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Target Journal: Plant Physiology Target date for submission: Late Winter or Spring (March) 2011 *If we submit a full research article, it will probably go under the section 'bioinformatics'. May want to ask for permission to use a non-standard format. See: [http://www.plantphysiol.org/misc/ifora.shtml Author instructions] *Could also consider submitting an “update” (7000 word max). Has to be invited, pretty long shot. '''Update:''' "Updates are solicited reviews of recent progress and meant to be teaching tools. Updates are not to exceed 7000 words, including references but excluding supplemental data. Although these are primarily associated with Focus Issues, scientists wishing to contribute an Update to a regular issue must first correspond with Don Ort (d-ort@uiuc.edu). All uninvited Updates will be returned to the author(s)." See: [http://www.plantphysiol.org/misc/updates.dtl PLANT PHYSIOLOGY® ANNUAL UPDATE COLLECTION] =Issues with the ontology arising during writing:= This section is for questions about the PO that came up while were writing the manuscript. These are issues that need to be addressed by the curators, preferably before publication and the next release. ==Rename Plant Structure Ontology (PSO) to Plant Anatomical Entity Ontology (PAEO)?== Reason: better reflects the new upper structure, highlights the changes we have done over the past year Problem: How do you pronounce PAEO? PAY_O? RW: I like PAY-O! How about Plant Anatomy Ontology (matches other animal anatomy ontologies)? ==Use of ontology id's in definitions== We have been inconsistent in where we put ID's for terms from other ontologies that we reference in the PO. For the top level PSO terms, we have CARO ID's in the definitions, but also have them as xrefs. For plant cell, we reference GO ID in the comment, but also have it as an xref. ==in vitro plant structures== What are the boundaries for an in vitro structure? What about a whole plant that is grown in culture? ==embryonic plant structure== Do we want dual parentage for embryonic structures? Should be use intersection_of relations, instead of asserting dual parentage? ==has_part relation== How will we deal with has_part relation? for this release? for future releases? ==Topics/goals to include:== Intro, results, methods: Update on the changes to PO in the past 18 months, focus on how it is now applicable to all plants. Challenges in incorporating such a phylogenetically broad group of species -Compare to previous publication [http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Ilic et al, Plant Phys]. '''Introduction:''' * What the PO is and types of data available on PO (background information), (use info from the grant proposal) * Overall goals of the PO - take from grant introduction, screen shots of browser * PO-based annotation can be used to improve analysis * How to improve the analysis aspect of genomics using ontology-based annotation of expression and phenotypes * Engage community, encourage folks to provide more annotations Discussion: how this will help move research forward in non-angiosperm model species and all non-model species future directions Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions. Ideas from PJ Apple-Pseudo fruit, microarray data, florets in rice and compositae. Compare large scale sequencing data sets. -We have been keeping track of the changes on the 'Summary of Changes' page Look at [http://qifa.ncpgr.cn/ Qifa Zhang] rice datasets see microarry data [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2009.04100.x/abstract Gene Expression Atlas] ==Examples/use cases:== * Compare gene expression data sets from Arabidopsis and rice: -find common datasets- one each for a '''tissue''' and and '''growth stage'''*** Sources: from [https://www.genevestigator.com/gv/index.jsp Genevestigator] Also: [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2009.04100.x/abstract Wang et al, 2010] To do: Lol- find list of datasets and their descriptions- See: [[List of useful Datasets]] * In the PO we currently have a large # of annotations to Arabidopsis (~532,000, from TAIR and NASC), but not as many to rice (from Gramene, how many?) * Since the PGDSO will be undergoing major revision between the time this paper is submitted and comes out, it would be better to use two or three examples from the PSO. -Highlight how we are bridging the range of taxa Currently we have the comparison between: *palea/lemma vs petal/ sepal (rice vs Arabidopsis) *Compare datasets between a leaf vs frond vs needle (example on poster)? * Include an example from the reproductive shoot system branch: strobilus vs spikelet vs panicle. '''Questions to ask/answer:''' 1. What are the genes that are over or under expressed in each set? Annotate those genes based on that, 2. Then go back to data set from arab and how many genes expressed in flower from arab overlap with gene ontology. 3. How many dots (genes or GO categories) connect these two data sets? Genevesitgator –Look for common data sets for rice and Arabidopsis? '''*Example: Comparison of palea/lemma in rice and petal/sepal expressed genes in Arabidopsis:''' -Used the PO to identify homologous organs, eg: in monocots vs dicots (arab vs rice) and then go look at the diffs/similarities in expressed genes (stretch?) -Extracted the set of genes expressed in palea/lemma in rice from the [http://dx.doi.org/10.1111/j.1365-313X.2009.04100.x Wang et al paper] (using the supplemental data files, not the CREP database) -Found their Arabidopsis homologs using the Gramene tool: [http://www.gramene.org/biomart/martview/ac390df26dacff841f75e01c2efe3588 GrameneMart] details: -Compared them to petal/sepal expressed genes in Arabidopsis in Genevestigator -Next step: Determine how many genes or GO categories connect these two data sets? [http://genome.cshlp.org/content/13/11/2498.abstract Cytoscape] and [http://bioinformatics.oxfordjournals.org/content/21/16/3448 BinGO]

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