Authorship and Acknowledgement Guidelines

= This Page is an Archive of an old discussion - June 11th 2010 =

This a revised draft by Joanne Luciano of the initial draft below horizontal line. Revised 28 Dec 2005

This page describes the authorship and acknowledgement guidelines that members of the BioPAX project should adhere to. BioPAX is a community effort that has benefited from contributions by many individuals from a variety of institutions. A balance needs to be achieved between ensuring that all significant contributors receive proper credit and the appropriate promotion and dissemination of the results of the project. The guidelines set forth on this page are designed to ensure that these individuals receive due credit in publications, presentations, technical documentation, and other media while at the same time making it possible for participants to report of their efforts and contributions in a timely and effective manner.

Format / Ontology Papers
It is our expectation that there will be at least one reference journal paper concerning the BioPAX project which will act as the prime citation. It is desirable that this paper should arise out of common consensus between the participants of the workgroup and should be written collaboratively. Prior to submission, the draft manuscript should be sent to the biopax-discuss email list and any other authors for review. All authors must agree to the text of the final submitted manuscript. The author list should be an alphabetical listing of all members of the BioPAX Workgroup. A contributions section of the paper should list the specific contributions of those authors who merit additional recognition, such as the primary authors of the manuscript or those that developed parts of the BioPAX ontology, converters, etc. that are presented in the paper. Given the longer gestation period that journal papers usual have, this process can be effectively undertaken. However, if a participant has not commented or provided input to the manuscript within six weeks of its dissemination on the BioPAX email list, the active authors will take this as tacit agreement.

In addition, we expect further journal publications regarding particular aspects of the project, its development, application, challenges encountered etc. Such journal papers (if published) should include the names of authors who actively contributed to the writing and intellectual content. An acknowledgement section will provide recognition to the wider BioPAX consortium and the context in which the work was done.

BioPAX News Articles
Papers written by BioPAX Workgroup members that do not contain technical details of the BioPAX ontology/format, but present news or commentary on its utility or application to pathway research, do not need to list all members of the BioPAX Workgroup as authors. However, these papers should contain a clear statement of acknowledgment to the BioPAX workgroup.

Papers Describing Projects Making Use Of BioPAX
Papers that present technical details of databases, software tools, or other projects that make use of BioPAX that are undertaken by members of the BioPAX Workgroup or other community members should list as authors those who contributed directly and significantly to those projects. Such papers should reference BioPAX by citation to an official BioPAX paper (such as the reference journal paper) listed on the BioPAX website (or directly reference the BioPAX website, if no paper is available to cite). Acknowedgment should be made to the BioPAX workgoup.

Lecture Presentations
Presentations specifically about BioPAX should list the presenter as the sole author, but should provide an acknowlegement to the BioPAX workgroup.

Posters
Presentations specifically about BioPAX should list as authors those who have contributed directly to the work reported and provide an acknowledgment to the BioPAX Workgroup.

Technical Documentation
BioPAX technical documentation, such as Level Specification Documents, should list as authors those who have contributed directly to the work reported and provide acknowledgment to the BioPAX Workgroup. Major contributors to the text of these documents should be listed as editors, below the author list.

Internet Resources
The About page of the BioPAX website should list all members of the BioPAX Workgroup and their affiliation. Workgroup members who have made significant contributions in the past, but are no longer active in BioPAX development, should be listed as "Past Contributors". All others will be listed as "Active Contributors". The minimal requirement to be listed as a Workgroup Member is attendance at a BioPAX face-to-face meeting and contribution to the resolution of a significant development issue. The About page will also list the current contacts for administrative coordination, such as meeting preparations, travel reimbursements, etc.

Joanne Luciano Comment: I have been thinking about the authorship guidelines and realized that in a certain sense they were too restrictive. One of the important objectives we have is to ensure the project is promoted in every possible sphere of potential application. I believe if every publication about BioPAX needs approval from everyone this will hinder rather than promote the project.

Equally it will be odd if authorship is ascribed to every member of the workgroup on every paper. I propose that the reference paper which we will write will include everyone's name as co-author but other papers, conference presentations etc. will name the authors actively involved and in addition provide an acknowledgement to the workgroup. This will allow responsibility to be clearly defined and also speed up the process of publication and dissemination. We need to avoid a 'design by committee' culture where it is not needed.

I look forward to people's views on this matter. I am hoping that people will not insist on being named as co-authors just because the are part of the consortium and wish to be authors by default.

This initial draft is to be discussed and refined.

This page describes the authorship and acknowledgement guidelines that members of the BioPAX project should adhere to. BioPAX is a community effort that has benefited from contributions by many individuals from a variety of institutions. It is critical to the BioPAX effort that all contributors feel they receive proper credit for the efforts. The guidelines set forth on this page are designed to ensure that these individuals receive due credit in publications, presentations, technical documentation, and other media.

Format / Ontology Papers
Papers whose primary focus is the structure of the BioPAX ontology or the use of BioPAX as a data exchange format should be developed collaboratively with the BioPAX Workgroup. Permission for the paper should be received from the BioPAX Workgroup, via consensus, before choosing to write such a paper. Prior to submission, the draft manuscript should be sent to the biopax-discuss email list and any other authors for review. All authors must agree to the text of the final submitted manuscript. The author list should be an alphabetical listing of all members of the BioPAX Workgroup. A contributions section of the paper should list the specific contributions of those authors who merit additional recognition, such as the primary authors of the manuscript or those that developed parts of the BioPAX ontology, converters, etc. that are presented in the paper.

BioPAX News Articles
Papers written by BioPAX Workgroup members that do not contain technical details of the BioPAX ontology/format, but present news or commentary on its utility or application to pathway research, do not need to list all members of the BioPAX Workgroup as authors. However, these papers should contain a clear statement that BioPAX is the work of the BioPAX Workgroup, and should list the Workgroup members. This statement should be prominent and appear early in the article, preferably as a preface to the main text. As a courtesy, co-authorship of the article should be offered to other members of the Workgroup and the draft manuscript should be sent to the biopax-discuss email list prior to submission for comment.

Papers Describing Projects Making Use Of BioPAX
Papers that present technical details of databases, software tools, or other projects that make use of BioPAX that are undertaken by members of the BioPAX Workgroup or other community members should list as authors those who contributed directly and significantly to those projects. Such papers should reference BioPAX by citation to an official BioPAX paper listed on the BioPAX website (or directly reference the BioPAX website, if no paper is available to cite).

Lecture Presentations
Presentations specifically about BioPAX should list the presenter as the sole author, but should list all BioPAX developers clearly in an acknowledgements slide.

Posters
Posters specifically about BioPAX should list as authors all members of the BioPAX Workgroup or "The BioPAX Workgroup" if there is not enough room for all authors in the poster abstract book. If this is the case, all of the authors should still be listed on the poster in the normal place where authors are listed. A small contributions section of the poster should optionally list the specific contributions of those authors who merit additional recognition, such as the primary authors of the poster or those that developed parts of the BioPAX ontology, converters, etc. that are presented in the poster.

Other posters, not specifically about BioPAX, but mentioning BioPAX should reference the BioPAX website or official paper.

Technical Documentation
BioPAX technical documentation, such as Level Specification Documents, should list as authors all members of the BioPAX Workgroup. Major contributors to the content of these documents should be listed as editors, below the author list.

Internet Resources
The About page of the BioPAX website should list all members of the BioPAX Workgroup and their affiliation. Workgroup members who have made significant contributions in the past, but are no longer active in BioPAX development, should be listed as "Past Contributors". All others will be listed as "Active Contributors". The minimal requirement to be listed as a Workgroup Member is attendance at a BioPAX face-to-face meeting and contribution to the resolution of a significant development issue. The About page will also list the current contacts for administrative coordination, such as meeting preparations, travel reimbursements, etc.