my journal paper

How to store ...

Archive file name

Format:	<author(s)>_<journal>_<year>.zip
Example:	Bakker_TREE_2008.zip Bakker_vdBurg_PlosOne_2010.zip vdBurg_etal_JEB_2009

To ensure general accessibility of the archives, all file names, metadata and other description files and comment lines in code must be in English. File names should not contain special characters other than dashes (-) or underscores (_); use underscores instead of spaces.

Contents of the .zip archive

The final version of the published paper as pdf-file, including early-online versions as referred to by DOI, but excluding preliminary author copies without proper DOI reference.
All supplementary material that is included and referred to in the paper, as pdf-files.
All primary (raw) data underlying the document. Primary data include a scanned pdf of original data sheets, field books etc. by preference; if this is not possible raw data should be at least included in some electronic way, i.e., in a table, spreadsheet or text file.
All secondary (processed) data used in the preparation of the document.
All program code and scripts used to produce the final results such as figures, tables, statistical analyses etc.
Relevent metadata: a text file read_me_first.txt describing the data sources in relation to (corresponding sections of) the paper. If many data files are present, additional metadata can be included in a spreasheet or database that is referred to in the read_me_first.txt file.

Example 1: Revilla_etal_TE_2013.zip

bever.ode
read_me_first.txt
revilla_etal-theorecol12.pdf

Example 2: Gerritsma_etal_JIP_2013.zip

Main file:
1.Final_version [file folder] 2.Manuscript [file folder] 3.Raw_data [file folder] 4.Processed_data [file folder] 5.Protocols [file folder] 6.Fieldwork [file folder] 7.Scanned_labbooks [file folder] Description.txt read_me_first.txt Folder 3.Raw_data:
Scanned_datasheets [file folder] Dissections_ER_22022012.xlsx Encapsulation_Assay_2010_sheets_A_to_I.xls Raw_data_Hemocytes_feb2012.xlsx

Contents of the metadata file

The following metadata fields:
- Author(s)
- Author affiliation(s)
- Title of the publication
- Year of publication
- Journal
- DOI
- Contact information of the first/corresponding author
- The complete reference of the paper using the Annual Review of Ecology, Evolution and Systematics journal format for the bibliographic reference. Do not abbreviate the author list to et al., and include the DOI of the paper
A short description of all data files in the archive.
If relevant: A short description of external data sets used for the paper, including a reference to their home institute & the principal scientist responsible for their quality.
A short description of the purpose of program code and script files in the archive, and their associated parameter files.
If relevant: references to any on-line programs that were used to produce (parts of) the paper.

Download metadata template file

Example 1: read_me_first.txt

Authors: T.A. Revilla, G.F. Veen, M.B. Eppinga, F.J. Weissing
Affiliations: Theoretical Biology, Community and Conservation Ecology
Title: Plant-soil feedbacks and the coexistence of competing plants
Year: 2013
Journal: Theoretical Ecology
DOI: 10.1007/s12080-012-0163-3.
Compiled by: [Tomas Revilla] <thomas.revilla[at]ecoex-moulis.cnrs.fr>
Description: Revilla TA, Veen GF, Eppinga MB & Weissing FJ (2013): Plant-soil feedbacks and the coexistence of competing plants. Theor. Ecol. 6:99-113, DOI:10.1007/s12080-012-0163-3

                              

Files
-----
* revilla_etal-theorecol12.pdf: the article in PDF format
* bever.ode: source code used to create the data for Figure 7

                              

Software employed
-----------------
* The final revision of the article was edited in MS-Word by the second author (corresponding author)
* Figures 1-6,8 and Appendix were made with [TGIF]
* Figure 7 data was created generated using [XPPAUT] and edited with [GRACE]

                              

[Tomas Revilla]:http://tomrevilla.sdf.org/
[TGIF]:http://bourbon.usc.edu/tgif/
[XPPAUT]:http://www.math.pitt.edu/~bard/xpp/xpp.html
[GRACE]:http://plasma-gate.weizmann.ac.il/Grace/

Example 2: read_me_first.txt

Authors: S. Gerritsma, A. de Haan, L. van de Zande, B. Wertheim
Affiliations: Evolutionary Genetics
Title: Natural variation in differentiated hemocytes is related to parasitoid resistance in Drosophila melanogaster
Year: 2013
Journal: J. Insect Physiol.
DOI: 10.1016/j.jinsphys.2012.09.017
Contact: S.Gerritsma[at]rug.nl
Description.txt: full citation of the publication

                              

This folder contains five subfolders with the following information:

                              

1.Final_version
Pdf of the online version of the publication

                              

2.Manuscript
-Manuscript_text: Manuscript text
-Tables&Figures

                              

3.Raw_data
-Dissections_ER_22022012.xls: contains the raw data results from dissection experiment of Feb 2012 (Individual encapsulation ability)
-Raw_data_Hemocytes_feb2012.xls: raw data of hemocyte counts feb 2012
-Encapsulation_Assay_2010_sheets_A_to_I.xls: Raw data of encapsulation assay 2010 (Population level encapsulation rate). NOTE: only sheets A to I hold the raw data
-Folder Scanned_datasheets: contains all raw data from datasheets (scanned) for hemocyte experiments and encapsulation assay (population level encapsulation rate)
...

complete example file

Which papers to archive

Required:	All publications in a scientific journal or book where GELIFES or a GELIFES group is the work address of the first or equal author (also in case of multiple addresses of the first or equal author)
Voluntary:	Publications with a first author from a different institute than GELIFES

NOTE: Chapters in a PhD thesis that have been previously published in a journal/book and have been archived as a publication, must be archived (again) as part of the PhD thesis archive. Similarly, chapters of a PhD thesis that have been archived as part of the PhD thesis archive and are published in a journal/book at a later moment, must be archived again as a publication.

When to deposit the archive

Each MSc student, PhD student, postdoc and other researchers (including professors) should compile a documented archive of all data underlying a publication and send this in for storage in the repository within 3 months after the paper appears online, including ‘early online’ publication.

How to deposit the archive

The data are deposited by sending an email with the full reference of the publication, and the zip file of the data archive to gelifes-data rug.nl. For sending larger files (>5 MB) the service SURF File Sender can be used, or other file transfer services such as Unishare, Dropbox, Google Drive, WeTransfer.

For questions or problems, contact the data managers.

Last modified:

11 December 2020 4.51 p.m.