POC Conf. Call 6-8-10
POC meeting, Webex Conference Call; Date: June 8th, 2010 10am (PDT)
In attendance: POC members:
Collaborators:
Absent:
Acceptance of the minutes from the 6-1-10 meeting? All in favor?
Agenda:
1. POC workshop to be held in Corvallis on June 29th/30th.
I have set up a page on the POWiki [Corvallis Workshop June 29th and 30th, 2010]
The goals of the meeting will be
and who will be invited, etc.
Laurel will assist with local arrangements.
2. Term Requests from Naama Menda, Solanaceae Genomics Network
a. tuber flesh
Proposed def'n: The flesh layer of the tuber (SGN:NM).
We looked at a diagram of the potato tuber anatomy online and saw that the 'flesh' is actually several different layers.
a1. Updated term names and definitions of relevant parent terms:
- ground tissue became portion of ground tissue. Had no definition.
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.
- parenchyma became portion of parenchyma
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. (Original def: Relatively unspecialized tissue composed of polyhedral cells typically with thin, non-lignified cellulose cell walls and nucleate living protoplasts.)
Two Important Questions:
1. Do we need to prefix all these terms like parenchyma with the 'portion of' or can the terms like parenchyma be used as count nouns? Not doing so would simplify the term names considerably (see diagram below), but may not be ontologically correct. If these terms are all children of 'portion of plant tissue" then aren't they all 'portions of' already?
If we decide to use the 'portion of ' prefix, we will also have to change all the other tissue types like collenchyma, sclerenchyma, pith, cortex, etc.
2. 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.
a2. Created new terms to deal with tuber flesh as a general term:
- Portion of storage parenchyma (child of portion of parenchyma tissue): A portion of parenchyma tissue specialized for carbohydrate storage. (Can add XP to carbohydrate: CHEBI:23008 or
starch: CHEBI:28017; GO does not have a term for carbohydrate storage, may want to request). Comment: This tissue could be found in any organ, but often occurs in fruits or tubers.
- Portion of fruit storage parenchyma: A portion of storage parenchyma tissue that is part of a fruit. Syn: fruit flesh
- Portion of tuber storage parenchyma: 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: A portion of tuber storage parenchyma tissue that is part of an aerial tuber.
- Portion of subterranean tuber storage parenchyma: A portion of tuber storage parenchyma tissue that is part of a subterranean tuber. Syn: potato tuber flesh
Comment: This term is used to refer to potato tuber flesh. See part_of children for individual components of subterranean tuber flesh.
a3. Parts of the tuber flesh
These terms can be used to annotate specific parts of the tuber storage parenchyma:
tuber pith (PO:0025052): A pith that is part of a portion of tuber storage parenchyma.
aerial tuber pith (PO:0025054): A tuber storage pith that is part of a portion of aerial tuber storage parenchyma.
subterranean tuber pith (PO:0025053): A tuber storage pith that is part of a portion of subterranean tuber storage parenchyma. Comment: In potatoes, this is part of the flesh. Syn: medulla, water core
Tuber cortex (PO:0025055): A stem cortex that is part of a portion of tuber storage parenchyma.
Aerial tuber cortex (PO:0025056): A tuber cortex that is part of a portion of aerial tuber storage parenchyma.
Subterranean tuber cortex (PO:0025057): A tuber cortex that is part of a portion of subterranean tuber storage parenchyma. Syn: outer storage tissue, Reeve et al. 1969
tuber interfascicular region (PO:0025050): An interfascicular region that is part of a portion of tuber storage parenchyma. Comment: Occurs in tubers. Part_of tuber storage pith.
aerial tuber interfascicular region (PO:0025051): A tuber storage interfascicular region that is part of a portion of aerial tuber storage parenchyma. Part_of aerial tuber storage pith.
subterranean tuber interfascicular region (PO:0025049): A tuber storage interfascicular region that is part of a portion of subterranean tuber storage parenchyma. Part_of subterranean tuber storage pith. Comment: In potatoes, the interfascicular region extends to the subterranean tuber axillary vegetative buds (eyes). Syn: medullary ray, pith ray.
- Also updated definitions and structure for pith, cortex, and interfascidular region
Image of all new or updated terms for tuber flesh:
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 tuber 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).
- Axil Axillary bud is currently defined as: Bud formed in the axil of a leaf or shoot. [source: POC:curators]. There are no scholarly references to shoot axil. PO has the term leaf axil. Should change def. of axillary but to remove reference to shoot.
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):
- 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.
Also updated term names and definitions of relevant parent terms:
- change dermal tissue (PO:0009014) to portion of dermal tissue
Original definition: Tissue derived from the protoderm that covers the surface of the plant body. [source: GR:pj, ISBN:0122151704]
Proposed def: A portion of plant tissue that covers the surface of the plant.
Original def: An outermost cell layer of primary tissues of the plant, sometimes comprised of more than one layer. [source: GR:pj, ISBN:0080374913]
Proposed def: A portion of dermal tissue composed of epidermal cells that develops from the protoderm and covers the plant in the primary state.
Comment: The epidermis can be composed of one or more layers of cells.
Original def: Secondary protective tissue that replaces the epidermis in stems and root, rarely in other organs. [source: GR:pj, ISBN:047124529]
Proposed def: A portion of dermal tissue that is secondarily derived and composed of phellogen, phellem, and phelloderm.
Comment: Replaces the epidermis in stems and roots, rarely in other organs.
This is an old request. 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.
e. Added new subset for potatoes
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:
* 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. 62 people are signed up! 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: http://www.doodle.com/6n4pmknkeebk9khg
* Infectious Disease Ontology Workshop
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.
Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.
For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html
8. Next meeting scheduled for Tuesday June 15th at 10am PDT.
