POC Conf. Call 10-18-11

POC meeting, Webex Conference Call; Date: Tuesday Oct 18th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-11-11?

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PO Releases

Current release

Release 16 should occur on or around Oct. 12, 2011.

Any issue to deal with arising from the release?

Next PO Release

Goals and Priorities:

• First major revision of PDSO (formerly PGDSO)

• Complete old user requests/SF tracker items

• New association files: Physcomitrella, grape, potato (?)

• fix dbxrefs for Fragaria annotations

• ABRC annotations to PO and TO terms

• Links to images on PlantSystematics.org

Collaborative projects:

-Mapping of Flora of North America Glossary to PO terms

-Others (These may be longer term than the next release):

-leaf character ontology for Phenotype RCN?

-linking ontology terms to character matrices using Morphobank?

Timeline

• Target date for finishing edits:

• Target date for release:

PDSO Revisions - Review

Review of changes discussed at NYBG meeting in on Saturday_Sept_10th,_2011.

PGDSO was renamed PDSO (See below).

General changes

We agreed to make the following changes:

• Use only stage, instead of phase. Can add phase as synonym, where appropriate.

• Keep numbers in term names for now (so they line up properly), but put them in parentheses.

• Change any names that suggest that they are not stages into stage names, e.g., vegetative growth to vegetative growth stage.

• Make any plural names singular.

• Convert definitions to genus-differentia form, as we are doing with PAO.

• Define stages as occurring between some landmarks (beginning and end points), rather than starting and ending at some landmarks. In this way, stages that are sub-parts of a larger stage will have is_a relations to the larger stage, rather than part_of. For example, protonema stage is_a gametophyte stage.

• The landmarks used to define the beginnings and ends of stages will general fall within the domain of GO biological process, not be part of PO. Will request new terms in GO as needed.

Changes to upper level hierarchy and definitions

New root term: Plant Structure Development Stage

It was decided that whole plant development stage should be is_a plant structure development stage, because a whole plant is a plant structure. This left plant structure development stage as the only sub-type of plant growth and development stage. It was decided to merge these two terms into one new root term: plant structure development stage.

proposed def. of plant structure development stage: A stage in the life of a plant structure during which the plant structure undergoes developmental processes.(POC:curators).

comment: developmental processes refers to GO:developmental process (get ID).

(image of new ontology structure here)

whole plant development stage and sub-types

This section is under construction.

proposed def. of whole plant development stage: A plant structure development stage that has as participant a whole plant.

Added a new term, child of whole plant development stage:

proposed def. of life of whole plant: A maximal whole plant development stage.

Comment: There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.

In order for the definition of life of whole plant to work (and for other reasons), we decided that seed (PO:0009010) should no longer be a subtype of whole plant. It will be is_a plant structure.

We will not have a term plant life cycle as a child of plant structure development stage, because there is not single plant structure that participates in an entire life cycle.

more

Gametophyte development stage and sporophyte development stage (formerly gametophyte phase and sporophyte phase) are direct children of whole plant development stage. These are defined as any interval between their beginning and end, so other whole plant growth stages are subtypes of gametophyte and sporophyte stages.

proposed definition, gametophyte development stage: A whole plant development stage that has as a participant a whole plant during the interval between meiosis or apospory and its death or fertilization.

proposed definition, sporophyte development stage: A whole plant development stage that has as a participant a whole plant during the interval between fertilization or apogamy and its death.

Existing terms for vegetative, reproductive, senescent and dormant stages are actually referring only to the sporophyte stage, so they will be made subtypes of sporophyte development stage, and renamed sporophyte vegetative development stage, etc. Corresponding stages will be created as subtypes of gametophyte stage.

We had an extensive discussion of what senescence is, and how to define the landmarks for the beginning and end of the senescent development stage. Some key points:

-Need differnt definitions for a senescent stage in a whole plant and a senescent stage in a part of a plant (like a leaf).

-Even though a plant may die from other causes before the end of normal senescence, the senescent stage of a whole plant ends with death.

proposed definition, senescence: A plant structure development stage that is (1) initiated by an event of cell death within the plant structure, (2) terminated in the death of the plant structure in such a way that (3) the former is connected to the latter by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism. [source: POC:curators, BS]

This definitions can be modified for specific structures (like sporophyte, gametophyte, leaf, etc.).

proposed definition, gametophyte reproductive development stage: A gametophyte development stage that is initiated with the development of a gamete producing structure and terminated with fertilization.

Comment: Some gametophytes may dies before fertilization.

proposed definition, gametophyte vegetative development stage: A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.

Worked on new children of gametophyte reproductive development stage and gametophyte vegetative development stage. Whole plant development stages that are named after a plant structure that is not a whole plant will need to have the words "whole plant" in their name, to distinguish them from other structure development stages. For example, gametophore reproductive whole plant development stage is a whole plant development stage, while gametophore development stage is a stage in the development of an individual gametophore.

proposed definition, gametophore reproductive whole plant development stage (needs work): A gametophyte reproductive development stage in which gametophores and gametangia are being produced.

proposed definition, gametophore vegetative whole plant development stage (needs work): A gametophyte vegetative whole plant development stage during which a gametophore is being produced but no gametangia are being produced. Succeeds a protonema stage.

proposed definition, protonema whole plant development stage (PO:0030006): A gametophyte development stage during which a gametophyte undergoes filamentous growth. This succeeds spore germination and precedes a thalloid development stage (planar growth) or gametophore development stage.

Can also add new terms for thalloid reproductive whole plant development stage and thalloid vegetative whole plant development stage.

Upcoming meetings and Presentations 2011/2012:

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011 Abstract Deadline: September 9, 2011...

Academic/Student No-Housing Package $720

RW registered and submitted abstract (Media:PO_abstract_PGBatCSHL2011.pdf). Will need to present a preliminary data analysis for the talk/poster.

No word yet on talk vs poster. Data analysis for presentation; This presentation should involve the larger analysis for the PO paper with the data from Physco and grape etc.

PAG 2012

January 14-18, 2012, San Diego, California

PO will host an Ontology workshop for PAG on Saturday January 14th from 10:20am-12:30pm

Use of Ontologies for Organizing Plant and Animal Genomics Data

Please see the PAG 2012 Ontology workshop wiki page.

LC is working on inviting speakers. Additional suggestions are welcome.

Important Dates:

• Registration and Abstract submissions: open on Sept 22
• Early Pre-Registration Deadline: October 31
• Travel Grants Deadline: November 1
• Abstract Submission Deadline: November 11

PJ may be tied up on Sat am, so we will not plan on him giving a talk. LC will also do a computer demo.

LC is also presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00am - 10:10am.

We need to discuss what the PO approach and strategy to phenotypes is. Abstract deadline is November 11

The PO will take part in an Outreach booth organized by MaizeGDB and host a computer demo

Who is attending: LC, PJ (weekend), maybe JP, JE??

Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

Call for abstracts is now open: Need to clarify the deadlines

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation)

2. Poster only

3. Workshop only

• Submission deadline November 30, 2011

• Notification of acceptance February 3, 2012

Instructions

There are seven topic sessions from which submitters are invited to select:

  1. Ontologies, standards and best practices, including gold standard datasets.
  2. Protein annotation; sequences, structures and pathways.
  3. Community annotation and Wikis.
  4. Genomics and metagenomics data curation.
  5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
  6. Literature collection, text mining and curation.
  7. Tools to assist curation, including automated pipelines. 

There are four submission tracks:

  1. Paper, with consideration for oral presentation
  2. Talk
  3. Workshop
  4. Poster 

PJ planning to attend and will be running a biocuration workshop, LC and RW can go, DWS will be away,

'From 9-27-11: PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide.

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open. Deadline for submissions is Saturday, October 15th, 2011 at 11:59 PM PST.

RW, DWS and MAG will put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes. RW will put the draft plant PATO on the SVN.

• We need to have a section sponsor for the workshop proposal, DWS suggested the structural section (Head: Bruce Kirchoff), paleo section or systematists. Development and structural, genetics, and teaching sections would also be appropriate co-sponsors.

From meeting website:

When you submit your proposal, you will be asked for the following information:

• What Societies and Sections will be sponsoring the session. Please provide contact information for any persons who have approved the sponsorship
• The societies participating in Botany 2012 of which you are a member
• The names, email and street addresses of the organizers, and which of them will lead the session
• A title and description of the session
• Keywords and web links that are relevant
• Requirements, such as room type, food, special equipment or transportation, depending on the type of proposal
• An estimate of anticipated attendance
• A list of invited speakers or leaders, if relevant.

Proposal was circulated to the group- please respond by end of the week

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012)

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

22-25 July 2012; Graz, Austria.

Conference Web site: http://purl.bioontology.org/ICBO/

We also have the opportunity to organize an anatomy workshop as well along with CM and MH- need to decide about this soon

Relevant dates

31 December 2011: Workshop and tutorial proposal submission deadline

25 January 2012: Notification of acceptance of workshops and tutorials

31 January 2012: Paper submission deadline

28 February 2012: Notification of paper acceptance

15 March 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline

15 April 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance

30 June 2012: Deadline for all camera-ready copies for the proceedings

We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?

Possible topics?