POC Conf. Call 11-8-11

POC meeting, Webex Conference Call; Date: Tuesday Nov 8th, 2011 10am (PST)

In attendance: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell University), Pankaj Jaiswal (OSU), Justin Elser (OSU),Ramona Walls (NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Justin Preece (OSU)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-1-11? There were no additions, deletions, or changes except for minor typos

Back to POC Meetings Minutes

• Note: LC will miss the meeting Tuesday Nov 22nd. Do we want to have one that week or are others traveling for the holiday? We will try to do it an hour earlier or later

New Glossary page

We now have a glossary page up on the dev site at http://dev.plantontology.org:8080/db/glossary/glossary1.

Note, this is currently limited to just structure terms as there are several terms in the PGDSO that do not lend themselves to obvious inclusion in a glossary. For example, 1 leaf flower stage, 2 leaf flower stage, SE.00 stem elongation begins, etc...

Any comments or suggestions before moving to the live site and announcing?

There is currently a problem as the script is creating entries for each synonym of the terms- BS noted there were 5 entries for whole plant. JE is working on fixing it. Other comments: RW felt that "aspect" would be confusing to users, might be better to use a more descriptive word, such as "Ontology, or Term type.

Discussion about the title: More descriptive name such as ..."Glossary of ... "Plant Anatomy and Development Terms" or maybe eventually "Glossary of Plant Biology", when the scope of the glossary is expanded. In the meantime, should have an explanation on the page (work in progress... etc) and/or a link to a wiki page that describes the source of the terms.

May eventually include Plant species names, pathogens, appropriate GO terms etc ?

Usually the 'Glossary' refers to terms used in the Ontology; such as 'aspect'. May want to create one of these some.

Future directions- will eventually include many things besides PO terms so it might be good to be able to filter by PO terms or GO terms etc.

"Browse by Alphabets"- this is poor grammar, need a search box and also may need to break down by second letter. Would also be good to have a few navigation buttons, like "return to top"

There is something strange on the 'S' page- starting with 'shoot axis stele', all the headings are inset/indented.

It would be good if we could specify the type of synonym, such as

PSDSO revisions: whole plant development stages: Continued from last week

At last week's meeting (see: POC Conf. Call 11-1-11), we started working on the the sub-types of whole plant development stage.

Here are the links to the SF trackers for the items discussed last week:

• gametophyte/sporophyte senescent stage

We need to look up more info and contact GO to add whole plant senescence term- analogous to aging in animals. All these terms are siblings of each other.

We need to decide if we are going to include the word development in all the child term names and be consistent. The names would read better with out it.

for example: 'sporophyte dormant development stage' vs 'sporophyte dormant stage'.

We all agreed that shorter names are better- and if the parent term includes the word, and it is also in the definition.

Should try to get GO to address the issue of inconsistency in the terminology of stages- development, growth and aging. They have different way of dividing up the stages- may result in conflicts as we use their process terms. The should all be dev stages, simplest possible way to describe development stages and then we can just say 'stage'

Only Tanya B (TAIR) and David Hill work on the GO development terms

Other sporophyte development stages:

gametophyte/sporophyte development stages

Proposed definitions:

• sporophyte dormant stage (PO:0007132): A sporophyte development stage that occurs during the interval between a suspension of physiological activity and the reactivation of physiological activity.

propose revised def'n:

sporophyte dormant stage (PO:0007132):A sporophyte development stage that occurs during the interval between the suspension of and reactivation of physiological activity.

new proposed def'n: A sporophyte development stage that occurs during the interval between the suspension of physiological activity and its reactivation.

dormancy vs dormant, include other as a synonym, need to review what occurs during dormancy- suspension of growth and cell division.

• sporophyte vegetative (development) stage (PO:0007134): A sporophyte development stage that occurs during the interval between seed germination and initiation of reproductive structures.

From the dev site: "A sporophyte development stage that has as a participant a whole plant during the interval between seed germination and the initiation of reproductive structures". [source: RW:test]

• sporophyte reproductive (development) stage (PO:0007130): A sporophyte development stage that has as a participant a whole plant during the interval between the initiation of reproductive structures and something (onset of dormancy, senescence, or resumption of vegetative stage). Has participant whole plant and sporangium

What about embryonic stage?

Is it a vegetative development stage, or does it precede it?

Proposed new term:

• embryo development stage: A sporophyte development stage (or a sporophyte vegetative development stage) that occurs during the interval between the first cell division of a zygote and ...

Note: Definition of plant embryo (PO:0009009): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote.

The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryonic phase ends when organs (roots, shoot axes, or leaves) begin to form.

We can work on more specific subdivisions of the embryonic stage later.

Proposed new term:

• embryo development stage: A sporophyte vegetative development stage that occurs during the interval between the first cell division of a zygote and ...

In both angiosperms and gymnosperms use the term 'proembryo': how does this fit in?- first few divisions in the development of the embryo

embryo development stage: Part of vegetative stage, from the 1st division of the zygote (beginning of embryonic stage), ends with what?. Is a whole plant dev stage, a sporophyte dev stage. Ploidy level is not nb, based on definition of sporophyte.

Reproductive stage starts with inflorescence formation and ends when, the plant is ready for seed germination??

DWS: We should consult Singh's "Embryology of the gymnosperms"

Other gametophyte development stages

gametophyte/sporophyte development stages

proposed definitions:

• gametophyte dormant stage (PO:0025342): A gametophyte development stage that has as a participant a whole plant during the interval between a suspension of physiological activity and the reactivation of physiological activity.

Proposed revised def'n: gametophyte dormant stage (PO:0025342): A gametophyte development stage that occurs during the interval between the suspension of and reactivation of physiological activity.

• gametophyte vegetative development stage (PO:0025340): A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.

• gametophyte reproductive development stage (PO:0025341): A gametophyte development stage that is initiated with the development of a gametangium and terminated with fertilization.

Comment: Some gametophytes may die before fertilization.

TraitNet PAO term requests on SourceForge, continued from last week

Last week (see: POC Conf. Call 11-1-11) we also discussed some of the outstanding requests from Traitnet:

• corm/bulb

• pneumatophore

• tendril

-These are all modifications of the structure to which they are attached- all subtypes, no general structure "tendril". Otherwise we would have to make it a modified plant structure. All should have a broad synonym "tendril"

• sorus

What is the status of these terms? Proposed definitions are open on SF, please comment

podarium

Comment from Traitnet: is synonym to tubercle

Rebman and Pinkava, Florida Entemologist (2001) describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:

"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."

Beentje's definition of podarium: (in cacti or other succulents): a modified leaf base functioning as the photosynthetic organ.

Beentje's definition of tubercle: (in ball- or barrel- shaped cacti), cone-shaped protuberances that are enlarged modified leaf bases fused with adjacent stem tissue (also lists two other definitions for tubercle).

Gibson and Nobel (1986, A Cactus Primer) describe a tubercle as developing form a leaf base, but they never clearly define it. -

Gibson and Nobel's description is based on work by Boke (AJB 1941 and 1944), who also does not clearly define tubercle. Boke: "The surface of the plant consists of spirally arranged protuberances which represent persistent leaf bases and on the adaxial sides." Then later, after describing the development of the leaf base: "The writer prefers to regard the leaf base as a part of the stem." He never actually uses the words tubercle or podarium.

Usage of the word tubercle by Papafotiou et al. (2001, Plant Cell, Tissue and Organ Culture)suggests that they are referring to the leaf base: "explants of the normal form were single tubercles excised (with part of the branch tissue at their base)"

Butterworth et al. (2002, Systematic Botany): "Zimmerman (1985) states that ribs and tubercles are mutually exclusive terms, although a number of intermediates are found. He recommends the use of the term podarium, suggesting that in reality ribs are series of podaria joined end-to-end. Tubercles, however, represent free or distinct podaria. This terminology allows for intermediacy between ribs and tubercles. The size and shape of tubercles range from long and leaf-like (as in Leuchtenbergia Hooker, Obregonia Fric, and some species of Ariocarpus Scheidweiler) to broad with shallow axils, as in Turbinicarpus."

(Zimmerman, A. D. 1985. Systematics of the genus Coryphantha (Cactaceae). PhD. thesis, University of Texas, Austin.)

Tubercle seems to be more widely used than podarium (no hits for podarium on Web of Science, 9 hits for tubercle and cactus).

proposed def. tubercle: A conical shaped swollen leaf base that is fused with adjacent shoot axis tissue.

Comment: Found in cacti and other succulents. May elongate and swell, as in species of pincushion cacti (Mammillaria). Tubercles may merge with those directly above and below to form ribs, as in saguaro (Carnegiea). The upper part of a leaf from which a tubercle develops is usually shed early in development.

is_a leaf base

synoyms: podarium, podaria (plural)

ref.: Systematic Botany 27(2):257-270. 2002 Molecular Systematics of Tribe Cacteae (Cactaceae: Cactoideae): A Phylogeny Based on rpl16 Intron Sequence Variation (http://www.jstor.org/pss/3093870)

Get diagram images from Troll.

new proposed def'n. tubercle: An enlarged leaf base that is fused with adjacent shoot axis tissue. Refer to PATO for enlarged

How is this compared to Eichornia plants? In Eichornia (and other plants with swollen leaf bases), the rest of the leaf is still attached, in the podarium, only the leaf base is there.

DWS: hierarchy is 'axillary bud, areole , tubercle, podarium. Should also add the term 'areole' to the PO. (RW: a tubercle is not really a type of areole, although the areole may be displaced to the tip of a tubercle.

areole: a specialized axillary bud in Cacti, small light- to dark-colored bumps, out of which grow clusters of spines, branches, and flowers. (source?)

cladode/phylloclade

These are related terms. Suggest we add them for use in cacti. Also need them for FNA mappings.

From Beentje:

cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf

phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.

FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.

proposed definition:

cladode: A shoot axis that is flattened and expanded.

comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.

synonyms: phylloclade, cladophyll

Need to open a SF tracker for these

Should also add 'rib' for cacti and other plants

diaspore

definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.

Do we want to add this term as a kind of upper level bin term?

Problem is that the definition is based on function (reproduction) rather than structural, positional, or developmental information, and we don't have a way to define it as a cross product right now.

proposed def.: A plant structure that is a dispersed for reproduction. Examples: seed, fruit, spore, bulbil, gemma, tureon

We all agreed that it would be better to add it as a broad synonym for the terms listed above.

Collaborations

Wood anatomy and Forest trees

Wood anatomy: PO will work with a group of scientists to develop ontology terms to describe wood anatomy.

From Jill Wegrzyn at UC Davis: The forest tree community (and in particular the conifers), are interested in collaborating with the Plant Ontology project to develop terms specific to our communities. I currently coordinate efforts on the TreeGenes database (http://dendrome.ucdavis.edu) and will be leading efforts to integrate ontologies into our existing database.

We should start by looking at wood anatomy books and online resources from the IAWA (International Association of Wood Anatomists). They have two main glossaries - one for gymnos and one for angiosperms. They want to have categories for wood structures.

We need to start on this now by dealing with basic terms like tracheary element. These really need work in the PO, so we need to get them in order before we can describe wood anatomy.

Location: NYBG, OSU, more enable more people to take part.

3 Goals:

• wood development and timecourse- formation
• terms for wood structure in the PAO
• Terms to describe wood quality and phenotype, traits

probably will not cover forests or communities, part of pine genome project. Also woody stems in other plants. Loblolly pine.

Suggested speakers: Elizabeth Wheeler, Barb L, Fredich Lens, authors of recent book, Peter Gaston Kew

When:TBA

LC set up a wiki page to organize the Info for this meeting Wood_Anatomy

FNA

See last week's minutes for details of the mappings (POC_Conf._Call_11-1-11#FNA).

Next steps:

• add 364 synonyms to existing terms
• fix several errors that were discovered while doing the mappings
• add 143 unique new terms, plus their synonyms

-FNA provides definitions, so this will be relatively easy

• work with FNA to create an official mapping file

-will need to get unique IDs for duplicate FNA terms

-will need to figure out how to handle FNA terms that map to >1 PO term

-discuss how to map terms that are too general for PO (101 character terms)

• begin work on phenotype/character terms, inlcuding the 101 from this list plus all of the FNA character terms

Conference call with FNA

They would like to set up a conference call with us to discuss the outstanding issues. Hong and James are available available Nov 14 (Monday). Suggested time 1PM ET/10AM PT.

Who else needs to attend this call? (RW, LC, others?)

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). This presentation should involve the larger analysis for the PO paper with the data from Physco and grape etc.

Will be a poster. Can also set up laptop in the poster room to give demo.

Sematic web conference focused on life science

JP will attend the SWAT4LS meeting in December. Folks such as TW from NCBO will be there.

PAG 2012

January 14-18, 2012, San Diego, California

Please see the PAG 2012 Ontology workshop wiki page.

PO will be represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. We have 5 speakers and time at the end for a panel discussion.

PJ may be tied up on Sat am, so we will not plan on him giving a talk at the Ontology workshop, but hopefully he can take part in the Panel Discussion.

• LC is also presenting in the Non-Seed Plant Workshop} (Saturday, Jan 14th, 3:50-6pm) and in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am).

• LC will also do a computer demo for the PO, unless one of the Justins is there and wants to do it.

• The PO will take part in an Outreach booth organized by MaizeGDB.

Important Dates:

• 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.

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

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. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.