Appendices, Supplements, and Data Papers Instructions for Authors
Introduction
Appendices and Supplements. Authors are encouraged to submit digital appendices and supplements at the time of article submission, or subject-matter editors may request such material. At the time of submission of your article for review, you need only submit your files in a format acceptable for reviewing; for example, as Word documents in the case of appendices. This should be done through the online tracking system following guidelines found there. Once the manuscript is accepted then your files must conform to the guidelines found here (for example, once accepted, the archives must be submitted as separate e-mail attachments to <esa_journals@cornell.edu> rather than through the online tracking system). The digital appendices and supplements normally will be evaluated by the subject-matter editor and the peer reviewers selected for the manuscript. The metadata of supplemental material may be subject to additional review to determine acceptability for Ecological Archives. Appendices and supplements accepted for Ecological Archives will be assigned permanent accession numbers, which will be published at the end of the original print article. Failure to submit copies of all materials for Ecological Archives to the Publications Office by the time of submission of the final accepted manuscript could result in significant delay in publication of the article.
There are specific downloadable templates for preparing appendices and supplements. Material for appendices and metadata for supplements should generally be in HTML, although some heavily formatted material, such as mathematical proofs, may need to be presented in pdf (in addition to the HTML). Material in supplements should be formatted for ease of use rather than display.
More detailed instructions appear below. See also FAQs.
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 Ecological Archives accession numbers. 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].
Special instructions are available for authors of Data Papers
Ecological Archives electronically publishes two types of materials that are supplemental to articles that appear in the ESA print journals: Appendices and Supplements. Appendices and Supplements to articles published in Ecology, Ecological Applications, or Ecological Monographs normally will be archived electronically in Ecological Archives. Please adhere to the following guidelines in preparing your Appendices or Supplements prior to submitting them to the ESA Publications Office (e-mail: esa_journals@cornell.edu). Examples can be found within recent issues of Ecological Archives. Please use examples from 2000 or later in preparing your submission.
In the printed journal article, a brief description and an accession number will be listed for each digital appendix and/or supplement following the Literature Cited section, as in this example:
Readers/users will be able to link directly to each appendix and supplement via the online version of the article.
Appendix or Supplement -- what's the difference?
Appendices in Ecological Archives are directly viewable (or executable in the case of sound or video) with a standard web browser. They are self-contained; all critical supporting materials are present in the caption, footnotes, or are in the associated original article. These supporting materials will typically take the form of tables, graphs, or photographs. Authors of field studies are encouraged to submit a photograph of their study site for inclusion as a digital appendix. An example appendix appears below:
Supplements can include, but are not limited to, original and derived data sets, source code for simulation models, and details of and 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 must be provided in a standard format. (Materials previously submitted to the ESA Supplemental Publication Service are now treated as Supplements.)
Another 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. The main supplement page will look something like this:
Preparing Appendices
Authors are encouraged to submit digital appendices and supplements at the time of article submission, or subject-matter editors may request such material. At the time of submission of your article for review, you need only submit appendix files in a format acceptable for reviewing; for example, as Word documents. This should be done through the online tracking system following guidelines found there. Once the manuscript is accepted then your files must conform to the guidelines found here.
Appendices of accepted manuscripts destined for Ecological Archives should be sent as e-mail attachments in web-browsable formats to the ESA Publications Office (e-mail: esa_journals@cornell.edu).
When submitting an Appendix of an accepted manuscript for Ecological Archives, you need to submit at least two files: a main (home) page that lists and is linked to all appendices for the article, and at least one linked page (or pages), each containing a single file. The main (home) page must be submitted in HTML, whereas the associated file(s) (page[s]) should be in one of the following formats: HTML for tabular or textual material; .GIF, .JPG, or .PNG for still graphics, .MPG for video graphics or animation, and .MP3 or .WAV for sound. Authors of mathematical appendices are encouraged to submit a pdf file in addition to, but not in place of, the html version using the most recent Adobe Distiller software. Appendices that are predominately mathematical will be examined on a case-by-case basis to determine whether the presentation is best served by posting a pdf file only. No other formats are acceptable for Appendices (unless special permission is granted by the Data Editor). Do not submit appendix tables that have been formatted by using spaces or tabs across a page. For example, a table created in MS Word must be in actual table format before converting to HTML. You can download HTML templates that you can use to create your files. Click here to download the Appendix templates.
The home page -- Appendices on Ecological Archives consist of a 'default' (home) page listing all the appendices, and one or more linked pages, each containing one file. The main page begins with a title line, which includes the author(s) names (first name, middle initial, last name), date of publication, title of article, journal in which the article appears, volume number, and page numbers. The title line is an HTML large heading (HTML tag <H3> or font size = +1). Please use Times New Roman font for all entries.
The title line is followed by the word Appendices (or Appendix and a letter, if there is but one digital appendix). This is also an HTML large heading (HTML tag <H3> or font size =+1). If there are multiples appendices, each of the entries starts as Appendix A, Appendix B, etc. The link is applied to the label Appendix N.
Following the header, the included appendices are listed. Each has a descriptive title (HTML large heading: HTML tag <H3>) and an Ecological Archives accession number. The ESA Publications Office will assign the accession number.
Note that while a single journal article can have only one entry in Ecological Archives, individual appendices and supplements receive separate accession numbers.
When using the HTML templates, please do not alter embedded links to the ESA Copyright page or the Ecological Archives Home Page.
Linked pages -- Linked pages contain the actual appendices. Like the home page, the linked pages are produced in HTML, but may have embedded still graphics (.JPG, .GIF, .PNG), video clips (.MPG), or sound clips (..MP3 or .WAV).
The first line of the file is the Ecological Archives accession number (HTML Large Heading: HTML tag <H3>). The second line is the full citation, as on the main page (HTML Large Heading: HTML tag <H3>). The ESA Publications Office will assign page numbers.
The third line (HTML paragraph) is the title of the file. Note that it is the same as on the main page.
The bulk of the file is taken up by the Appendix itself. For example, it is common for the appendix to be a simple table, constructed in HTML. It could also be a figure, photograph, video clip, or sound clip.
If literature is cited in the Appendix, there should be a Literature Cited section at the end of the page. See FAQs page, number 10, for more details. If URLs are included as Literature Cited, please include the date the web page was last accessed by you.
The last line of the file provides a hyper-link back to the main page.
Additional questions about preparing and formatting Appendices for publication in Ecological Archives should be directed to the Data Archives Manager or the Data Editor.
Preparing Supplements
Authors are encouraged to submit digital appendices and supplements at the time of article submission, or subject-matter editors may request such material. At the time of submission of your article for review, you need only submit your files in a format acceptable for reviewing. This should be done through the online tracking system following guidelines found there. Once the manuscript is accepted then your files must conform to the guidelines found here.
Supplements destined for Ecological Archives should be sent as an e-mail attachment in appropriate formats to the ESA Publications Office. The format for supplement pages is fixed and templates are provided. You will notice that we provide two separate template pages for supplements (a main page and a download page) but often use only one. This is because if your file list is short enough, it is unnecessary to list all the same files again on a separate page. However, if your downloadable files consist of zipped files and large numbers of unzipped files, it may be preferable to place them on a separate download page.
See http://esapubs.org/archive/ecol/E085/020/suppl-1.htm for an example of the former and http://esapubs.org/archive/ecol/E085/022/suppl-1.htm for an example of the latter. The main (home) page must be submitted in HTML, while the associated file(s) (page[s]) should be in a usable format.
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. In order to guarantee the accessibility of data for the long-term, we cannot accept Excel spreadsheets for posting. Tab or comma-delimited ASCII files should be submitted instead.
Software should be submitted both as source code and compiled (executable) code.
Compiled code submitted without accompanying source code is not acceptable.
Before submitting other types of supplemental files, please consult the Data Editor to discuss appropriate submission formats. Supplements of programs should include information on how the programs are run. We discourage including links to other web pages for additional components since we cannot guarantee availability. If you do include links to other web pages please include the date last accessed as in "Smith, J. B. 1997. Ultimate tree ring Web pages. (14 January 2002; www.utk.edu/~grissino)".
As with Appendices, the formats for the main page and download page are fixed. You can download HTML templates that you can use to create your files. Click here to download the Supplement templates.
The home page -- Supplements on Ecological Archives consist of a 'default' (home) page (if you have more than one supplement) listing all the associated supplements, a main page, a download page if appropriate, and one or more linked pages, each containing one file. If you have only one supplement, then the home page file is not necessary, and if your file list is brief, then the download page is unnecessary.
The main page begins with a title line, which includes the author(s) names (first name, middle initial, last name), date of publication, title of article, journal in which the article appears, volume number, and page numbers. The title line is an HTML large heading (HTML tag <H3> or font size = +1). Please use Times New Roman font for all entries.
The title line is followed by the word Supplement(s). This is also an HTML large heading (HTML tag <H3>).
Following the Supplement header, the included supplements are listed. Each has a descriptive title (HTML large heading: HTML tag <H3>) and an Ecological Archives accession number. The ESA Publications Office will assign the accession number. When more than one supplement is included, start the entry with the title Supplement 1, 2, etc.
Note that in Ecological Archives, multiple supplements can be assigned to a single paper, and each supplement receives its own accession number.
The main page has three principal hyper-links (in addition to the hyper-link to the ESA Copyright page). These hyper-links reference the Authors of the Supplement, the File list, and the Description of the supplement, including the individual files, and including download instructions. These sections generally follow on the main page linked via anchors, but in the case of complicated supplements, or multiple supplements, extra linked pages may be necessary for clarity.
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.
The File list indexes all available files associated with the Supplement. This is a simple, indented paragraph (use the HTML tag <BLOCKQUOTE>). All file names should be formatted inCourier font. Each file should be hyper-linked to the associated file itself. This provides one way to either view or download these files. Where many files constitute a supplement, individual files can be listed on a separate linked page.
The Description describes the available files. Such descriptions should include file layout, variable names (also in Courier font) and interpretations, any required software, instructions on using the supplemental files (file names in Courier font), and any literature cited. There is no limit to the length of these descriptions. Please be concise, but complete. See details above on requirements for data and software.
When using the HTML templates, please do not alter embedded links to the ESA Copyright page or the Ecological Archives Home Page.
The Download page, if included, links the files that can be downloaded across the internet by the users. This page is relatively simple. It is titled with the Ecological Archives accession number (assigned by the ESA Publications Office), and then contains the list of files available for downloading. If there are several files associated with the Supplement, a file archive containing all the files, should also be provided. Use WinZip to create archive files for PC, or tar for creating archive files for Unix/Linux. The archive file facilitates downloading of multiple files. This allows the user the option to either download all the files at once, or download individual files.
The file list is an indented paragraph, formatted with Courier font.
Data Editor
Additional questions regarding formatting Supplements or Appendices for Ecological Archives can be directed to either the Data Editor or the Data Archives Manager.
Preparing Data Papers
Data Papers consist of 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. Tabular data in proprietary spreadsheet formats (e.g., Excel, Lotus) are not acceptable and will be returned for reformatting in ASCII. 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 HTML (preferred) file. If multiple files are required to adequately document the data, provide a group of HTML files linked in a hierarchical format to a default.htm master 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. Although formal metadata content standards for Ecological Archives are still in the development stage, useful examples are available online. Text portions of the metadata should generally adhere to manuscript submission guidelines developed for ESA journals.
General instructions for preparing metadata in data papers
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 to submit a Data Paper for peer review
Please begin by checking the author instructions found at: http://esapubs.org/esapubs/authors_main.htm
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 reviewers of Data Papers
Instructions for reviewers of Data Papers
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 author(s) (data compiler(s)) 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.
All reviews must be submitted electronically http://esapubs.esapubs.org
