Ecological Society of America

APPENDICES, SUPPLEMENTS, AND DATA PAPERS INSTRUCTIONS FOR AUTHORS

• START HERE: Quick guide to submitting archives
  • Step #1: The index page
  • Step #2: The appendices
  • Step #3: The supplements
  • Step #4: Sending the archives
• Appendices and supplements
• Data papers
  • Data vs. metadata
  • Author instructions
• Reviewer instructions

QUICK GUIDE TO SUBMITTING ARCHIVES

This guide is for the submission of archives after a manuscript has been accepted for publication. The instructions here do not apply to archives for manuscripts not yet accepted for publication. If your paper is still in the pre-review or review process, archives should be uploaded along with other manuscript files through the online system, EcoTrack.

Please be aware that the posting of the archives are scheduled to coincide with, or slightly precede, the posting of that issue of the journal online and are not made available earlier for preprints. The data editors for Ecological Archives will be responsible for ensuring your files display properly and conform to ESA style before being placed online for readers to see. To expedite this process, a few preparations must be made.

STEP #1: Prepare the index

The index is the first page readers will see when viewing your archives. Index pages are required for appendices, supplements, and data papers. It contains the basic information regarding your archives. The following information should be included in a separate .DOC/.DOCX (preferred), HTML, or PDF file:

• Full list of authors (names only)
• Title of manuscript
• Journal
• A list of all appendices/supplements with titles
  • Please be sure you are classifying your submissions appropriately - appendices are not the same as supplements. If you are unsure what the difference between appendices and supplements are, the distinction is explained here.
  • Titles should be short and concise, approximately one sentence each but also descriptive of the contents. For instance, the title "Additional methods" is not descriptive enough. These titles will appear after the literature cited of your main manuscript, as can be seen in the example image below.
    
  • Appendices use alphabetical designations - Appendix A, Appendix B, C, etc.
  • Supplements use numeric designations - Supplement 1, Supplement 2, 3, etc.

With this information, the data editors will create the index page. Here are a few examples of index pages, after being converted and formatted: #1, #2, #3.

STEP #2: Prepare the appendices

If your archives do not contain any appendices, skip to the next step.

Within each appendix, every table, figure, and equation requires an alphanumeric designation. Figures in Appendix A, for example, would be designated Fig. A1, A2, etc., tables in Appendix C would be Table C1, C2, and so on. Include detailed descriptions of each figure and table. If literature is referenced, include a literature cited section at the end of each appendix, exclusive to that appendix and adhering to ESA style. Ensure all images are displaying clearly and properly.

Below is an example image of an appendix, after conversion and formatting by a data editor:

See the following links for more examples of finished appendices: #1, #2, #3.

STEP #3: Prepare the supplements

If your archives do not contain any supplements, skip to the next step.

For each supplement, a page will need to be created containing short descriptions of all of the data files in the supplement. The following information should be included in a separate .DOC/.DOCX (preferred), HTML, or PDF file:

• Full list of authors, including addresses for each author and emails for the corresponding author(s)
• A list of all files contained in the supplement
• A short description of the files, including variable descriptions, use, checksum values if appropriate, and any other useful or relevant information.

This information will be used by the data editors to create the supplement pages. Below is an example image of a supplement, after being converted and formatted:

See the following links for more examples of finished supplements: #1, #2, #3.

STEP #4: Send the archives

The data editors will need all of your files in their original format, including any images and figures. All of the files should be placed into a .ZIP or .RAR archive and emailed to the publications office <esa_journals@cornell.edu>.

For additional information on the submission and acceptance process of appendices, supplements, and data papers, please see the FAQ or continue reading below. Any remaining questions may be directed to Jane Bain, the Associate Data Editor <jlb40@cornell.edu>.

APPENDICES AND SUPPLEMENTS

Ecological Archives publishes two types of materials that are in addition to articles that appear in Ecology, Ecological Applications, Ecological Monographs, Ecosphere, or The Bulletin.

Appendices will typically contain additional methods, tables, graphs, figures, equations, or other supporting information that the author, editors, or reviewers may deem unnecessary or too large to include in the main article. Authors do not need to know HTML to submit appendices - the data editors will be responsible for converting the submitted files into an accessible format for online viewing. To facilitate conversion, Ecological Archives requires appendices to be in .DOC, .DOCX, or HTML; image files should be in .GIF, .JPG, or .PNG; movies should be in .MPG; sound files should be in .WAV or .MP3. Please do not submit tables that are formatted using spaces or tabs - all tables should be explicitly defined as such in your word processing software. Authors using LaTeX should submit their files in PDF format, making sure that all tables, figures, and equations are appropriately numbered (see here for details). There are are also LaTeX to HTML converters available (see FAQ for details). Authors of field studies are encouraged to submit a photograph of their study site for inclusion as a digital appendix. Including links to other web pages for additional components is discouraged since availability cannot be guaranteed.

Supplements can include, but are not limited to, original and derived data sets, source code for simulation models, and details of software for unusual statistical analyses. Authors are encouraged to submit supplements so as to facilitate new analyses as well as validation of analyses already conducted. Appropriate metadata are required and may be submitted in .DOC, .DOCX, or HTML format. The list of authors should include the names, affiliations, and correspondence addresses of all authors. Because users may need to contact authors for additional information on using supplements, please provide e-mail addresses whenever possible. In order to ensure all archives are kept open and available for the future, Ecological Archives avoids the use of proprietary formats. As such, Ecological Archives does not accept Excel spreadsheets, unless special permission is granted from the data editors (see FAQ for how to convert spreadsheets). Data files should be submitted in separate ASCII (text)-based files using comma or tab-separated variables. In the textual description of the data files you must include information on what the rows and columns comprise, checksum values for download verification, information on specific codes incorporated into the files (i.e., "blank values are denoted as "-9999"), and any additional information for using the files. It's a good idea to test the usability of the files by passing them by an unfamiliar user first. Software should be submitted both as source code and compiled (executable) code. Compiled code submitted without accompanying source code is not acceptable.

One way to think of the distinction between appendices and supplements is that appendices generally are meant to be read, while supplements generally are meant to be used. There is no length limit for appendices or supplements and no charge for file size, as long as files stay under 10MB (see financial arrangements for more details on data charges). Authors are encouraged to submit appendices and supplements at the time of article submission, or subject-matter editors may request such material. The appendices and supplements will be evaluated by the subject-matter editor and the peer reviewers selected for the manuscript, and then revised and formatted by the data editors before being posted online.

Additional questions regarding supplements or appendices for Ecological Archives can be directed to either the Data Editor or the Associate Data Editor.

DATA PAPERS

Data papers are subject to full peer-review and oversight by subject-matter editors and a Data Editor. The review process will evaluate ecological significance and overall quality first, but data papers also will be subject to further technical review to maintain the highest standards of usability, especially with respect to associated metadata. Full titles, author(s), abstracts, and key words of peer-reviewed data papers will be published in Ecology or Ecological Applications as appropriate, along with accession numbers for Ecological Archives. A data paper abstract published in Ecology can be cited as an Ecology publication in the literature in much the same fashion as a book review, and may appear as an Ecology publication on the author's vitae.

One way in which data papers differ from traditional web publication of data is that ESA provides long-term maintenance of a publicly accessible archival copy. In addition, ESA accepts periodic updates. Long-term maintenance carries a financial liability for ESA. For this reason, ESA charges a one-time fee at publication for data papers [see Financial arrangements].

For examples of recently published data papers, visit the Ecological Archives section for data papers.

Data papers contain two parts: data and metadata

Data should be logically and consistently formatted. For tabular data, ASCII (fixed-format, tab-delimited, comma-delimited, or space-delimited) is the preferred format for submission. In order to ensure all archives are kept open and available for the future, Ecological Archives avoids the use of proprietary formats. As such, Ecological Archives does not except Excel spreadsheets (see FAQ for how to convert spreadsheets). Rasterized digital geospatial data should be submitted in IDRISI or ERDAS-compatible formats; vectorized geospatial data should be submitted in ARC/INFO export format. For other types of data, consult the Ecological Archives Data Editor. Multiple files should be compressed and submitted together as self-extracting .ZIP or .TAR files. Generally, synthetic data (e.g., figures) can accompany, but not substitute for, raw data in data papers; such synthetic results normally should be placed within the accompanying metadata text.

Metadata fully describes the content, context, quality, and structure of the data. The metadata ideally should be submitted in a single .DOC, .DOCX, or HTML file. Metadata content should adhere strictly to the Ecological Archives metadata content standards derived from Michener et al. (1997; Ecological Applications 7:330–342); questions about relevance of specific fields should be directed to the Data Editor.

Instructions for preparing metadata

Please begin by checking the author instructions found at: http://esapubs.org/esapubs/AuthorInstructions.htm

Metadata text should generally adhere to the instructions for ESA print journals. Write with precision, clarity, and economy; use the active voice and first person wherever appropriate; avoid footnotes.

Please italicize scientific names and the symbols for all variables and constants except Greek letters. Italics should not be used for emphasis.

Use leading zeroes with all numbers < 1, including probability values (e.g., P < 0.001).

Note that many symbols used in equations cannot be reproduced in HTML. Either (1) format the equation as an embedded graphic (.JPG, .GIF, or .PNG):

(2) use XML equation tags (produced, for example, by the LaTeX2HTML converter), or (3) write out (e.g., dN_1/dt = r_1 N_1 [K_1-N_1-(alpha_12)N_2]/[K_1]. Note that superscript can be denoted either by ^ or 'sup', and subscript can be denoted either by _ or 'sub'.

Use the International System of Units (SI) for measurements. Consult Standard Practice for Use of the International System of Units (ASTM Standard E-380-93) for guidance on unit conversions, style, and usage. An abbreviated version may be downloaded from the ASTM website.

Title. Titles should conform in style to those found in ESA print journals.

Authors/Data Compilers. For each author, state the relevant address--usually the institutional affiliation of the author(s) during the period when all or most of the data were collected. The authors' present address(es), if different from this, should appear in parentheses. Provide a current, corresponding e-mail address to which questions regarding the dataset can be directed. Inform the Data Editor when contact e-mail address(es) change.

Abstract and Key Words. An abstract and key words should be included in the metadata. The abstract should be brief (< 350 words) and provide a brief summary of the database, including the purpose, methods, and results of completed analyses. Avoid speculation in the Abstract; if included, speculation about possible interpretations or applications of your data should play a minor role. Do not include any literature citations in the Abstract. Common names may be used when convenient after stating the scientific names. Please supply up to 12 key words for indexing purposes.

Metadata. The organization of the metadata should correspond to the Ecological Archives Metadata Standard (see recent examples of data papers) and all appropriate fields must be completed.

The motivation or purpose of your research should appear in the "Research Origin Descriptors", where you state the questions you sought to answer, and the background of those questions. In the "Methods" section you should provide sufficient information to allow someone to repeat your work. A clear description of the experimental design, sampling procedures, and statistical procedures is especially important in metadata describing field studies, simulations, or experiments. If you list a product (e.g., animal food, analytical device), supply the name and location of the manufacturer. Give the model number for equipment used. Supply complete citations, including author (or editor), title, year, publisher, and version number, for computer software mentioned in the metadata.

Particular attention should be paid to providing comprehensive documentation of the physical structure of the data, known data anomalies, and quality assurance and quality control procedures employed. Contributors to Ecological Archives are encouraged to provide comprehensive documentation of supplemental descriptors that would facilitate secondary data use and interpretation. Before submitting the data paper, contributors should thoroughly review the metadata and verify that physical structure descriptors are sufficient to permit secondary usage of the data.

Statistical analysis of the data can appear in the metadata section, but it should be kept to a minimum. Such detailed analyses of datasets could, however, form the core of a companion paper submitted to an ESA print journal.

Acknowledgments. Be brief.

Literature Cited. Before submitting the metadata, check each citation in the text against the Literature Cited to see that they match exactly. Format references to conform in style to the ESA print journals.

Tables, Figures, and Appendices. Tables and Figures should be embedded in the metadata where appropriate. Tables should be in HTML and Figures should be embedded .JPG, .GIF, or .PNG files. Appendices are not acceptable parts of data papers.

Assembly of Metadata file. Assemble the metadata file in the following order: Title, Authors (data compilers), Abstract, Key Words, Metadata, Acknowledgments, Literature Cited.

How are data papers reviewed?

All data papers will receive at least two independent reviews; final acceptance of data papers is by the Data Editor or the Editor-in-Chief.

INSTRUCTIONS FOR DATA PAPER REVIEWERS

The following instructions are sent to each reviewer, along with directions for how to access the data and metadata.

Confidentiality. This data paper is a privileged communication. Please do not show it to anyone or discuss it, except to solicit assistance with a technical point. If you feel a colleague is more qualified than you to review the data paper, do not pass this responsibility on to that person without first requesting permission to do so from the Data Editor. Your review and your recommendation should also be considered confidential.

Time. In fairness to the author(s), you should return your review within 3 weeks. If it seems likely that you will be unable to meet this deadline, please e-mail the Data Editor today.

Conflicts of Interest. If you feel you might have any difficulty writing an objective review, please contact the Data Editor. If your previous or present connection with the authors, data compilers, or an author's institution might be construed as creating a conflict of interest, but no actual conflict exists, please discuss this issue in the cover letter that accompanies your review.

Comments for the authors. What is the major contribution of the data paper? What are its major strengths and weaknesses, and its suitability for publication? Please include both general and specific comments bearing on these questions, and emphasize your most significant points.

General Comments

• 1) Importance and interest to Ecological Archives' users and readers.
• 2) Scientific and technical soundness of the database.
• 3) Originality.
• 4) Degree to which metadata fully describe the content, context, quality, and structure of the database.

Specific Comments

Support your general comments with specific evidence in "Comments for the Author(s)". Comment on any of the following matters that significantly affected your judgment of the database:

• 1) Metadata Presentation. Are the metadata logically organized and do they adhere to the Ecological Archives Metadata Content Standard (see recent examples of data papers)? Do the title, abstract, and key words accurately and consistently reflect the major point(s) of the database? Is the writing concise, easy to follow, interesting?
• 2) Metadata Completeness. Are the metadata complete and sufficient to facilitate interpretation and secondary use of the data? What portions of the metadata should be expanded? Condensed? Deleted?
• 3) Data Organization. Are the data logically and consistently organized? Is the data format consistent with the format defined in the metadata?
• 4) Data Quality. Were suitable methods employed to maintain the integrity of the original data and datasets? Are all data anomalies well-documented? Are the metadata sufficient to allow a secondary user to determine how outliers were identified and treated?
• 5) Data Integrity. Have adequate procedures been employed to allow a secondary user to determine whether errors may have been introduced during data transmission (e.g., checksum techniques, file size)?
• 6) Methods. Are they appropriate? Current? Described clearly enough so that the work could be repeated by someone else?
• 7) Study Design. Is the design appropriate and correct? Can the reader readily discern which measurements or observations are independent of which other measurements or observations? Are replicates correctly identified? Are significance statements justified?
• 8) Errors. Point out any errors in technique, fact, calculation, interpretation, or style. (For style we follow the "CBE Style Manual, Fifth Edition," and the ASTM Standard E380- 93, "Standard Practice for Use of the International System of Units.")
• 9) Citations. Are all (and only) pertinent references cited?

Fairness and Objectivity. If the research premise for the database is flawed, criticize the science, not the scientist. Harsh words in a review will cause the reader to doubt your objectivity; as a result, your criticisms will be rejected, even if they are correct! Comments directed to the authors should demonstrate that:

• You have carefully and thoroughly reviewed the data and metadata.
• Your criticisms are objective and correct, are not merely differences of opinion, and are intended to help the data originator improve his or her data paper.
• You are qualified to provide an expert opinion about the research that served as the impetus for the data paper.

If you fail to win the data originator's respect and appreciation, your efforts will have been wasted.

Anonymity. You may sign your review if you wish. If you choose to remain anonymous, avoid comments to the authors that might serve as clues to your identity.