POC Conf. Call 11-1-11

POC meeting, Webex Conference Call; Date: Tuesday Nov 1st, 2011 10am (PDT)

In attendance:

POC members: Ramona Walls (NYBG), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell University), Pankaj Jaiswal (OSU), Justin Elser (OSU), Justin Preece (OSU)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-18-11? There were no additions, deletions, or changes except for minor typos.

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Infectious disease ontology for plants

At last weeks meeting, BS asked if anyone wanted to co-author a preliminary paper on infectious diseases in plants, as an extension of the IDO. RW said she would like to do this, if BS thought that her limited knowledge of plant diseases was not a problem. He said it shouldn't be at this stage.

Need to go through IDO and pick out those terms/regions in the ontology that are relevant to plants, and how plant diseases would fit into IDO's framework. How might we test the results in specific disease in plants. e.g., host, pathogen, vector - already have those.

We discussed whether or not there are non-infectious diseases in plants. Closest thing is a gall, which is a plant response to a insect or other foreign organism. This leads to a cancer like growth that is not contagious. IDO has that covered. There are also endophytes in plants -- fungi that live within the plant but are not pathogenic. Maybe be comparable to the bacteria and other organisms that live in and on humans with little known effect.

Crown galls - caused by virus - may be infectious

What about chronic disease like Lyme disease? Are plants ever killed by galls? Plants can get so many of them that they die, but one gall does not spread to another. May be other diseases that can start out small and either remain small or spread to become chronic.

Do plants have immune systems? They have systematic responses to pathogens and pests. That work needs to be done in IDO.

We should also think about plant structures as they relate to diseases (e.g. gall, blister) - "patho-anatomical structures".

LC: I am interested in taking part in this as well. I have some background in plant pathology and access to many experts in this dept. Crown gall is caused by the bacterium, Agrobacterium tumefaciens, or closely a related species. Crown Galls could be transmitted in the case of a graft- the Agrobacterium can be transmitted to the new plant. Galls also form on plants in response to wounding and from chemicals produced by insect invaders.

In answer to BS' question: here is a link to a 2006 Nature Review: The Plant Immune System.

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).

Differs from bulb, because bulb is leaf bases.

Maybe request perrenation in GO biological process?

Should be is_a shoot system. Often has scale leave that form a protective covering and are part of the corm, and it contains at least one bud.

new proposed def. of corm: A shoot system that has as parts a short, enlarged stem in which the internodes do not elongate, and one or more buds.

comment: May serve as a storage or perennating organ. Usually underground. Differs from a bulb (PO:xxxx) in that it does not have fleshy leaves or leaf bases, but usually has scale leaves or remnants of dry leaf sheaths (tunics) that form a protective covering around it. May bear remnants or scars of detached leaves. Adventitious roots may develop from the base of a corm, and these may be contractile, pulling the corm into the soil. Examples include Gladiolus and Crocus. The pseudobulb of an orchid is equivalent to a corm. A corm is very similar to a rhizome (PO:0004542) with very short sympodial units, although not all corms have sympodial growth

Narrow synonyms: cormel, cormlet, pseudobulb. Reference: Bell and Bryan

LC: By definition, I think corms are always underground.

add term bulb; Beentje: underground storage organ, the bud enclosed by fleshy scale leaves or leaf bases. Example: Alium

Bulb should be is_a shoot system.

Use Bell and Bryan as source.

proposed definition of bulb: A short, enlarged shoot system that has as parts a short stem and one or more buds enclosed by fleshy leaves or leaf bases.

Comment: The internodes between the leaves of a bulb do not enlongate. May serve as a storage and/or perennating organ. Usually underground. Differs from a corm (PO:xxxx) by having fleshy leaves or leaf bases. The outer leaves of a bulb are often dry and membranous, rather than fleshy. May bear adventitious roots. Examples include Alium and Tulipa.

narrow syn.: bublet (bulbil is different, should be a different term)

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

add synonym: breathing root

Cypress knee is a knee root - is it a type of pneumataphore with a bend? Need to find out what people call them in cypress and figure out if knee root should be added as a separate term.

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. If the tendril is derived from the terminal leaflet, use the term leaflet tendril (PO:xxxxxxx). 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. Get list of tendril types form Bell and Bryan.

(German: Ranke)

We should not create a general class for tendril, because it does not have a structural basis. The only thing they have in common is shape/function.

Should request "tendril-shaped" in PATO and define all these as tendril-shaped - if it is indeed true that what unites these structures is their shape. Then, in the future, we could add an intersection_of statement that says has_quality tendril shape. Then one could create a category for tendrils that is the intersection_of is_a plant structure and has_quality tendril-shaped. For now, we will have to define the shape separately in each term.

Tendril is an abbreviation for referring to several types of structures that have the same shape -- it does not merit its own ontology class.

We should put a comment on the different types of tendrils referring users to the other kinds of tendrils, in case they end up on the wrong one.

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 on the surface of a vascular leaf that has as part a cluster of two or more adjacent sporangia.

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 on the surface of a vascular leaf that has as parts two or more fused sori.

Need to add term indusium to PO.

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?

(after meeting) -- yes. that would be a good idea.

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.

Should work with PATO to get a set of relevant diagrams of shapes, like tendril-shaped or helix or leaf shapes, that they could link to.

Wood anatomy and Forest trees

Do we need to talk about these at the meeting?

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.

FNA

This includes the run on 07/18/2011 by C. Mungall using the OBOL program. When the software returned multiple matches, RW chose the correct match, or used both if appropriate. Other matches added manually by RW.

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

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

NOTE: OBOL 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	Matches to both term names and syonyms. This is high, because many of these were not accurate (OBOL matched all concepts with the same name in FNA to the same PO term)
Total number of one to one matches to existing terms:	126	includes one to one matches that are slight variants on name (e.g., FNA:fascicle to PO:flower fascicle, FNA:cell to PO:plant cell)
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 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 unique new terms needed:	143	if all are approved
Total number of FNA terms that should be added as characters:	101	Too general for PO structures, better scored as phenotypes
FNA terms that could not be mapped to PO:	17	actually, some of these might be plant substances (e.g., raphide)
~belong in GO:	5
~too vague for PO structures:	12	some of these could be scored as phenotypes

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

LC: We need to make sure this information is also on the FNA collaborators page.

PSDSO revisions

sub-types of whole plant development stage: senescent stage

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 September, 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 (this won't actually go in PO): 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.).

note: clause (3) should say "...the latter is connected to the former..."

GO:0010260 organ senescence: The process that occurs in an organ near the end of its active life that is associated with the dismantling of cell components and membranes, and an overall decline in metabolism. An example of this process is found in Arabidopsis thaliana.

GO does not have a term for senescence of an organism. They did have a general term "senescence" but it was made obsolete because it overlapped with organ senescence and cell aging.

GO:0007568 aging:The inherent decline over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility.

We could use definitions as below, or we could request a new term in GO biological process called organism senescence and define gametophyte and sporophyte senescence based on that.

We need to work with GO on their definition of aging, which is not appropriate for all its subtypes (e.g., cell aging does not involve decline from optimal fertility). Organism senescence should be a subtype of aging, so definition of aging will have to cover that.

Definition of senescence for GO would be similar to definition of senescent stage, above.

We will have to address cell senescence for terms like fibers or tracheids which are dead at maturity.

Aging in plants is not like aging in animals. In plants, you can have an organ aging (that is; senesncing) while the rest of the plant is not. We will need a process term for 'organ senescence', as well as cell and organism senescence.

Add new child of aging - organism aging - and add organisms senescence as a synonym of it. Aging could be just the general decline over time.

RW will start a GO SF tracker item for senescence/aging.

If an organism is dying due to disease, is that considered senescence? Acute, progressive and chronic diseases - with chronic you can go a long time without dying. Dying with chronic disease can occur by senescence (unless it become progressive), but with an acute disease (just as with an accident) you die before senescence occurs. Senescence is not caused by environmental factors -- an endogenous process -- although certainly environmental factors can speed it up or slow it down.

proposed terms and definitions

See SF link: gametophyte/sporophyte senescent stage

proposed definition, gametophyte senescent stage: A gametophyte development development stage that has as a participant a gametophyte/occurs during the interval between an event of cell death and the death of the gametophyte, such that the initial cell death is connected to the death of the organism 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 has as a participant a sporophyte/occurs during the interval between an event of cell death and the death of the sporophyte, such that the initial cell death is connected to the death of the organism by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.

Comment: In annual angiosperms, the sporophyte senescent stage follows the sporophyte reproductive stage. (Are there annuals in other types of vascular plants?)

Do we need to repeat "has as a participant a gametophyte/sporophyte" in child terms? No! If you have to repeat parts of definitions of parent terms, there is a problem.

What about using "occurs"? BS says this is okay. We know what it means.

This could also be applied to the definitions of gametophyte/sporophyte development stage, because has participant whole plant is already inherited from whole plant development stage.

new proposed definition, gametophyte senescent stage: A gametophyte development stage that occurs during the interval between an event of cell death and the death of the gametophyte, such that the death of the organism is connected to the initial cell death by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.

Occurs after the production of gametiangia. May produce many archegonia, but usually only one sporophyte is produced -- once one archegonium is fertilized, gametophyte starts to senescence. Development depends on whether it is pleurocarpus or acrocarpous moss -- need to look into this.

new proposed definition, sporophyte senescent stage: A sporophyte development development stage that occurs during the interval between an event of cell death and the death of the sporophyte, such that the death of the organism is connected to the initial cell death by processes of dismantling of cell components and membranes, loss of functional chloroplasts, and an overall decline in metabolism.

Comment: In annual angiosperms, the sporophyte senescent stage follows the sporophyte reproductive stage. (Are there annuals in other types of vascular plants?)

We need to find a plant phys book that covers senescence.

LC: Looked in Raven et al, (5th edition) and in my old Salisbury and Ross (3rd edition)- not defined but discussed in terms of the plant hormones cytokinin (preventative) and ethylene (promotes senescence). In this sense senescence can be induced by an environmental factor. See also this site: Senwiki

Also located a 2007 Annals of Botany review: "Senescence processes in plants". Annual Plant Reviews, Volume 26. S. Gan. ed. 2007. Oxford: Blackwell Publishing Ltd. Not in the OSU library, but requested by interlibrary loan

Upcoming meetings and Presentations 2011/2012:

No news on meetings at this week's meeting

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 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 host the following events:

• Ontology workshop for PAG on Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data. LC is working on inviting speakers. Additional suggestions are welcome.'

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.