cytoplasm, it is the same single cell, with the same cytoplasm. No plasma membrane forms around. "syncytial"- A multinucleated mass of cytoplasm that is not separated into individual cells."
Notes after the call: I am not sure this is exactly true in all cases: McCue at al clearly show that a cytoplasmic membrane surrounds the sperm nuclei.
McCue et al (2011) Cytoplasmic connection of sperm cells to the pollen vegetative cell nucleus: potential roles of the male germ unit revisited. Journal of Experimental Botany 62: 1621–1631
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).
Does the gametangium ever exist outside the gametophyte development stage? If not, we need to restrict it.
revised def'n: A plant organ (PO:0009008) that produces one or more gametes (PO:0025006) and participates in the gametophyte development stage (PO:0028003).
The definition should include all the essential information. Should we say "when mature?
PJ: The multicellular plant gametangium includes an individual cell that divides to form gametes, so that is a conflict with the definition.
Will follow up on SourceForge, perhaps we could add a comment or deal with this in the respective definitions for archegonia and antheridia.
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."
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:
- To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
- To identify potentially fruitful applications which such enhanced coordination might bring
- To enhance the Protein Ontology treatment of plant-related proteins
- To address coordination issues between the GO and PO, for example as concerns treatment of development stages
- 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
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
