POC Conf. Call 11-1-11

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POC meeting, Webex Conference Call; Date: Tuesday Nov 1st, 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_10-18-11?

Back to POC Meetings Minutes


Old user requests on Source Forge

TraitNet requests

corm

proposed def: A short, enlarged stem in which the internodes do not elongate.

Comment: May serve as a storage and/or perennating organ. Usually underground.

child of stem (PO:0009047).

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def: A lateral root that is erect and protrudes above the soil.

Comment: Pneumatophores are found in trees that live in flooded habitats such as mangroves. May provide oxygen to below ground roots growing in flooded soils.

is_a lateral root

tendril

Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.

tendrils can be (evolutionarily) derived from multiple types of structures. Suggest we make separate terms:

branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.

leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaflet tendril (child of leaflet): A leaflet that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.

Can add other types of tendrils if they come up or users need them.

This is the way we defined spine (no parent class spine, only leaf spine and stipule spine with is_a relations to leaf and stipule).

Also need to add terms for petiole tendril and maybe root tendril.

(German: Ranke)

sorus

from Crum (2001): a cluster of fern sporangia

from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.

Proposed definition: A collective plant structure has as part a cluster of two or more adjacent sporagia on the surface of a leaf.

Comment: Found in ferns. May be enclosed by an indusium.

Part_of vascular leaf, has_part sporangium


Can also add coenosorus – A collective plant structure that has as parts two or more fused sori.

PGDSO revisions

sub-types of whole plant development stage: vegetative, reproductive, senescent, and dormant stages

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.

senescent stages

At the NYBG meeting in Sepetember, 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 different 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.

general definition for senescent stage: 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 senescent stage: A gametophyte development development stage that is initiated by an event of cell death within a gametophyte and terminated by the death of the gametophyte in such a way that the initiation is connected to the death by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.

proposed definition, sporophyte senescent stage: A sporophyte development development stage that is initiated by an event of cell death within a sporophyte and terminated by the death of the sporophyte in such a way that the initiation is connected to the death by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.

Comment: In annual plants, the sporophyte senescent stage follows the production of flowers seeds (sporophyte reproductive stage).

other sporophyte stages

proposed definition, sporophyte reproductive development stage: A sporophyte development stage that


proposed definition, gametophyte vegetative development stage: A sporophyte development stage that.

proposed definition, gametophyte dormant development stage:

other gametophyte stages

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 die before fertilization.


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

proposed definition, gametophyte dormant development stage:

Collaborations and other items

  • Dr. Judy Jernstedt of the Department of Agronomy & Range Science/Plant Sciences, UC Davis will be visiting the OSU BPP Dept on Friday, November 4

She is Editor-in-Chief of the the American Journal of Botany, Should we try to set up a time to meet with her to introduce the PO?

PlantSystematics.org

We had a PO PlantSystematics conference call 10-21-11 with KN, where we set forth the following tasks:

short term:

  • KN will send list of all PS.org keywords to RW at PO. (see update below)
  • RW will work with JP to create a mapping file between PS.org keywords and PO IDs. This will go on PO's SVN and will follow standard mapping file format.
  • JP, JE and RW will work create a few test cases of keyword searches (e.g., some with a single word, some with multiple words) and send these to KN so he can figure out the best format for the url.
  • JE will create the links from pages on the dev version of PO's AmiGO brower, to make sure they work properly.

longer term

  • PO will work on method of automatically adding links to images from PO based on PO term names and synonyms.
  • PO will work with KN to devise a strategy for associating PO id's directly with PO.org images. These can then be used to link back to PO.


Update from KN:

I wrote something to extract individual keywords, but I would like to do some editing of the actual keywords before continuing. Because we did not enforce any kind of delimiters, there are some compound keywords that will otherwise be broken up into individual words.

So, I am making a different schema for keywords which will both be easier to manage and allow indexing of words (links to images by unique word/phrase), sorting into hierarchies (e.g., flower features, leaf features) etc. I should have this ready soon, probably next week.

At this point, there are only about 1900 images with keywords, and about 1800 unique ones (but of course, this is overcounting those with multiple words).


Note: We can add keywords to PlantSystematics.org to associate them with images that we want to match to PO terms.

Wood anatomy and Forest trees

Do we need to talk about these at the meeting?

FNA

This includes the run on 07/18/2011 by C. Mungall using xxx software. When the software returned multiple matches, RW chose the correct match. Other matches added manually by R. Walls.

Exact duplicates (same term, category, and limitation) represent multiple defiintions for the same term in FNA glossary. RW added numbers to correspond to FNA numbers.

Definitions from PO were check against defintiions from the FNA glossary at http://128.2.21.109/fmi/xsl/FNA/home.xsl

NOTE: the automatching program will match to obsolete terms, with no warning.


Number of FNA terms: 839 including duplicates with different meanings
Number of PO anatomy terms: 1080 release 16
Number of matches: 930 including duplicates with different meanings, plus those with the same meaning that map to multiple PO terms
Number of matches made by software: 264
Number of multiple matches made by software: 49 Automatched to more than one term. 26 of the multiples are because the Spanish and English names are the same
Total number of matches to existing synonyms: 193 Includes 3 obsolete terms
Total number of one to one matches to existing terms: 126 (includes one to one matches that are slight varients on name {e.g., FNA:fascicle to PO:flower fascicle, FNA:cell to PO:plant cell}) DB:Reference) PMID:2676709
7. * Evidence IMP
8. With (or) From
9. * Aspect G
10. DB_Object_Name lesion resembling disease-10
11. Synonym) bl5|spotted leaf-4
12.* DB_Object_Type gene
13.* taxon) taxon:4527
14.* Date 20050303
15.* Assigned_by GR
16. Annotation_extension part_of(PO:0028002)
17. Gene Product Form ID UniProtKB:P12345-2


Total number FNA terms that map to >1 PO term 14

Total number of matches to obsolete terms: 8 (Inlcudes duplicate plural forms, 5 unique. 3 have been replaced by GO terms, other 5 have no explanation as to why obsolete.)

Total number of new synonyms needed for existing terms: 364 (includes plural forms, so many of these will go to the same PO term)

Total number of uniquenew terms needed: 143 (if all are approved)

Total number of FNA terms that should be added as charactersl: 101 (Too general for PO structures, better scorred as phenotypes)

FNA terms that could not be mapped to PO: 17

~belong in GO: 5

~too vague for PO structures: 12

Upcoming meetings and Presentations 2011/2012:

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011

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.

Sematic web conference focused on life science

JP will attend this meeting in December. Folks such as TW from NCBO will be there.

Will put more notes when they are available.

PAG 2012

January 14-18, 2012, San Diego, California

Please see the PAG 2012 Ontology workshop wiki page.

PO will host the following events:

PJ may be tied up on Sat am, so we will not plan on him giving a talk.

  • LC is also presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00am - 10:10am.
  • Stefan Rensing has asked us to present a talk on expanding the PO to include bryophytes, as part of a non-seed plant workshop (Saturday, Jan 14, 3:50-6PM). LC will give this presentation.
  • LC will also do a computer demo.
  • The PO will take part in an Outreach booth organized by MaizeGDB.


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

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


Abstract deadline is November 11. Will need abstracts for plant phenotype workshop, computer demo, non-seed plant workshop, and any talks going into the Ontologies workshop.

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:


RW, DWS and MAG 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.

Proposal was submitted, waiting for news.


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.

exhibitor's booth

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.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

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

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts.

Could also consider organizing a phenotype ontology workshop.

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: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?

BS would like to collaborate on a preliminary paper on Plant Disease Ontology if anyone is interested.

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