Transparency In Authors’ Contributions And Responsibilities To Promote Integrity In Scientific Publication

Authors: Marcia McNutt, Monica Bradford, Jeffrey Drazen, R. Brooks Hanson, Bob Howard, Kathleen Hall Jamieson, Veronique Kiermer, Michael Magoulias, Emilie Marcus, Barbara Kline Pope, Randy Schekman, Sowmya Swaminathan, Peter Stang and Inder Verma

Abstract: In keeping with the growing movement in scientific publishing toward transparency in data and methods, we argue that the names of authors accompanying journal articles should provide insight into who is responsible for which contributions, a process should exist to confirm that the list is complete, clearly articulated standards should establish whether and when the contributions of an individual justify authorship credit, and those involved in the generation of scientific knowledge should follow these best practices. To accomplish these goals, we recommend that journals adopt common and transparent standards for authorship, outline responsibilities for corresponding authors, adopt the CRediT (Contributor Roles Taxonomy) methodology for attributing contributions, include this information in article metadata, and encourage authors to use the digital persistent identifier ORCID. Furthermore, we suggest that research institutions have regular open conversations on authorship criteria and ethics and that funding agencies adopt ORCID and accept CRediT. Scientific societies should further authorship transparency by promoting these recommendations through their meetings and publications programs.

Citation: Marcia McNutt, Monica Bradford, Jeffrey Drazen, R. Brooks Hanson, Bob Howard, Kathleen Hall Jamieson, Veronique Kiermer, Michael Magoulias, Emilie Marcus, Barbara Kline Pope, Randy Schekman, Sowmya Swaminathan, Peter Stang, Inder Verma. (2017). Transparency In Authors’ Contributions And Responsibilities To Promote Integrity In Scientific Publication.
bioRxiv 140228; doi:


Copyright and the Use of Images as Biodiversity Data

Authors: Willi Egloff, Donat Agosti, Puneet Kishor, David Patterson, Jeremy A. Miller

Abstract: Taxonomy is the discipline responsible for charting the world’s organismic diversity, understanding ancestor/descendant relationships, and organizing all species according to a unified taxonomic classification system. Taxonomists document the attributes (characters) of organisms, with emphasis on those can be used to distinguish species from each other. Character information is compiled in the scientific literature as text, tables, and images. The information is presented according to conventions that vary among taxonomic domains; such conventions facilitate comparison among similar species, even when descriptions are published by different authors. There is considerable uncertainty within the taxonomic community as to how to re-use images that were included in taxonomic publications, especially in regard to whether copyright applies. This article deals with the principles and application of copyright law, database protection, and protection against unfair competition, as applied to images. We conclude that copyright does not apply to most images in taxonomic literature because they are presented in a standardized way and lack the creativity that is required to qualify as ‘copyrightable works’. There are exceptions, such as wildlife photographs, drawings and artwork produced in a distinctive individual form and intended for other than comparative purposes (such as visual art). Further exceptions may apply to collections of images that qualify as a database in the sense of European database protection law. In a few European countries, there is legal protection for photographs that do not qualify as works in the usual sense of copyright. It follows that most images found in taxonomic literature can be re-used for research or many other purposes without seeking permission, regardless of any copyright declaration. In observance of ethical and scholarly standards, re-users are expected to cite the author and original source of any image that they use.

Citation: Willi Egloff, Donat Agosti, Puneet Kishor, David Patterson, Jeremy A. Miller,  2017. “Copyright and the Use of Images as Biodiversity Data” 


Re-envisioning a future in scholarly communication

Author: Chris H.J. Hartgerink

Abstract: Scholarly communication is in need of disruption. Commodifying knowledge as is currently done with journals, is not sustainable any longer. An alternative is the commodification of how information is consumed. By focusing on the commodification of consumption instead of commodification of the resource, the problem of access to knowledge can be resolved in a sustainable manner. Additionally, commodification of consumption removes several perverse incentives from the scholarly system that now produces unreliable knowledge. The main tenet underlying the themes of Open Access, Open Data, Open Science, and replication initiatives in scholarly communication is sustainability through transparency of the scholarly process in all facets. The sustainability of any networked system is threatened by single points of failure (i.e., the entire system can be manipulated from one node in the network). The scholarly process is ridden with such single points of failures at all stages. Distributing the scholarly communications system would remove the problems of single points of failure. Distributing and decentralizing the scholarly communications system is achievable with newly developed peer-to-peer (p2p) Internet protocols. Alongside decentralization and distribution of the content, integrity of the scholarly record can also be reformed to transform sections of a paper into different, reusable nodes of knowledge. These nodes can be logged on a blockchain based ledger of which everyone can have a copy. In order to deposit nodes onto the ledger, the depositor needs to agree that the contents are licensed CC 0, in order to maximize legal certainty regarding reuse of the contents. This is key to create a sustainable eco-system where scholars and companies can cooperate instead of compete, as we currently do.

Citation: Chris H.J. Hartgerink. (2017). Re-envisioning a future in scholarly communication. For the 2017 IFLA conference.

Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

Authors: Gil Yolanda, Cedric H. David, Ibrahim Demir, Bakinam T. Essawy, Robinson W. Fulweiler, Jonathan L. Goodall, Leif Karlstrom, Huikyo Lee, Heath J. Mills, Ji-Hyun Oh, Suzanne A. Pierce, Allen Pope, Mimi W. Tzeng, Sandra R. Villamizar, Xuan Yu

Abstract: Geoscientists now live in a world rich with digital data and methods, and their computational research cannot be fully captured in traditional publications. The Geoscience Paper of the Future (GPF) presents an approach to fully document, share, and cite all their research products including data, software, and computational provenance. This article proposes best practices for GPF authors to make data, software, and methods openly accessible, citable, and well documented. The publication of digital objects empowers scientists to manage their research products as valuable scientific assets in an open and transparent way that enables broader access by other scientists, students, decision makers, and the public. Improving documentation and dissemination of research will accelerate the pace of scientific discovery by improving the ability of others to build upon published work.

Citation: Gil, Y., et all (2016). Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance. Earth and Space Science, 3, 388-415. 


Open Access and the Graduate Author: A Dissertation Anxiety Manual

Author: Jill Cirasella & Polly Thistlehwaite

Abstract: The process of completing a dissertation is stressful—deadlines are scary, editing is hard, formatting is tricky, and defending is terrifying. (And, of course, postgraduate employment is often uncertain.) Now that dissertations are deposited and distributed electronically, students must perform yet another anxiety-inducing task: deciding whether they want to make their dissertations immediately open access (OA) or, at universities that require OA, coming to terms with openness. For some students, mostly in the humanities and some of the social sciences, who hope to transform their dissertations into books, OA has become a bogeyman, a supposed saboteur of book contracts and destroyer of careers.

This chapter examines the various access-related anxieties that plague graduate students. It is a kind of diagnostic and statistical manual of dissertation anxieties—a “Dissertation Anxiety Manual,” if you will—describing anxieties surrounding book contracts, book sales, plagiarism, juvenilia, the ambiguity of the term online, and changes in scholarly research and production.

Citation: Cirasella, J., & Thistlethwaite, P. (2017). Open access and the graduate author: A dissertation anxiety manual. In K. L. Smith & K. A. Dickson (Eds.), Open access and the future of scholarly communication: Implementation (pp. 203-224). Lanham, MD: Rowman & Littlefield.



Structuring supplemental materials in support of reproducibility

Author: Dov Greenbaum

Abstract: Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable, and reusable (i.e., “FAIR”). Moreover, properly off-loading to them the data and detail in a paper could make the main text more readable. We propose a hierarchical organization for supplements, with some parts paralleling and “shadowing” the main text and other elements branching off from it, and we suggest a specific formatting to make this structure explicit. Furthermore, sections of the supplement could be presented in multiple scientific “dialects”, including machine-readable and lay-friendly formats.

Citation: Greenbaum, Dov, et al., 2017.Structuring supplemental materials in support of reproducibility. Genome Biology 18:64, 10.1186/s13059-017-1205-3.