PO Paper Winter 2011

Plans for a publication- TIPS paper

-This is a priority for the fall to promote the application of "Ontologies for Plant Sciences"

First manuscript will target journal: 'Trends in Plant science' for a Review/Opinion article.

-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 and GO, 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 et al, 2003

• Use info from the grant proposal.

Possible topics to include:

What the PO is and types of data available on PO (background information) Overall goals - take from grant introduction, screen shots of browser, improve analysis, -PO based annotation

• How to improve analysis aspect of genomics using ontology-based annotation of expression and phenotypes

Example/use case, maybe for box:

Have expression based data sets from Arabidopsis– from genevesitgater

If microarray from a tissue maps to a gene, then gene expresses in that Take data set from Qifa and (15 tissues) What are the genes that are over or under express, and annotate those genes based on that, Then go back to data set from arab and how many genes expressed in flower form arab overlap with gene ontology. Genevesitgator –any common data sets for rice and arab? Come up with enriched data set (list of genes and expression profile). How many dots connect these two data set in terms of gene orthology.

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

-Compare to previous publication Ilic et al, Plant Phys.

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 Qifa Zhang rice datasets see microarry data Gene Expression Atlas