Focus and Scope

This electronic journal focuses on the emerging field of biodiversity informatics--the creation, integration, analysis, and understanding of information regarding biological diversity. The journal encourages submissions in any area of the biodiversity informatics enterprise. We distinguish between two types of submissions; full manuscripts and application notes. Application notes are shorter papers (typically not exceeding ten manuscript pages) that announce and describe a new biodiversity informatics application. Full manuscripts may still include details on any particular biodiversity informatics tool, but the scope of the paper should be larger than that single application. Full manuscipts should include more details about shared development challenges and solutions for the whole community, and how the work fits in with broad development or research questions of importance to the biodiversity research or biodiversity tool development community.

POTENTIAL AUTHORS SHOULD NOTE: When users register with the journal three check boxes are available towards the end of the form that allow a user to select potential roles: choices are "Reader," "Author," and "Reviewer"--anyone considering contributing to the journal should select all three. Once a user is registered, however, apparently only managers can alter their roles(!). This seems to be a (minor) flaw / oversight in the software, and may--for the moment--require that readers who wish to become authors have to re-register using a different username and email, and checking the 'author' box.

Biodiversity Informatics Training Modules

These modules are the portal to an online curriculum of subjects in biodiversity informatics. Each is peer-reviewed, and thereby has some degree of reliability in terms of authoritative summary of a sub-field of biodiversity informatics.

Privacy Statement

The names and email addresses entered in this journal site will be used exclusively for the stated purposes of this journal and will not be made available for any other purpose or to any other party. 

Peer Review Process

Biodiversity Informatics typically seeks two peer reviews per manuscript submission. In cases of conflict between those two reviews, a third opinion or that of one of the editors may be sought. In some cases, the editors may decide to return manuscripts to authors prior to review with preliminary comments designed to improve the manuscript's chances of eventual acceptance. Each manuscript is inspected for non-original text and other unethical practices via a variety of means.

Publication Frequency

BI will be published continuously, with papers appearing as they are ready throughout the year.

Copyright Notice

Copyright for articles published in this journal is retained by the authors, with first publication rights granted to the journal. All articles are licensed under a Creative Commons Attribution Non-Commercial license.

Open Access Policy

This journal provides open access to all of it content on the principle that making research freely available to the public supports a greater global exchange of knowledge. Such access is associated with increased readership and increased citation of an author's work. For more information on this approach, see the Public Knowledge Project, which has designed this system to improve the scholarly and public quality of research, and which freely distributes the journal system as well as other software to support the open access publishing of scholarly resources.

Biodiversity Informatics provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge. Authors will never be charged to submit or publish a manuscript through Biodiversity Informatics and all articles will be published under a Creative Commons Attribution Non-Commercial license.

Archiving

Biodiversity Informatics is archived in Portico (www.portico.org) and at the University of Kansas

Author Guidelines

INSTRUCTIONS TO AUTHORS

Biodiversity Informatics publishes articles in all areas related to information regarding biodiversity: creation of electronic data sets, and their management, integration, analysis, interpretation, and understanding. We welcome manuscripts presenting significant and original results that extend our understanding of biodiversity informatics.

Papers follow several formats:

  1. ARTICLES: Regular articles report either important additions to biodiversity informatics, or careful empirical studies that bear on significant questions in the field. They should include an abstract that summarizes the results and their implications. Demonstrating well-established phenomena in another taxon or context may fall short of being acceptable. Similarly, papers that simply apply existing models are less likely to be accepted than those that materially extend our understanding or provide practical applications.
  2. COMMENTARIES: Commentaries express new points of view or set out speculations based on scholarly review of recently published works. They must go beyond the works being reviewed and include discussions of new directions, new syntheses, and/or resolutions to old questions. These contributions will normally be solicited, but authors may submit proposals to the Editors.
  3. SHORT COMMUNICATIONS: Short Communications are brief papers reporting new data or ideas. They should be 15 or fewer typed pages (including literature cited) and include up to 2 figures and 2 tables. They should include abstracts no longer than five percent of the paper's length.
  4. BOOK/MEDIA REVIEWS: Reviews evaluate recently published books or monographs and set the reviewed work in the context of the field. Book Reviews are normally solicited, but aspiring reviewers may propose writing a review to the Editors. 

GUIDELINES FOR MANUSCRIPT PREPARATION Manuscripts follow The Chicago Manual of Style, the CBE Style Manual, and the style and format of recent articles published in the journal Evolution, save that web links or URLs should be placed in footnotes. The names of journals in the Literature Cited section must be abbreviated according to BIOSIS. Do not hyphenate words at the right margin or justify the right margin. Footnotes to text should be avoided; they can usually be included in the text (parenthetically if necessary). All tables (including appendices) must be double spaced. Do not separate tables from their footnotes. Mathematical expressions must be clearly typed; leave two blank lines before and after each equation. Illustrations, when published, will be reduced to a maximum of 88 mm (single column) or 180 mm in width and 230 mm in length; calculate line thickness and symbol sizes accordingly. Figure legends must be double spaced.

SPECIAL GUIDELINES FOR BIODIVERSITY INFORMATICS TRAINING MODULES: We are trying out a new idea … peer-reviewed teaching modules that treat different aspects of the new field of biodiversity informatics. The idea is to provide diverse learning materials for colleagues around the world who might benefit from hearing authoritative lectures from experts in aspects of the field.

Here are some relevant links about the project:

  1. The main project page is located at http://biodiversity-informatics-training.org.
  2. Publicity/announcements are handled through a Facebook page, at http://www.facebook.com/groups/BiodiversityInformatics/.
  3. The modules are published in the journal Biodiversity Informatics, located at https://journals.ku.edu/jbi.
  4. An example of a training module (the first one to be ‘published’) can be seen at https://journals.ku.edu/index.php/jbi/article/view/4300.

The teaching modules are quite simple. As you can see in the link (#4 above), they consist of four elements:

  1. Abstract – keep it relatively short, just outlining the set of topics.
  2. Links to YouTube videos of your lecture (see excellent guidelines at http://support.google.com/youtube/bin/static.py?hl=en&guide=1728585&page=guide.cs). You are welcome to develop and post these videos yourself, or we can help out, as we have the protocols pretty much in hand. If you develop and post your own videos, be sure to choose the “Creative Commons License” option for posting, as that option retains the copyright for you.
  3. Reading materials (best supplied as a permanent URL … perhaps to an object in an institutional repository; if you are without ideas as to how to achieve this, we can help)
  4. Practice materials or sample data or worked examples (whatever is appropriate to the particular topic) In sum, preparation of these teaching modules is not a huge task, other than the process of accumulating and synthesizing the expertise with which to free brave enough to give the lecture in the first place. We (i.e., the BITC project personnel, or the Biodiversity Informatics editorial group) are very willing to help with any questions or complications. Please contact Town Peterson (town@ku.edu), if you have any remaining questions or doubts about this project.

SUBMISSION INSTRUCTIONS: Manuscripts must be in English, Spanish, or Portuguese. Manuscripts are submitted online via the Biodiversity Informatics website.

REVIEW: After a paper has been reviewed by the Editors and outside reviewers, the Editor will decide whether to accept or reject it. Acceptance is based on the quality of the work and writing and significance of the article to our understanding of evolution. Each paper must stand on its own merits and be a substantial contribution to the field. Authors of accepted papers will be asked to send an electronic version (Microsoft Word or Rich Text Format) of the accepted manuscript to the BI website for editing and publication.

STATEMENT ON AUTHORSHIP: Authorship of a paper carries with it responsibility as well as credit. All those whose names appear as authors should have played a significant role in designing or carrying out the research, writing the manuscript, or providing extensive guidance to the execution of the project. They should be able to present and defend the work in a public forum. Honorary authorship is to be avoided. All authors must be in agreement on both the submission and full content of any article carrying their name. Any violation of these conditions represents academic misconduct and will be dealt with accordingly.

CHARGES FOR PUBLICATION: Biodiversity Informatics is founded on the principle of free and open access to information, in this case information about biodiversity informatics. Hence, no page charges are requested.

COPYRIGHT: Copyright for articles published in this journal is retained by the authors, with first publication rights granted to the journal. All articles are licensed under a Creative Commons Attribution Non-Commercial license.

Publication Ethics and Malpractice Statement

The journal Biodiversity Informatics expects all persons involved in the publication process (author, journal editor, peer reviewer, publisher) to follow standards and norms of expected ethical behavior. These statements are based on COPE’s Best Practice Guidelines for Journal Editors (see http://publicationethics.org/resources/guidelines for various resources), and follow the template (roughly at least) of the National Journal of Community Medicine (http://www.njcmindia.org/home/about/22).

Publication Decisions: The editor decides which of the manuscripts submitted will be published. The editor will follow the journal’s stated policies, constrained by the relevant legal requirements regarding libel, copyright infringement, and plagiarism. The editor may confer with other editors or peer-reviewers in making these decisions.

Fair Play: The editor’s decisions regarding publication of manuscripts will be based on their intellectual content, without regard to race, gender, sexual orientation, religious belief, ethnic origin, citizenship, or political philosophy of the authors.

Confidentiality: The editor will not disclose any information about manuscripts submitted to any other parties, save for the corresponding author, reviewers and potential reviewers, and other editors.

Disclosure and Conflicts of Interest: Unpublished materials in submitted manuscripts will not be used in the editor's own research without the express written consent of the author.

DUTIES OF REVIEWERS

Contribution to Editorial Decisions:  Peer review assists the editor in editorial decisions; through the editor, review may also assist the author in improving manuscripts.

Expertise and Promptness: Potential referees who do not feel qualified to evaluate a manuscript, or who will not be able to provide reviews within reasonable periods of time should advise the editor and excuse him/herself from the review process.

Confidentiality: Manuscripts received for review will be treated as confidential, and cannot be shared with others without editorial authorization.

Standards of Objectivity: Reviews should be objective, and with appropriate supporting information and argument. Ad hominem comments should be avoided at all costs.

Acknowledgement of Sources: Reviewers should identify relevant published work not cited by the authors, and should provide sufficient reference that the authors can find such previous work. Reviewers should make known to the editor any substantive overlap between a manuscript under consideration and other work of which they have personal knowledge.

Disclosure and Conflict of Interest:  Information and ideas disclosed to peer reviewers is confidential and cannot be used for personal advantage. Reviewers should not review manuscripts in any case in which they have real or apparent conflicts of interest of any sort (competition, collaboration, personal relationships, institutional connections) with any of the authors, companies, or institutions connected to the manuscript.

DUTIES OF AUTHORS

Reporting Standards: Authors should present careful accounting of work performed, together with objective discussion of significance of results. A paper should present data and methods in sufficient detail so that others can replicate the work. Fraudulent or known-inaccurate statements constitute unethical behavior and are unacceptable.

Data Access and Retention: Authors may be asked to provide access to relevant raw data used in development of a paper for the review process. Authors should be prepared to provide access to such data (consistent with the ALPSP-STM Statement on Data and Databases) as practical, and should retain such data for a reasonable time after publication. Whenever possible, authors should deposit such data in openly accessible repositories.

Originality and Plagiarism: The authors attest that the work submitted to the journal is original. Any use of work or words of others must be appropriately cited or quoted.

Multiple, Redundant, or Concurrent Publication: Authors should not publish manuscripts describing essentially the same research in multiple primary publications. Concurrent submissions of the same manuscript to multiple journals is unethical behavior and is unacceptable.

Authorship: Authorship should be limited to persons who have made a significant intellectual contributions specifically to the paper in question. These contributions may be to the conception, design, execution, or interpretation of the study. All who have made such contributions should be listed as co-authors. Others who participated in aspects of the research should be acknowledged appropriately. The corresponding author must ensure that all co-authors have seen and approved the final manuscript version and have agreed to its submission for publication.

Hazards and Human or Animal Subjects: Any work involving any hazardous materials or procedures, or that involves direct interaction with individual humans or other vertebrate animals must follow accepted norms for such work.

Disclosure and Conflicts of Interest: Authors must disclose any financial interests or other substantive conflicts of interest that might be construed as potentially influencing their results or interpretation of their manuscript. All sources of financial support for the research must be disclosed.

Errors in Published Works: Authors who discover significant errors or inaccuracies in the published work must notify the journal editor immediately, and cooperate with the editor to retract or correct the paper.