Difference between revisions of "PO Paper Winter 2011"
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==Plans for a publication to detail the updates in the PO== | ==Plans for a publication to detail the updates in the PO== | ||
| − | -This is a priority for the fall to | + | -This is a priority for the fall to promote the application of the Ontologies for Plants |
-We have been keeping track of the changes on the 'Summary of Changes' page | -We have been keeping track of the changes on the 'Summary of Changes' page | ||
| − | First manuscript will target journal: 'Trends in Plant science | + | First manuscript will target journal: 'Trends in Plant science' |
-Laurel and Ramona will prepare a summary preproposal to be sent to [http://www.cell.com/trends/plant-science/Presubmission Trends in Plant Science] for their consideration. Focus will be on the benefits and usefulness of the PO, global perspective, links between PO and GO | -Laurel and Ramona will prepare a summary preproposal to be sent to [http://www.cell.com/trends/plant-science/Presubmission Trends in Plant Science] for their consideration. Focus will be on the benefits and usefulness of the PO, global perspective, links between PO and GO | ||
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-two papers to consider when writing this [http://dx.doi.org/10.1016/j.tig.2009.11.004 He et al, 2009] and [http://www.sciencedirect.com/science/article/B6TD1-49R5G9N-2/2/d2ad592124aa644953568e2ae2cfaf6f Vincent etal, 2003] | -two papers to consider when writing this [http://dx.doi.org/10.1016/j.tig.2009.11.004 He et al, 2009] and [http://www.sciencedirect.com/science/article/B6TD1-49R5G9N-2/2/d2ad592124aa644953568e2ae2cfaf6f Vincent etal, 2003] | ||
| − | Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions. Use info from the grant proposal. Focus will be on updates to PO, and how it is now applicable to all plants. | + | Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions. |
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| + | * Use info from the grant proposal. Focus will be on updates to PO, and how it is now applicable to all plants. | ||
-Compare to previous publication [http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Ilic et al, Plant Phys]. | -Compare to previous publication [http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Ilic et al, Plant Phys]. | ||
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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] | 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] | ||
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==TIPS Paper== | ==TIPS Paper== | ||
Revision as of 16:39, 1 November 2010
Plans for a publication to detail the updates in the PO
-This is a priority for the fall to promote the application of the Ontologies for Plants
-We have been keeping track of the changes on the 'Summary of Changes' page
First manuscript will target journal: 'Trends in Plant science'
-Laurel and Ramona will prepare a summary preproposal to be sent to Trends in Plant Science for their consideration. Focus will be on the benefits and usefulness of the PO, global perspective, links between PO and GO
Review/Opinion article pre-submission enquiries: provide a 500-600 word summary outlining
- what will be discussed in the article,
- why the suggested topic would be timely,
co-author information, plus up to 20 key references that indicate the intended breadth of the proposed article (most references should be to work published in the past 2-3 years).
-two papers to consider when writing this He et al, 2009 and Vincent etal, 2003
Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions.
- Use info from the grant proposal. Focus will be on updates to PO, and how it is now applicable to all plants.
-Compare to previous publication Ilic et al, Plant Phys.
PSO- Plant Physiology paper
Ideas from PJ Apple-Pseudo fruit, microarray data,
florets in rice and compositae. Compare large scale sequencing data sets.
Look at Qifa Zhang rice datasets see microarry data Gene Expression Atlas
TIPS Paper
From Ramona (10/29/10)
Possible topics to include:
What the PO is and types of data available on PO (background information)
Potential uses of PO
-interspecies comparison using Genevesitgater
-hot topics in plant genomics and how the PO can help research in those areas
--e.g., rice data sets described above, new genomes being sequenced
-systematics (character descriptions), see Teleost Anatomy Ontology paper.
-evolutionary studies of homology and convergence, evo-devo, GO-type analyses
-crop improvement for non-model species (trait descriptions and gene expression as in SGN or Generation Challenge Program, gene exploration for non-model species based on model organism database in PO)
Actual use cases
-Virtual Plant
-GCP
-SGN
-Traitnet
-others?
Recruiting more contributors
-use the article as a way to get encourage contribution of annotations from more groups
List of possible citations (required for proposal):
Gene Expression Atlasin rice (Zhang)
Plant Phys paper
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
Discussion:
how this will help move research forward in non-angiosperm model species and all non-model species
future directions
