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| − | =Status of New Annotation Files for data release in Dec:=
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| − | This content below needs updating: Copied from 9-27-11 meeting
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| − | ===Physcomitrella Annotations===
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| − | LC has been working with DL and SR to get the Physcomitrella annotations added
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| − | ===Gramene Annotations===
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| − | During the last release cycle, LC worked with the Gramene collaborators to get their files updated. They were also going through a realase as well. Have not received any new annotations, even though they said they should be coming from Gramene in the next 1-2 weeks''
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| − | ===Grape and Strawberry===
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| − | * LC working on grape file, see sample
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| − | * Strawberry is on SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]
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| − | What links do we need to use for these and how do we get AmiGO to recognize them?
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| − | ''See notes above''
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| − | ===Potato Annotations===
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| − | LC has been in contact with the group who published the [http://www.nature.com/nature/journal/v475/n7355/full/nature10158.html#/f4 potato genome paper] and they are interested in collaborating with us to assign ontology terms to the annotations.
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| − | From Dr. Richard Finker (Wageningen, The Netherlands):
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| − | "We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
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| − | ''This will go in the next release, do they have expression data- RNA Seq?''
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| − | ===Comments from PJ about Annotation Guidelines===
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| − | Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info.
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| − | Maybe co-author it with SR
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| − | -This will also be helpful when applying for new grants
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| − | -it would be helpful to have a detailed guide on our wiki for collaborators
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| − | ==Whole plant development stages==
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| − | ''postponed until next week''
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]===
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| − | ====GO terms====
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| − | GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.
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| − | '''dormancy process (GO:0022611):''' The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity. (They also have a term for seed dormancy.)
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| − | '''proposed new definition for dormancy process:''' A developmental process in which a dormant state is induced, maintained or broken.
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| − | Comment: A dormant state is characterized by a suspension of most physiological activity, and, in plants, by a suspension of growth.
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| − | '''seed dormancy (GO:0010162):''' The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated.
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| − |
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| − | '''proposed new definition for seed dormancy:''' A dormancy process that has as participant a seed.
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| − | comment: Seed dormancy is characterized by a suspension of physiological activity that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.(''work on comment'')
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| − | '''organism dormancy (new term):''' A dormancy process that has as participant a whole organism.
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| − | ====PO terms====
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| − | '''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in a dormancy process (GO:0022611).
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| − | comment: This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure, although dormancy of buds is an essential part of the sporophyte dormant stage. A sporophyte dormant stage involves the formation of dormant buds. These may be above ground (in woody plants), at ground level (in herbaceous plants), or underground (in plants with tubers, bulbs, corms, or perennating rhizomes). Dormancy may be preceded by the senescence of other plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. Evidence of the end of dormancy is the resumed growth of buds and/or the growth of vascular cambium. The dormant stage is an evolved response to environmental conditions such as seasonality, extreme heat, drought, or cold.
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| − | '''gametophyte dormant stage (PO:0025342):''' A gametophyte development stage during which a gametophyte participates in a dormancy process (GO:0022611).
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| − |
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| − | comment: This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage is an evolved response to environmental conditions such as seasonality, extreme heat, drought, or cold.
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| − | References:
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| − | [http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.15.060164.001153 Vegis; Dormancy in Higher Plants ARPP 1964]
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| − | [http://www.jstor.org/stable/3244383 paper on sporophyte dormancy in a bryophyte]
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| − | Dormancy of gemmae in a liverwort: DOI: 10.1034/j.1600-0706.2001.940314.x. In this case, the gemma is a whole plant.
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| − | Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3432979&group_id=76834&atid=835555 gametophyte/sporophyte senescent stage]===
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| − | Work on these terms is ongoing. Will present new definitions and GO proposal for senescence at a future meeting.
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3439459&group_id=76834&atid=835555 embryo stage] and [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo]===
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| − | ====embryo stage====
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| − | We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed '''embryo stage''' and made is_a sporophyte vegetative stage.
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| − | proposed def.:
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| − | '''embryo stage (PO:0007631):''' A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.
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| − | Comment: The embryo stage generally starts 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 begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.
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| − |
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| − | ====plant embryo====
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| − | Now that we have a working term for embryo stage, we can define '''plant embryo''' in terms of the stage.
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| − | '''existing def. plant embryo (PO:0009009):''' A whole plant in the early part of a sporophytic phase after the first cell division.
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| − | '''proposed def. plant embryo (PO:0009009):''' A whole plant that participates in the embryo stage (PO:0025369).
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| − | comment (basically the same as existing comment): 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 embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.
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| − | -change from participates_in sporophyte development stage to participates_in embryo stage
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 zygote stage]===
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| − | We already have a term "A zygotic stage" (PO:0001097), is_a embryo stage. This was renamed '''zygote stage''' and made is_a sporophyte development stage.
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| − | '''proposed def. zygote stage (PO:0001097):'''A sporophyte development stage that occurs during the interval between syngamy and the first cell division.
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| − | =Upcoming meetings and Presentations 2011/2012:=
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| − | ==Sematic web conference focused on life science==
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| − | JP will attend the [http://www.swat4ls.org/workshops/london2011/ SWAT4LS] meeting in December. Folks such as TW from NCBO will be there.
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| − | Poster presentation: "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes [http://wiki.plantontology.org:8080/images/6/62/SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf link]
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| − | ==[http://www.intl-pag.org/ PAG 2012]==
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| − | January 14-18, 2012, San Diego, California
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| − | '''PO will be represented at the following events:'''
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| − | *Ontology workshop, Saturday January 14th from 10:20am-12:30pm: [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data]. We have 5 speakers and time at the end for a panel discussion.
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| − | PJ will give the introductory remarks at the Ontology workshop, and hopefully take part in the Panel Discussion.
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| − | For more info, see the [[PAG 2012 Ontology workshop]] wiki page.
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| − | *LC is also presenting in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm) and in the [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes] workshop on Sunday, Jan. 15th, (8:00am - 10:10am).
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| − | *LC will also do a computer demo for the PO, unless one of the Justins is there and wants to do it.
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| − | *The PO will take part in an Outreach booth organized by MaizeGDB.
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| − | ==Phenotype RCN meeting, 23-25 February 2012==
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| − | The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.
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| − | It will be held again at NESCent (Durham, NC).
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| − | RW has a friend there she can stay with and is interested in going.
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| − | ==Maize Genetics Meeting, March 15-18, 2012==
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| − | The maize meetings are being held in Portland, OR this year.
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| − | For more info see: [http://www.maizegdb.org/maize_meeting/2012/index.php Maize Genetics Meeting 2012]
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| − | Registration Link:
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| − | 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.
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| − | Deadlines:
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| − | Advance meeting registration is due by January 31, 2012.
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| − | ==[http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]==
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| − | April 2-4, 2012, Washington DC
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| − | Call for abstracts is now open:
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| − | There are three submission categories for abstracts:
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| − | 1. Talk or Poster (with consideration for oral presentation) (LC would prefer a talk)
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| − | 2. Poster only
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| − | 3. Workshop only
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| − | • '''Submission deadline December 9, 2011'''
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| − | • Notification of acceptance February 3, 2012
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| − | [http://pir.georgetown.edu/biocuration2012.html/instructions.html Instructions]
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| − | There are seven topic sessions from which submitters are invited to select:
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| − | 1. Ontologies, standards and best practices, including gold standard datasets.
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| − | 2. Protein annotation; sequences, structures and pathways.
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| − | 3. Community annotation and Wikis.
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| − | 4. Genomics and metagenomics data curation.
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| − | 5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
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| − | 6. Literature collection, text mining and curation.
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| − | 7. Tools to assist curation, including automated pipelines.
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| − | PJ planning to attend and will be running a biocuration workshop, LC and RW can go, DWS will be away,
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| − | 'From 9-27-11: PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide.
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| − | ==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==
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| − | Annual meeting of the Society for the Preservation of Natural History Collections
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| − | Yale University, New Haven Connecticut
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| − | June 11-16, 2012
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| − | 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).
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| − | 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).
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| − | ''From PJ: If we can show progress in the FNA work or Morphobank yes we should''
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| − | ==[http://www.2011.botanyconference.org/info/Botany2012.php Botany 2012]==
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| − | July 7 - 11, 2012 - Columbus, Ohio
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| − | Call for Symposia, Colloquia and Workshops:
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| − | 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.
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| − | Proposal was submitted, waiting for news.
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| − | 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.
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| − | ===exhibitor's booth===
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| − | We should also consider hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].'''
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| − | 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!)
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| − | • 2 months of Rotating Banner Ads in the online American Journal of Botany
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| − | • A Rotating Banner Ad in one edition of the online Plant Science Bulletin
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| − | • A Rotating Banner Ad on the Botany 2012 abstract submission site
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| − | • A Rotating Banner Ad on the 2012 Conference Registration site.
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| − | ''PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.''
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| − | ===Annotation wiki===
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| − | JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.
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| − | ==ICBO 2012==
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| − | '''International Conference on Biomedical Ontologies''' ([http://purl.bioontology.org/ICBO/ ICBO 2012])
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| − | co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)
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| − | 22-25 July 2012; Graz, Austria.
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| − | Conference Web site: http://purl.bioontology.org/ICBO/
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| − | *The consensus with CM, MH and DOS was not to organize an Anatomy Ontology Workshop this year.
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| − | BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts.
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| − | Could also consider organizing a phenotype ontology workshop.
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| − | ===Relevant dates ===
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| − | 31 December 2011: Workshop and tutorial proposal submission deadline
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| − | 25 January 2012: Notification of acceptance of workshops and tutorials
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| − | '''31 January 2012: Paper submission deadline'''
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| − | 28 February 2012: Notification of paper acceptance
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| − | 15 March 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
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| − | 15 April 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
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| − | 30 June 2012: Deadline for all camera-ready copies for the proceedings
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| − | We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?
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| − | 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?
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| − | 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.
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| − | ==ASPB Plant Biology 2012==
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| − | July 20 - 24, 2012 - Plant Biology 2012, Austin, TX
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| | =Next meeting scheduled for Tuesday, Dec. 13th, 2011 at 10am PST/1pm EST= | | =Next meeting scheduled for Tuesday, Dec. 13th, 2011 at 10am PST/1pm EST= |
