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| | '''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)''' | | '''POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)''' |
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| − | In attendance: | + | In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU) |
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| − | POC members:
| + | Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY) |
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| − | Absent:
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| − | Collaborators:
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| | + | Collaborators: none |
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| | Acceptance of the minutes from the [[POC_Conf._Call_3-8-11]]? | | Acceptance of the minutes from the [[POC_Conf._Call_3-8-11]]? |
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| − | ==Issues arising from last week's meeting:==
| + | ''There were no changes, additions, or deletions.'' |
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| − | ==Continuing User requests: for PSO==
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| − | - Deal with and complete the list of user requests on SourceForge-
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]===
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| − | submitted by Austin Mast
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| − | Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3165981&group_id=76834&atid=835555 fascicle] The term fascicle can refer to different structures in different taxa. Suggest we use the term '''floral fascicle''' or '''flower fascicle''' in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
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| − | From Tucker, 2003, Flora:
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| − | (in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
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| − | that two to several flowers are initiated in each bract axil rather than
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| − | just one as in a raceme. '''The cluster of flowers at each node is called a fascicle.''' The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows
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| − | '''the fascicle to be a short shoot topped by a second order inflorescence apical meristem'''. This meristem initiates
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| − | flowers in a bilaterally symmetrical order: a single abaxial flower, then
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| − | two lateral flowers, another median abaxial, then two more laterals. The
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| − | number of flowers per fascicle depends on the duration of the axillary
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| − | inflorescence apex of the short shoot, which ceases activity after
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| − | initiating the few flowers in the fascicle. No flowers are initiated
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| − | adaxially (toward the first order axis) on the short shoot (Tucker, 1987b;
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| − | Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be
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| − | distinguished from a cyme in that every flower is bract subtended in a
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| − | pseudoraceme."
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| − | Suggested def: A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated. Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle] (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
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| − | We added the term stipule spine. Could also add the term '''stipule bristles''': A stipule that has a brush-like appearance.
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| − | Alternative is to suggest bristled to PATO
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode] Suggested def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]
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| − | '''Banner''' (as in a legume flower) - suggest using name 'banner petal'
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| − | Suggested def: A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
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| − | '''Wing''' (as in a legume flower) - suggest using name 'wing petal'
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| − | Suggested def: One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.
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| − | '''Keel''' (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name 'corolla keel'
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| − | Suggest three new terms:
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| − | fused petal: A petal that is fused to another petal. Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
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| − | fused corolla: A corolla in which the petals are fused. Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
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| − | corolla keel: A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae. Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3166008&group_id=76834&atid=835555 locule] The term locule can be used to refer to the cavity in an carpel or in an anther. In the PGDSO, we have the term PO:0001026 locules established, which is an anther development stage. For clarity, we may want to add two terms: locule, anther locule and carpel locule.
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| − | anther locule: A plant anatomical space that is a cavity in an anther formed by a single pollen sac.
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| − | carpel locule: A plant anatomical space that is a cavity in a carpel that contains at least one ovule. Comment: A syncarpous gynoecium may have multiple locules, and the locules of multiple carpels may be fused.
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| − | May want to add general parent terms locule: A plant anatomical space that is a cavity within a sporophyll. Synonym: loculus
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| − | ===TraitNet requests===
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]
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| − | proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
| + | =Issues arising from last week's meeting:= |
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| − | child of stem (PO:0009047).
| + | Special technical meeting? |
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| | + | ''The conference call will take place on 3-17-11, at 4PM PDT.'' |
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium] | + | ''RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it. Will post possible alternative solutions on the [[POC Technical Issues Page]].'' |
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| − | Their comment: is synonym to Tubercle
| + | =Physcomitrella terms= |
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| − | podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
| + | ''Discussion of new terms was postponed until next week, due to low attendance.'' |
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| − | tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
| + | ==[https://sourceforge.net/tracker/?func=detail&aid=3109542&group_id=76834&atid=835555 Gametangium, antheridium, archegonium and related terms]== |
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| − | proposed def:
| + | ==apical cell== |
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| | + | ==Collective plant structures:== |
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
| + | ==Plant organs:== |
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| − | definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
| + | ==Additional moss terms:== |
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| − | proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
| + | ==Cardinal organ parts== |
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| − | | + | ''See [[POC_Conf._Call_3-22-11]] for details.'' |
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore] | |
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| − | 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.
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| − | We could add this term as a kind of upper level bin term (similar to trichome)
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone] | |
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| − | Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]
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| − | from Crum (2001): a cluster of fern sporangia
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| − | from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
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| − | Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
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| − | Part_of vascular leaf, has_part sporangium
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| − | [https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
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| − | Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
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| − | tendrils can derived from multiple types of structures. Suggest we make separate terms:
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| − | branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
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| − | leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
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| − | leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
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| − | leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
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| − | Can add other types of tendrils if they come up or users need them.
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| − | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]===
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| − | submitted by Rich Zobel (Nov 2009)
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| − | ==User requests still open on Source Forge; PGDSO ==
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| − | ===[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]===
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| − | This item has been open on SF since 6/2009
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| − | I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
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| − | Suggested stages:
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| − | -sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
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| − | -tuber initiation
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| − | -tuber growth
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| − | -tuber maturation
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| − | How we work these in will depend on restructuring of PGDSO
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| − | l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
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| − | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed development stages]===
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| − | This is a fairly new request for terms for cotton
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| | =Upcoming meetings 2011:= | | =Upcoming meetings 2011:= |
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| | '''* ICBO 2011 Second International Conference on Biomedical Ontology''' | | '''* ICBO 2011 Second International Conference on Biomedical Ontology''' |
| | July 26-30, 2011 | | July 26-30, 2011 |
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| | LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" | | LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" |
| − | Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper | + | Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted) |
| | + | LC is working with the other organizers to develop the workshop plans and a call for papers. |
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| − | Submitted: February 15th, 2011
| + | '''Full-Day Workshops Schedule:''' |
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| − | - LC will attend and represent the PO. Invite other plant people? Will talk with Elizabeth Arnaud at the upcoming meeting. | + | '''July 26 9am-6pm''' The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies |
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| − | -BS suggested we might want to submit a short paper which could be published in longer form later- see above | + | '''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability |
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| | + | '''July 26 6.30pm-9pm''' Evening Workshop: Common Logic |
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| | + | '''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium |
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| | + | - LC will attend and represent the PO, will submit a short paper/poster for the workshop (deadline April 1st). |
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| | Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13. | | Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13. |
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| | + | Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster. |
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| | Abstract deadlines: Your abstract must be submitted by '''March 11''' if you want it to be considered for a minisymposium talk. | | Abstract deadlines: Your abstract must be submitted by '''March 11''' if you want it to be considered for a minisymposium talk. |
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| − | For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27. | + | For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''. |
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| | + | TAIR is organizing an Outreach Booth and we are invited to take part. |
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| | Dennis, Alejandra, Pankaj and Ramona are planning to attend. | | Dennis, Alejandra, Pankaj and Ramona are planning to attend. |
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| | + | Early bird registration deadline - Extended 1 March 2011 |
| | + | Deadline for registration by presenters 1 March 2011 |
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| | See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details | | See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details |
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| − | ==Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PST== | + | |
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| | + | ==Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PDT== |
POC meeting, Webex Conference Call; Date: Tuesday Mar 15th, 2011 10am (PST)
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Justin Preece (OSU)
Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
Collaborators: none
Acceptance of the minutes from the POC_Conf._Call_3-8-11?
There were no changes, additions, or deletions.
Issues arising from last week's meeting:
Special technical meeting?
The conference call will take place on 3-17-11, at 4PM PDT.
RW will look try to see if any other ontologies are using the has_part relation, and how they deal with it. Will post possible alternative solutions on the POC Technical Issues Page.
Physcomitrella terms
Discussion of new terms was postponed until next week, due to low attendance.
apical cell
Collective plant structures:
Plant organs:
Additional moss terms:
Cardinal organ parts
See POC_Conf._Call_3-22-11 for details.
Upcoming meetings 2011:
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
ICBO
LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted)
LC is working with the other organizers to develop the workshop plans and a call for papers.
Full-Day Workshops Schedule:
July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability
July 26 6.30pm-9pm Evening Workshop: Common Logic
July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium
- LC will attend and represent the PO, will submit a short paper/poster for the workshop (deadline April 1st).
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
Plant Biology 2011
Early-bird registration ends May 13.
Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.
Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.
For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.
TAIR is organizing an Outreach Booth and we are invited to take part.
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
Early bird registration deadline - Extended 1 March 2011
Deadline for registration by presenters 1 March 2011
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
Next meeting scheduled for Tues, Mar. 22nd, 2011 at 10am PDT
