POC Conf. Call 6-1-10

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POC meeting, Webex Conference Call; Date: June 1st, 2010 10am (PDT)

In attendance: POC members:

Collaborators:

Absent:

Acceptance of the minutes from the last meeting? All in favor?


Agenda:

1. Term Requests from Naama Menda, Solanaceae Genomics Network

a. tuber flesh

Proposed def'n: The flesh layer of the tuber (SGN:NM).

Comments from last week's meeting:

BS: Terms like 'flesh' are 'mass' nouns and should be avoided, better to use 'count' nouns.

DWS: the proper botanical term is storage parenchymal tissue, starch filled, could use 'flesh' as a synonym

PJ, RN: the ontology must be understandable to the users like plant breeders. There was discussion about how the users would be able to know where the annotations would go.

We looked at a diagram of the potato tuber anatomy online and saw that the 'flesh' is actually several different layers.


Created new terms to deal with tuber flesh (see dev browser):

  • Portion of storage parenchyma tissue (child of portion of parenchyma tissue): A portion of parenchyma tissue specialized for carbohydrate storage. (Still need to work on definition with possible XPs to GO or ChEBI terms). Comment: This tissue could be found in any organ, but often occurs in fruits or tubers.
  • Portion of fruit storage parenchyma tissue: A portion of storage parenchyma tissue that is part of a fruit. Syn: fruit flesh
  • Portion of tuber storage parenchyma tissue: A portion of storage parenchyma tissue that is part of a tuber. Syn: flesh, flesh tissue (maybe these should be synonyms of storage parenchyma rather than tuber storage parenchyma)
  • Portion of aerial tuber storage parenchyma tissue: A portion of storage parenchyma tissue that is part of an aerial tuber.
  • Portion of subterranean tuber storage parenchyma tissue: A portion of tuber storage parenchyma tissue that is part of a subterranean tuber. Syn: potato tuber flesh

Comments: This is the term that would be used to refer to potato tuber flesh. See more specific terms for different portions of subterranean tuber flesh (Still need to add these terms).

Also updated term names and definitions of relevant parent terms:

Proposed def: Any portion of plant tissue other than the dermal or vascular tissue. Develops from the ground meristem (meristem L2 and meristem L3).

This is a case of 'defining by what it's not,' but it is the most common definition out there. We can work on a better definition later.

Proposed def:A portion of ground tissue composed of polyhedral cells typically with thin, non-lignified cellulosic cell walls and nucleate living protoplasts. Comment: Parenchyma contains relatively unspecialized cells. Synonyms (exact): parenchyma, parenchyma tissue, ground tissue

This is a relatively minor change from the original definition, adjusted to fit the genus/differentia form: Relatively unspecialized tissue composed of polyhedral cells typically with thin, non-lignified cellulose cell walls and nucleate living protoplasts.


Questions:

  • Do we need to call parenchyma 'portion of parenchyma tissue,' or can the term parenchyma be used as a count noun? It would simplify the term names. If we change this, we will have to change all the other tissue types like collenchyma, sclerenchyma, epidermis, etc.
  • What is the rule/policy on having the same synonym for multiple terms? If someone is searching for flesh, they may mean either tuber flesh, fruit flesh, or flesh in some other tissue, so it might make sense to have flesh be a synonym of portion of storage parenchyma tissue, portion of fruit storage parenchyma tissue, portion of tuber storage parenchyma tissue, portion of aerial tuber storage parenchyma tissue, and portion of subterranean tuber storage parenchyma tissue.


b. tuber eye

Proposed def'n: The structure on the tuber surface that can sprout. It also has a significance in determining the processing quality.(SGN:NM).

Comments from last week's meeting:

DWS: the eye of a tube is an axillary bud or meristem


Created new terms to deal with tuber eye (see dev browser):

  • tuber axillary vegetative bud: An axillary vegetative bud that is part of
a tuber. 

  • aerial tuber axillary vegetative bud: A tuber axillary vegetative bud that
is part of an aerial tuber.
  • subterranean tuber axillary vegetative bud: A tuber axillary vegetative bud that is
part of a subterranean tuber. Syn: eye, potato eye, tuber eye. 
Comments: In potatoes, axillary vegetative buds (eyes) can determine
processing quality.


Problems with parent terms:

  • Axillary vegetative bud is both an axillary bud and a vegetative bud. Also, bud has no is_a parent (is part_of shoot).
  • We may need the term axil, so leaf axil and shoot axil can be children of it axil. Then we can define axillary as a bud that occurs in an axil. Right now we have leaf axil, and this may be enough. However, axillary bud is currently defined as: Bud formed in the axil of a leaf or shoot. [source: POC:curators]. Is there really such a thing as a shoot axil?


c. tuber epidermis

Proposed def'n: Epidermal layer of a tuber.(SGN:NM)

From last weeks meeting: the skin of a potato is actually a periderm, but there are tubers (including young dicot tubers and monocots) that have an epidermis, so we will need both tuber epidermis and tuber periderm.


Created new terms to deal with tuber epidermis (see dev browser):

(this section still under construction by RW)

Tuber periderm: A periderm that is part of a tuber.

Aerial tuber periderm: A tuber periderm that is part of an aerial tuber.

Subterranean tuber periderm: A tuber periderm that is part of a subterranean tuber. Syn.: potato skin

Tuber epidermis: A shoot epidermis that is part of a tuber.

Aerial tuber epidermis: A tuber epidermis that is part of an aerial tuber.

Subterranean tuber epidermis: A tuber epidermis that is part of a subterranean tuber.



d. On a related note, we have an old request for root tuber New term for root tuber.

We already have the terms aerial tuber (PO:0004548) and subterranean tuber (PO:0004547), which may have been added in response to this request. Suggest that we close this item while we are working on tubers.




2. Report on meeting with TraitNet

Ramona met with Dan Bunker (New Jersey Institute of Technology) and Farshid Ahrestani (Columbia University) to discuss possible collaborations with PO.

Items carried over from last week's agenda:

1. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.


Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312


Barry suggested that we reword the second half of the definition, because the final word 'it' was ambiguous about what it was referring to, and the use of the word 'other' was unclear. We agreed that the second part of the definition about other floral structures should go into the comments section. Started to discuss whether or not the seed should be included as part of the definition (fruit contains seed), but ran out of time. To be continued next meeting.



2. Embryo (See SF Tracker: embryo)

Discussion of embryo was postponed until next meeting.


Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants


(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes -add a comment?


Relationships:

(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity (2) develops_from zygote (see comment above) Usually (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)




x. Linking images to PO

  • We can put in hyperlinks to individual images posted on plantsystematics.org
  • More difficult to insert hyperlinks to collections of images, such as search results for keyword "pedicel," but it is possible
  • If each image has a unique ID, Amigo can automatically generate hyperlinks to the database, so we would only have to input the ID. For example, we would enter PS:00123 under exteral dbxrefs, where PS would stand for PlantSystematics.org, and 00123 would be the unique ID number for an image, and in the Amigo browser, there would be a link to the image in Plantsystematic.org.
  • Can we request that arrows be added to some of the existing images to highlight the feature we want to illustrate?


Upcoming Conferences and Meetings: Updates:

*Infectious Disease Ontology Workshop

To be held in Dallas, Dec. 8th and 9th, organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

It would be good to have someone there to represent the interests of the PO with regard to plant infectious diseases. This may be especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research. Either one of the POC coordinators could attend, or we could suggest a colleague who is an expert on plant infectious diseases.

Any suggestions?

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html


* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.

Alejandra cannot travel that day -- can attend via conference call.

Ramona will be in Portland June 26-29, Ramona has sent a requested to schedule her talk on the 27th or 28th. Barry will be in France this week and can't attend. DWS may be in England after all.

Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).

Laurel will be working on plans for the meeting in the next few weeks, will contact Chris and see if he can come up.


* Bio-Ontologies 2010: Semantic Applications in Life Sciences. July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona are registered.

Our one page write up has been selected for a 'flash update talk' along with the poster. Final revisions were submitted Friday May 14th.


* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation and Annotation Workshop with Gramene.

Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. more details TBA


  • Botanical Society of America (BSA)- July 31-Aug 4th 2010. Providence, Rhode Island. Dennis, Alejandra attending, Ramona presenting, 15 minute oral presentation, Abstract submitted 3/26/10.


  • Annotation workshops to be held at NYBG in fall 2010. Date TBD.

Will invite outside experts, scientists, students and postdocs.

Please fill out Doodle Poll re. dates that you are or are not available.


8. Next meeting scheduled for Tuesday June 7th at 10am PDT.

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