PO Paper Winter 2011

Link to proposed Plant Physiology paper- 2011

Plans for Publication(s)

-This is a priority for Feb to promote the application of "Ontologies for Plant Sciences" since the proposal we submitted to TIPs was turned down.

-Target journal? Ideas:

* Bioinformatics- see: Author info

-provides a forum for the exchange of information in the fields of computational molecular biology and post-genome bioinformatics, with emphasis on the documentation of new algorithms and databases that allows the progress of bioinformatics and biomedical research in a significant manner.

• categories of manuscripts: Genome analysis, Sequence analysis, Phylogenetics, Structural bioinformatics, Gene expression, Genetic and population analysis, Systems biology, Data and text mining, Databases and ontologies (see below)

• Types of papers:

- Original Papers (up to 7 pages; this is approx. 5000 words)

- Discovery Notes (up to 4 pages, this is approx. 3000 words)

- Application Notes (up to 2 pages; this is approx. 1300 words or 1000 words plus one figure)

- Reviews (3-8 pages) Most review papers are commissioned, although the editors welcome suggestions from prospective authors who should in the first instance submit a draft or abstract/summary no longer than a page.

- Letters to the Editor, Conference Papers

*Databases and Ontologies This category includes: Curated biological databases, data warehouses, eScience, web services, database integration, biologically-relevant ontologies. - will consider applications in any of the above areas. Descriptions of databases will not be published if they have been previously described unless there have been substantial changes or enhancements that represent a fundamental change in the database.

We encourage Application Notes describing programmatic interfaces to biological data and services.

Other journals to consider:

• Briefings in Bioinformatics: This one seems particularly relevant for a short article informing people about the PO

From their webpage:

"Briefings in Bioinformatics is an international forum for researchers and educators in the life sciences. The journal publishes reviews for the users of databases and analytical tools of contemporary genetics and molecular biology and is unique in providing practical help and guidance to the non-specialist. Papers range in scope and depth, from the introductory level to specific details of protocols and analyses encompassing bacterial, plant, animal and human data. "

"Detailed subject areas covered by the journal include: DNA sequencing, expression profiling, alignment methods, gene expression studies, protein profiles and HMMs, metabolic and signalling pathways, structure and function prediction, mapping and microarrays."

This could be an interesting forum for reaching a wider audience. They have a category for Software and Website Reviews, which seems good for the PO.

• Database: We aren't strictly a database, but still think this journal could be a decent fit

Database: The Journal of Biological Databases and Curation provides an open access platform for the presentation of novel ideas in database research surrounding biological information, and aims to help strengthen the bridge between database developers, curators, and users. In addition, the journal will provide a platform for the description of novel advances in the field of biocuration and promote the use of information from biological databases to assist in the planning and design of original research projects. Biocuration involves the translation of information relevant to biology and medicine, into an organized format, typically as a database, which enables the integration of scientific literature as well as large datasets such that information is accurately represented and readily accessible, as a source of information for scientists, and as a basis for computational analysis.

The journal will publish:

• Detailed descriptions of databases, and database tools, in the broad arena of biology - authors are strongly encouraged to include a biological discovery or a 'testable' hypothesis in their papers

• Shorter papers describing significant updates to established databases

• Objective reviews of complementary and ancillary databases and database tools

• User tutorials for database tools

• Methodology and technical notes on database development

• Improvements to automated prediction and annotation for biomedical datasets

• Detailed descriptions of the state and updating of the annotation of genomes

• Descriptions of the development and content of ontologies of relevance to the biomedical community and the tools specific to the use of these ontologies

• Articles relevant to the annotation process such as standards for curation, annotation best practices, annotation methodologies, the use of automated and semi-automated methods for annotation and the measures for annotation consistency

• BMC Bioinformatics

-for example, CL just published a paper there (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024222/?tool=pubmed - check out their figure 2 as a cross-species comparison example)

"BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics (ISSN 1471-2105) is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS, CAS, EMBASE, Scopus, ACM, CABI, Thomson Reuters (ISI) and Google Scholar.'

-also possible: BMC genomics or BMC plant biology

• American Journal of Botany

DWS has suggested this journal for a possible special invited paper. The editor is a plant morphologist/evo-devo person.

• PLOS One- open access, substantial page charges

Other journals to consider for later:

• Genome Biology

-Genome Biology publishes research articles, new methods and software tools, in addition to reviews and opinions, from the full spectrum of biology, including molecular, cellular, organism or population biology studied from a genomic perspective, as well as sequence analysis, bioinformatics, proteomics, comparative biology and evolution. (editorial@genomebiology.com)

See 'Instructions for Genome Biology authors' for descriptions of different article types and information about policies and the refereeing process.

-we would probably fit best under the 'review' or 'software' sections.

-"Key aims of reviews are to provide systematic and substantial coverage of mature subjects, evaluations of progress in specified areas, and/or critical assessments of emerging technologies. Reviews are usually commissioned from recognized experts in a particular field, and we ask authors to provide a balanced overview of the field and not to focus on their own work or that of their close colleagues."

-'software' section is probably a stretch as well.

• Nucleic Acids Research

Nucleic Acids Research (NAR) publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions.

It enables the rapid publication of papers under the following categories: Chemistry and synthetic biology; Computational biology; Gene regulation, chromatin and epigenetics; Genome integrity, repair and replication; Genomics; Molecular biology; Nucleic acid enzymes; RNA and Structural biology.

A Survey and Summary section provides a format for brief reviews.

The first issue of each year is devoted to biological databases, and an issue in July is devoted to papers describing web-based software resources of value to the biological community.

NAR Methods Online provides a forum for the online publication of methods papers.

Scope and Criteria

Instructions for Authors

They have an annual database issue (deadline July 2011,for Jan 2012 publication)

• Current Opinions in Plant Science:

2011 Contents: The subject of plant biology is divided into seven sections, each of which is reviewed once a year.

Subjects for 2011: -February: Growth and development

-April: Genome studies and molecular genetics

-June: Physiology and metabolism

-August: Biotic interactions

-October: Cell signaling and gene regulation

December: Cell biology

Each issue contains one or two of the sections, and the amount of space devoted to each section is related to its importance.

Contact details for submission: Submission to this journal is by invitation only. Please contact your Content Development Manager by email if you have any questions.

Next appropriate issue for consideration: April 2011: Genome Studies and Molecular Genetics; (Edited by Jeffrey L Bennetzen and Jian-Kang Zhu)- already full, focused on epigenetics

Topics/goals to include:

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

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 Genevestigator

http://www.nebion.com/ne/doc/services.jsp

Also: 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 Wang et al paper (using the supplemental data files, not the CREP database)

-Found their Arabidopsis homologs using the Gramene tool: 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?

Cytoscape and BinGO

Potential uses of PO

-interspecies comparison using Genevestigator

-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)

Sites that use the PO: use cases

-Virtual Plant

• VirtualPlant integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of genomic data. The goal of VirtualPlant is to provide the tools to aid researchers to generate biological hypotheses.

Note: They are still using the older version of the PSO, not the 10-10 version

-Generation Challenge Program-

-Solanaceae Genomics Network-

-Traitnet

Note: no actual mention of the PO on their site

-others?

Recruiting more contributors

-use the article as a way to get encourage contribution of annotations from more groups

Possible citations (up to 20)

(obviously this list will need to be edited somewhat)

x=papers that were tagged by both Lol and Ramona

Other plant genomic databases and data sets (mostly taxon specific)

x Wang, L. et al. A dynamic gene expression atlas covering the entire life cycle of rice. The Plant Journal 61, 752-766 (2010). Gene Expression Atlasin rice

Perez-Rodriguez et al. 2010 PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research

Dai et al. 2010 TrichOME: A Comparative Omics Database for Plant Trichomes. Plant Phys

xBhasi et al. 2010 RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. Bmc Plant Biology

Jung et al. 2008 GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Research

x Katari, M.S. et al. VirtualPlant: A Software Platform to Support Systems Biology Research. Plant Physiol. 152, 500-515 (2010).

Rengel et al. 2009 A new genomic resource dedicated to wood formation in Eucalyptus. Bmc Plant Biology

Wang et al. 2010 SoyDB: a knowledge database of soybean transcription factors. Bmc Plant Biology

Keller et al. 2009 Development and functional annotation of an 11,303-EST collection from Eucalyptus for studies of cold tolerance. Tree Genetics and Genomes

Miozzi et al. 2010 ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato. Plant Molecular Biology

Ogata et al. 2010 CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics

Proost et al. 2009 PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants. Plant Cell

Soldatos et al. 2010 Martini: using literature keywords to compare gene sets. Nucleic Acids Research

Takahashi et al. 2009 KNApSAcK gene classification system for Arabidopsis thaliana: Comparative genomic analysis of unicellular to seed plants. Plant Biotechnology

Fujita, M. et al. Rice Expression Atlas In Reproductive Development. Plant and Cell Physiology doi:10.1093/pcp/pcq165

Eveland, A.L. et al. Digital Gene Expression Signatures for Maize Development. Plant Physiol. 154, 1024-1039 (2010).

Examples of analyses (mostly using GO)

Hayes et al. 2010 Maize global transcriptomics reveals pervasive leaf diurnal rhythms but rhythms in developing ears are largely limited to the core oscillator. PLoS One

x Dharmawardhana, P., Brunner, A. & Strauss, S. Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics 11, 150 (2010).

Horan et al. 2008. Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Phys

Allen, A.M., Lexer, C. & Hiscock, S.J. Comparative Analysis of Pistil Transcriptomes Reveals Conserved and Novel Genes Expressed in Dry, Wet, and Semidry Stigmas. Plant Physiol. 154, 1347-1360 (2010). Allen etal, 2010

Jain, M. et al. F-Box Proteins in Rice. Genome-Wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic Stress. Plant Physiol. 143, 1467-1483 (2007).

Ontologies in systematics

Mabee et al. 2007 Connecting evolutionary morphology to genomics using ontologies: A case study from cypriniformes including zebrafish. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution

Cui 2010. Semantic annotation of morphological descriptions: an overall strategy. BMC Bioinformatics

Dahdul et al. 2010 Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS one

Comparative evo-devo (potential use of PO)

x Rensing, S.A. et al. The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319, 64-69 (2008).

Papanov et al. 2009 The evolution of nuclear auxin signalling. BMC Evolutionary Biology

van der Graaf et al. 2009 The WUS homeobox-containing (WOX) protein family. Genome Biology

Lang et al. 2010 Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity. Genome Biology and Evolution

Duarte et al. 2010 Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology

Krom and Ramakrishna 2008 Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and Populus. Plant Phys

Kawai et al. 2010 Class 1 KNOX Gene Expression Supports the Selaginella Rhizophore Concept. Journal of Plant Biology

Langdale 2008 Evolution of developmental mechanisms in plants. Current Opinion in Genetics & Development

x Mukherjee, K., Brocchieri, L. & Burglin, T.R. A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Mol Biol Evol 26, 2775-2794 (2009).

Miscellaneous

x He, Q., Berg, A., Li, Y., Vallejos, C.E. & Wu, R. Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends in Genetics 26, 39-46 (2010).

Lang et al. 2008 Exploring plant biodiversity: the Physcomitrella genome and beyond. TIPS

Wolf et al. 2010 The Molecular and Physiological Responses of Physcomitrella patens to Ultraviolet-B Radiation. Plant Physiology

Mungall, C. et al. Integrating phenotype ontologies across multiple species. Genome Biology 11, R2 (2010).

Castel, R., Kusters, E. & Koes, R. Inflorescence development in petunia: through the maze of botanical terminology. J. Exp. Bot. 61, 2235-2246 (2010)

Yadav, R.K., Girke, T., Pasala, S., Xie, M. & Reddy, G.V. Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proceedings of the National Academy of Sciences 106, 4941-4946 (2009).

Madin et al. 2007. Advancing ecological research with ontologies. Trends in Ecology and Evolution 23:159-168

Mari L. Salmi, Thomas J. Bushart, Stephen C. Stout and Stanley J. Roux. Profile and Analysis of Gene Expression Changes during Early Development in Germinating Spores of Ceratopteris richardii. Plant Physiology 138:1734-1745 (2005) http://www.plantphysiol.org/cgi/content/full/138/3/1734