About

Pensoft is an independent academic publishing company, well known worldwide for its innovations in the field of semantic publishing and for its cutting-edge publishing tools and workflows. Founded in 1992 "by scientists, for the scientists" and initially focusing on book publishing, it has grown to become a leading publisher of innovative open access journals, such as: Research Ideas and Outcomes (RIO), ZooKeys, Biodiversity Data Journal, PhytoKeys, MycoKeys, Nature Conservation, NeoBiota, Comparative Cytogenetics, and others. Pensoft has published more than 1,000 books and over 4,000 open access articles, mostly in the field of natural history.

Pensoft is a member or partner of several professional publishing organisations and data publishing platforms, including CrossRef, OASPA, PubMedCentral, CLOCKSS, Research Data Alliance (RDA), OpenAIRE, LifeWatch, DataONE, Dryad Data Repository, Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL), and others.

The content of most Pensoft journals is indexed by: ISI Web of Science, Scopus, BIOSIS, Google Scholar, Directory of Open Access Journals (DOAJ), Zoological Record, CAB Abstracts, Vifabio, BHL Citebank, Globalnames, JournalMap and others, and is archived in PubMedCentral, CLOCKSS and ZENODO.

In 2010, Pensoft was the first publisher to implement semantic tagging and enrichment of published articles as a routine editorial practice. The company is actively developing novel tools, workflows and methods for text and data publication and dissemination of scientific information, as well as technologies for semantic enrichment of content. In 2013, Pensoft launched the first ever, end-to-end, XML-based, authoring, reviewing and publishing workflow, as demonstrated by the Biodiversity Data Journal (BDJ) and the Pensoft Writing Tool (PWT), now upgraded to the ARPHA Publishing Platform. The company has also developed a number of tools for semantic publishing: Pensoft Markup Tool (PMT), Pensoft Taxon Profile (PTP), Pensoft Wiki Converter (PWC), the literature and data discovery tool Refindit.org, and others.

Innovations have always been at the core of Pensoft’s business to better serve our clients, partners and research communities. 

ARPHA Publishing Platform

We have been seeking a way to scrap the notion of academic publishing being a time-consuming and exhausting venture for any author ready to present a research. In the end, we came up with the first of its kind publishing platform to combine Authoring, Reviewing, Publishing, Hosting and Archiving all in one place. Bearing the name ARPHA, it is implemented to all Pensoft journals and offers a wide range of services also to other journals and publishers. ARPHA represents the first ever end-to-end, entirely XML-based commodity in the journal publishing industry.

Arpha Writing Tool (AWT) 

Being passionate advocates for open science, at Pensoft we have always made sure to not only provide freely accessible digital content, but also encourage collaboration in the peer-review, publication and dissemination process. Thus, we developed the ARPHA Writing Tool (AWT) to  allow authors, co-authors, external contributors, pre-submission reviewers, linguistic and copy editors to gather in the intuitive and user-friendly online authoring environment and work together on a manuscript.

Pensoft Markup Tool (PMT)

Another quite tiresome and painstaking task an author needs to complete, while submitting a manuscript, is a sweeping amount of importing, referencing, cross-linking, interlinking, mapping, and so on. Implementing our extensive experience in semantic technology and innovations, Pensoft has developed the Pensoft Markup Tool (PMT), which makes the following operations possible:

  • Import, retrieval and interlinking of XML, HTML and Adobe InDesign files
  • Tagging and auto-tagging of general and domain-specific terms at different granularity levels
  • Cross-linking of citations within the text and reference list
  • Exporting the text to semantically enhanced HTML version of the paper, visualising some of the important tag elements, the literature references cited in the text, and external links to them (when available)
  • Mapping geocoordinated localities listed in the papers
  • Generating the Taxon Pensoft Profile page for each taxon name cited in a paper, providing the reader with a quick and up-to-date summary information on a taxon from certified external sources
  • Exporting to generic JATS and TaxPub JAST XML file (http://sourceforge.net/projects/taxpub) in compliance with the requirements for archiving in PubMedCentral and indexing in PubMed
  • XML export of taxon treatments or any other tagged information in various formats acceptable by aggregators and indexers, for example Encyclopedia of Life, Plazi.org, Species-ID.net and other data aggregators.  

Pensoft Taxon Profile (PTP)

The web-based harvester Pensoft Taxon Profile (PTP) was developed to automatically harvest information about any biological taxon name mentioned within a publication and link it to external resources, for example CrossRef, PubMedCentral, PubMed, Biodiversity Heritage Library, NCBI/GenBank, ZooBank, International Plant Name Index (IPNI), Index Fungorum, International Union for Conservation of Nature (IUCN), Wikipedia, Encyclopedia of Life, Plazi.org and others. As a result, a dynamic web-page for that taxon name is being created in real time, which saves our readers a great amount of time and efforts.

Pensoft Wiki Converter (PWC)

While the Wiki environment is a fine example of a huge open access online space with immense potential in science, we have always known that we need to make use of it, in order to provide a best-quality experience to our users. This is how we came up with the Pensoft Wiki Converter (PWC), which turns the XML versions of our papers into Media-Wiki-based pages, such as Species-ID.net.

ReFindit

Led by our desire to provide our users with user-friendly and accessible knowledge, we created a handy literature and data discovery tool, called ReFindit. In order to access a publication, all you need to do is enter any relevant information, such as a Digital Object Identifier (DOI), author, title, or simply a bit of free text and click a ‘Search’ button. ReFindit searches and gathers information for you from metadata stored on CrossRef, DataCite, PubMed, Mendeley, RefBank, and the Global Names Usage Bank (GNUB).

General

The publishing ethics and malpractice policies follow the Principles of Transparency and Best Practice in Scholarly Publishing (joint statement by COPE, DOAJ, WAME, and OASPA), the NISO Recommended Practices for the Presentation and Identification of E-Journals (PIE-J), and, where relevant, the Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals from ICMJE.

Privacy statement

The personal information used on this website is to be used exclusively for the stated purposes of each particular journal. It will not be made available for any other purpose or to any other party. 

Open access

Pensoft and ARPHA-hosted journals adhere strictly to gold open access to accelerate the barrier-free dissemination of scientific knowledge. All published articles are made freely available to read, download, and distribute immediately upon publication, given that the original source and authors are cited (Creative Commons Attribution License (CC BY 4.0)).

Open data publishing and sharing

Pensoft and ARPHA encourage open data publication and sharing, in accordance with Panton’s Principles and FAIR Data Principles. For the domain of biodiversity-related publications Pensoft has specially developed extended Data Publishing Policies and Guidelines for Biodiversity Data. Specific data publishing guidelines are available on the journal website. 

Data can be published in various ways, such as preservation in data repositories linked to the respective article or as data files or packages supplementary to the article. Datasets should be deposited in an appropriate, trusted repository and the associated identifier (URL or DOI) of the dataset(s) must be included in the data resources section of the article. Reference(s) to datasets should also be included in the reference list of the article with DOIs (where available). Where no discipline-specific data repository exists authors should deposit their datasets in a general repository such as, for example Zenodo or others. 

Submission, peer review and editorial process

The peer review and editorial processes are facilitated through an online editorial system and a set of email notifications. Pensoft journals’ websites display stepwise description of the editorial process and list all necessary instructions and links. These links are also included in the respective email notification.

General: Publication and authorship

  • All submitted papers are subject to a rigorous peer review process by at least two international reviewers who are experts in the scientific field of the particular paper. 

  • The factors that are taken into account in review are relevance, soundness, significance, originality, readability and language. 

  • The journals allow a maximum of two rounds of review of a manuscript. The ultimate responsibility for editorial decisions lies with the respective Subject Editor and, in some cases, with the Editor-in-Chief. All appeals should be directed to the Editor-in-Chief, who may decide to seek advice among the Subject Editors and Reviewers.

  • The possible decisions include: (1) Accept, (2) Minor revisions, (2) Major revisions, (3) Reject, but re-submission encouraged and (5) Reject. 

  • If Authors are encouraged to revise and re-submit a submission, there is no guarantee that the revised submission will be accepted. 

  • The paper acceptance is constrained by such legal requirements as shall then be in force regarding libel, copyright infringement and plagiarism. 

  • No research can be included in more than one publication.

Responsibility of Authors

  • Authors are required to agree that their paper will be published in open access under the Creative Commons Attribution License (CC BY 4.0) license.

  • Authors must certify that their manuscripts are their original work. 

  • Authors must certify that the manuscript has not previously been published elsewhere. 

  • Authors must certify that the manuscript is not currently being considered for publication elsewhere. 

  • Authors should submit the manuscript in linguistically and grammatically correct English and formatted in accordance with the journal’s Author Guidelines.

  • Authors must participate in the peer review process. 

  • Authors are obliged to provide retractions or corrections of mistakes. 

  • All Authors mentioned are expected to have significantly contributed to the research. 

  • Authors must notify the Editors of any conflicts of interest. 

  • Authors must identify all sources used in the creation of their manuscript. 

  • Authors must report any errors they discover in their published paper to the Editors.

  • Authors should acknowledge all significant funders of the research pertaining to their article and list all relevant competing interests.   

  • Other sources of support for publications should also be clearly identified in the manuscript, usually in an acknowledgement (e.g. funding for the article processing charge; language editing or editorial assistance).

  • The Corresponding author should provide the declaration of any conflicts of interest on behalf of all Authors. Conflicts of interest may be associated with employment, sources of funding, personal financial interests, membership of relevant organisations or others.

Responsibility of Reviewers

  • The manuscripts will be reviewed by two or three experts in order to reach first decision as soon as possible. Reviewers do not need to sign their reports but are welcome to do so. They are also asked to declare any conflicts of interests.

  • Reviewers are not expected to provide a thorough linguistic editing or copyediting of a manuscript, but to focus on its scientific quality, as well as for the overall style, which should correspond to the good practices in clear and concise academic writing. If Reviewers recognize that a manuscript requires linguistic edits, they should inform both Authors and Editor in the report.

  • Reviewers are asked to check whether the manuscript is scientifically sound and coherent, how interesting it is and whether the quality of the writing is acceptable.

  • In cases of strong disagreement between the reviews or between the Authors and Reviewers, the Editors can judge these according to their expertise or seek advice from a member of the journal's Editorial Board.

  • Reviewers are also asked to indicate which articles they consider to be especially interesting or significant. These articles may be given greater prominence and greater external publicity, including press releases addressed to science journalists and mass media.

  • During a second review round, the Reviewer may be asked by the Subject Editor to evaluate the revised version of the manuscript with regards to Reviewer’s recommendations submitted during the first review round.

  • Reviewers are asked to be polite and constructive in their reports. Reports that may be insulting or uninformative will be rescinded.

  • Reviewers are asked to start their report with a very brief summary of the reviewed paper. This will help the Editors and Authors see whether the reviewer correctly understood the paper or whether a report might be based on misunderstanding.

  • Further, Reviewers are asked to comment on originality, structure and previous research: (1) Is the paper sufficiently novel and does it contribute to a better understanding of the topic under scrutiny? Is the work rather confirmatory and repetitive? (2) Is the introduction clear and concise? Does it place the work into the context that is necessary for a reader to comprehend the aims, hypotheses tested, experimental design or methods? Are Material and Methods clearly described and sufficiently explained? Are reasons given when choosing one method over another one from a set of comparable methods? Are the results clearly but concisely described? Do they relate to the topic outlined in the introduction? Do they follow a logical sequence? Does the discussion place the paper in scientific context and go a step beyond the current scientific knowledge on the basis of the results? Are competing hypotheses or theories reasonably related to each other and properly discussed? Do conclusions seem reasonable?  Is previous research adequately incorporated into the paper? Are references complete, necessary and accurate? Is there any sign that substantial parts of the paper were copies of other works?

  • Reviewers should not review manuscripts in which they have conflicts of interest resulting from competitive, collaborative, or other relationships or connections with any of the authors, companies, or institutions connected to the papers.

  • Reviewers should keep all information regarding papers confidential and treat them as privileged information. 

  • Reviewers should express their views clearly with supporting arguments. 

  • Reviewers should identify relevant published work that has not been cited by the authors.

  • Reviewers should also call to the Editors’ attention any substantial similarity or overlap between the manuscript under consideration and any other published paper of which they have personal knowledge.

Responsibility of Editors

  • Editors in Pensoft’s journals carry the main responsibility for the scientific quality of the published papers and base their decisions solely on the papers' importance, originality, clarity and relevance to publication's scope.

  • The Subject Editor takes the final decision on a manuscript’s acceptance or rejection and his/her name is listed as "Academic Editor" in the header of each article.

  • The Subject Editors are not expected to provide a thorough linguistic editing or copyediting of a manuscript, but to focus on its scientific quality, as well as the overall style, which should correspond to the good practices in clear and concise academic writing. 

  • Editors are expected to spot small errors in orthography or stylistic during the editing process and correct them.

  • Editors should always consider the needs of the Authors and the Readers when attempting to improve the publication. 

  • Editors should guarantee the quality of the papers and the integrity of the academic record. 

  • Editors should preserve the anonymity of Reviewers, unless the later decide to disclose their identities. 

  • Editors should ensure that all research material they publish conforms to internationally accepted ethical guidelines. 

  • Editors should act if they suspect misconduct and make all reasonable attempts to obtain a resolution to the problem. 

  • Editors should not reject papers based on suspicions, they should have proof of misconduct.

  • Editors should not allow any conflicts of interest between Authors, Reviewers and Board Members.

Human and animal rights

The ethical standards in medical and pharmacological studies are based on the Helsinki declaration (1964, amended in 1975, 1983, 1989, 1996 and 2000) of the World Medical Association and the Publication Ethics Policies for Medical Journals of the World Association of Medical Journals (WAME).

Authors of studies including experiments on humans or human tissues should declare in their cover letter a compliance with the ethical standards of the respective institutional or regional committee on human experimentation and attach committee’s statement and informed consent; for those researchers who do not have access to formal ethics review committees, the principles outlined in the Declaration of Helsinki should be followed and declared in the cover letter. Patients’ names, initials, or hospital numbers should not be used, not in the text nor in any illustrative material, tables of databases, unless the author presents a written permission from each patient to use his or her personal data. Photos or videos of patients should be taken after a warning and agreement of the patient or of a legal authority acting on his or her behalf.

Animal experiments require full compliance with local, national, ethical, and regulatory principles, and local licensing arrangements and respective statements of compliance (or approvals of institutional ethical committees where such exists) should be included in the article text.

Informed consent

Individual participants in studies have the right to decide what happens to the identifiable personal data gathered, to what they have said during a study or an interview, as well as to any photograph that was taken. Hence it is important that all participants gave their informed consent in writing prior to inclusion in the study. Identifying details (names, dates of birth, identity numbers and other information) of the participants that were studied should not be published in written descriptions, photographs, and genetic profiles unless the information is essential for scientific purposes and the participant (or parent or guardian if the participant is incapable) gave written informed consent for publication. Complete anonymity is difficult to achieve in some cases, and informed consent should be obtained if there is any doubt. If identifying characteristics are altered to protect anonymity, such as in genetic profiles, authors should provide assurance that alterations do not distort scientific meaning.

The following statement should be included in the article text in one of the following ways:

  • "Informed consent was obtained from all individual participants included in the study."

  • "Informed consent was obtained from all individuals for whom identifying information is included in this article." (In case some patients’ data have been published in the article or supplementary materials to it).

Conflict of interest

During the editorial process, the following relationships between editors and authors are considered conflicts of interest: Current colleagues, recent colleagues, recent co-authors, and doctoral students for which editor served as committee chair. During the submission process, the authors are kindly advised to identify possible conflicts of interest with the journal editors. After manuscripts are assigned to the handling editor, individual editors are required to inform the managing editor of any possble conflicts of interest with the authors. Journal submissions are also assigned to referees to minimize conflicts of interest. After manuscripts are assigned for review, referees are asked to inform the editor of any conflicts that may exist.

Appeals and open debate

We encourage academic debate and constructive criticism. Authors are always invited to respond to any editorial correspondence before publication. Authors are not allowed to neglect unfavorable comments about their work and choose not to respond to criticisms. 

No Reviewer’s comment or published correspondence may contain a personal attack on any of the Authors. Criticism of the work is encouraged. Editors should edit (or reject) personal or offensive statements. Authors should submit their appeal on editorial decisions to the Editorial Office, addressed to the Editor-in-Chief or to the Managing Editor. Authors are discouraged from directly contacting Editorial Board Members and Editors with appeals.

Editors will mediate all discussions between Authors and Reviewers during the peer review process prior to publication. If agreement cannot be reached, Editors may consider inviting additional reviewers if appropriate. 

The Editor-in-Chief will mediate all discussions between Authors and Subject Editors.

The journals encourage publication of open opinions, forum papers, corrigenda, critical comments on a published paper and Author’s response to criticism.

Misconduct

Research misconduct may include: (a) manipulating research materials, equipment or processes; (b) changing or omitting data or results such that the research is not accurately represented in the article. A special case of misconduct is plagiarism, which is the appropriation of another person's ideas, processes, results or words without giving appropriate credit. Research misconduct does not include honest error or differences of opinion. If misconduct is suspected, journal Editors will act in accordance with the relevant COPE guidelines

Responses to possible misconduct

All allegations of misconduct must be referred to the Editor-In-Chief. Upon the thorough examination, the Editor-In-Chief and deputy editors should conclude if the case concerns a possibility of misconduct. All allegations should be kept confidential and references to the matter in writing should be kept anonymous, whenever possible.

Should a comment on potential misconduct be submitted by the Reviewers or Editors, an explanation will be sought from the Authors. If it is satisfactory and the issue is the result of either a mistake or misunderstanding, the matter can be easily resolved. If not, the manuscript will be rejected or retracted and the Editors may impose a ban on that individual's publication in the journals for a certain period of time. In cases of published plagiarism or dual publication, an announcement will be made in both journals explaining the situation.

When allegations concern authors, the peer review and publication process for their submission will be halted until completion of the aforementioned process. The investigation will be carried out even if the authors withdraw the manuscript, and implementation of the responses below will be considered.

When allegations concern reviewers or editors, they will be replaced in the review process during the ongoing investigation of the matter. Editors or reviewers who are found to have engaged in scientific misconduct should be removed from further association with the journal, and this fact reported to their institution.

Retraction policies

Article retraction

According to the COPE Retraction Guidelines followed by this Journal, an article can be retracted because of the following reasons:

  • Unreliable findings based on clear evidence of a misconduct (e.g. fraudulent use of the data) or honest error (e.g. miscalculation or experimental error).
  • Redundant publication, e.g., findings that have previously been published elsewhere without proper cross-referencing, permission or justification.
  • Plagiarism or other kind of unethical research.

Retraction procedure

  • Retraction should happen after a careful consideration by the Journal editors of allegations coming from the editors, authors, or readers.
  • The HTML version of the retracted article is removed (except for the article metadata) and on its place a retraction note is issued.
  • The PDF of the retracted article is left on the website but clearly watermarked with the note "Retracted" on each page.
  • In some rare cases (e.g., for legal reasons or health risk) the retracted article can be replaced with a new corrected version containing apparent link to the retracted original version and a retraction note with a history of the document.

Expression of concern

In other cases, the Journal editors should consider issuing an expression of concern, if evidence is available for:

  • Inconclusive evidence of research or publication misconduct by the authors.
  • Unreliable findings that are unreliable but the authors’ institution will not investigate the case.
  • A belief that an investigation into alleged misconduct related to the publication either has not been, or would not be, fair and impartial or conclusive.
  • An investigation is underway but a judgement will not be available for a considerable time.

Correction

Journal editors should consider issuing a correction if:

  • A small portion of an otherwise reliable publication proves to be misleading (especially because of honest error).
  • The author / contributor list is incorrect (i.e. a deserving author has been omitted or somebody who does not meet authorship criteria has been included).
  • Other reasons that do not qualify as a sound evidence for retraction or expression of concern.