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Dill-PICL / GOMAP-Paper-2019.1

Data, code, and results for our paper Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants (https://doi.org/10.1093/gigascience/giac023). If you use any of our code or results in a scientific publication, we would be grateful if you cite the paper.
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Scout potential Journals and decide for one #6

Open Thyra opened 5 years ago

Thyra commented 5 years ago

We could publish in either of these three journals

To decide which one would best fit our intentions we should gather some information about each of these journals. This is what I think would be helpful to know, feel free to add to this list:

hhvu0102 commented 5 years ago

Oh I also drafted an email about this, waiting till tomorrow to send it off :'D

I have read through some journals and their description also, and I think the following ones could be for us:

I think we can narrow down our choices by the journal's aims and scope first, as this info will help answer a lot of the questions you raised above (free access or not, target readers,...)

hhvu0102 commented 5 years ago

Got trapped in -30 degree temperature so I made a small table so that we can compare the above journals.

Journal Impact Factor */ Circulation Aims and Scope/ Requirements Publishing Fee Special Edition/ Publication Frequency Free access
Frontiers in Plant Science 3.677 (2017); 29 million views and downloads Quantitative analysis need to be performed on a minimum number of 3 biological replicates. This includes quantitative omics studies (transcriptomics, proteomics, metabolomics) as well as phenotypic measurements, quantitative assays, and qPCR expression analysis. US$ 2,950 (max) No special issues seem to fit. There's a section called "Bioinformatics and Computational Biology" that appears in Plant Science and CJLD is an editor Yes
Plant Physiology 6.280 (2015) Welcomes original submissions that offer new and fundamental insights into the origins, development, and function of plants; encourages submissions that span a range of technologies. US$ 2,100 (max) Monthly, in three volumes per year; no special issues fit. See MAKER paper for example. Yes (with fee)
Plant Methods 4.269 (2017); 3,062,514 downloads Plant Methods’ goal is to stimulate the development and adoption of new and improved techniques and research tools and, where appropriate, to promote consistency of methodologies for better integration of data from different laboratories. [...] The main criteria for a Methodology/Database/Software article are that it should (1) describe a significant advance on what has been previously available, (2) be of potential interest to a broad spectrum of plant research scientists and (3) that the methodology/database/software should be properly validated. US$ 2490 ? Yes
The Plant Journal 5.775 (2017) Resource articles will typically be data-rich and provide an important, novel reference source for the field. Such an article could encompass a careful comparative analysis of ecotypes or strains of a model or reference organism, but also large-scale reference datasets derived from transcriptomics, proteomics, or metabolomics that the community will likely continue to use for metadata analysis leading to novel biological insights. Dependent on OpenAccess or not. Monthly Yes (with fee)
Plant Direct ? Plant Direct features original research articles and editorials and takes innovative approaches to encourage a rapid and transparent publication process and deliver excellent service to the plant science research community. US$ 2,200 (max) ? Yes

(*) I personally don't believe in the correlation between impact factors and the quality of an article, but this could be a good signal if a journal is well received or not.

iacornflake commented 5 years ago

Nice table! I'm looking for special issues...

Impact factor: I agree. I also "personally don't believe in the correlation between impact factors and the quality of an article." However! At some point you will get evaluated and that metric matters to people in positions of authority who cannot otherwise figure out how to measure things...

hhvu0102 commented 5 years ago

Most of the impact factors for those above I got from Wikipedia, except for the Frontiers in Plant Biology where they clearly state their impact factor on the site, and they also claim to be the world's most cited plant science journal. So I'm not too sure that I can trust those impact factors...

iacornflake commented 5 years ago

I think Plant Phys or Frontiers in Plant Science. Note that as an author, I have a freebie to submit for Frontiers in Plant Science section Bioinformatics and Computational Biology

If Plant Phys, we need at least one author added for each database involved.

hhvu0102 commented 5 years ago

I think Frontiers with BCB section will fit us as we do aim to do statistical testing/quantitative measure in our project.

Thyra commented 5 years ago

We are going with Frontiers in Plant Science in the Computational Biology section

iacornflake commented 5 years ago

If phylogenetically works, we should rethink to higher impact factor. Maybe PLoS One or e Life

Thyra commented 5 years ago

GigaScience could be another idea since we focus on reproducibility.

Thyra commented 3 years ago

Another idea by Carolyn:

Here's a back-up journal idea in case when we get reviewed we end up re-submitting somewhere else: https://www.mdpi.com/journal/plants/special_issues/gene_annotation

2.632 impact factor, so not great but a good fit.