Editorial Policies and Reporting Standards | GigaScience

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class="content-main js-main ui-base"> <section class="master-main row"> <div class="center-inner-row no-overflow"> <div id="skipNav" tabindex="-1"></div> <div class="page-column-wrap"> <div id="cloudCMS" class="secondary-cms"><div id="mainContent" class="secondaryPageMain"><div class="inner"><div class="main"><div class="secondaryContent"> <h1>Editorial Policies & Reporting Standards</h1> <script type='text/javascript' src='https://platform-api.sharethis.com/js/sharethis.js#property=6481b8a5cc05f10013916a95&product=sop' async='async'></script> <script> document.addEventListener("readystatechange" ,function() { const compactButton = document.querySelector("div.st-custom-button"); if(compactButton) { const mutationObserver = new MutationObserver(entries => { if(document.body.classList.contains("st-body-no-scroll")) { compactButton.ariaExpanded = true; } else { compactButton.ariaExpanded = false; } }) mutationObserver.observe(document.body, { attributes: true }); } }) </script> <ul class="unbulleted"> <li><a data-link-id="7790c51a-d7c5-4ffd-bfa6-1f70aef2f311" href="#General Policies">General Policies</a></li> <li><a data-link-id="0e62ab84-beaf-4212-9f8a-13fb644a7e7d" href="#Availability of Data and Materials">Availability of Data and Materials</a></li> <li><a data-link-id="ec569e96-6c67-4500-bf94-0b85d92ebc3b" href="#Reporting Standards">Reporting Standards</a></li> <li><a data-link-id="3fbb0e04-a8e6-43ef-a7e0-fc07898005e6" href="#Misconduct">Misconduct</a></li> </ul> <h2><a data-link-id="0af15566-6e09-4c31-806d-8b2b4b0e15de" id="General Policies" name="General Policies"></a>General Policies</h2> <p><em>GigaScience</em> is a member of the <a data-link-id="e7727f19-87be-459a-844a-6abd3203accc" href="http://publicationethics.org/">Committee on Publication Ethics (COPE)</a> and endorses the World Association of Medical Editors (WAME) <a data-link-id="4cb86344-910c-46e6-92ba-8278d933b6f5" href="http://www.wame.org/policy-statements#Geopolitical%20Instrusion">Policy Statement on Geopolitical Intrusion on Editorial Decisions</a>.</p> <p>When a manuscript is submitted to the <em>GigaScience</em> journal this implies that all authors have read and agreed to its content and that the manuscript conforms to the journal's policies.</p> <h3>Previous publication</h3> <p>Submission of a manuscript implies that it reports unpublished work, that it is not under consideration for publication elsewhere and that, if accepted, it will not be published elsewhere in the same form, either in English or in any other language, without the consent of the publisher. [Note that we actively encourage authors to submit manuscripts to a preprint server, and such sharing will not impact our decision process or be considered as prior work. See more in our Open Science statement below.]</p> <p>For manuscripts submitted for consideration at <em>GigaScience</em>, authors should provide the references of similar work that they have already published, or which is currently under consideration by another journal. The journal will consider publication of work that has previously been presented as either a published abstract or poster at a conference, but not as a full paper in conference proceedings. If the manuscript includes previously published tables, illustrations or more than 200 words of text, then the copyright holder's written permission must be obtained. You must include copies of any such permission letters with your paper. Please note that if considered appropriate, plagiarism checking software may be applied to your manuscript during the editorial review process.</p> <h3>Authorship</h3> <p>All persons included as authors should qualify for authorship according to our <a data-link-id="ef4aac99-4f45-4039-89de-e5651150f5a2" href="https://academic.oup.com/gigascience/pages/authorship_guidelines">authorship guidelines</a>, and to give appropriate credit, the individual contributions of authors should be specified in the manuscript. Each author should have participated sufficiently in the work to take public responsibility for the content. Authorship credit should be based on substantial contribution to conception and design, execution, or analysis and interpretation of data. All authors should be involved in drafting the article or revising it critically for important intellectual content, and must have read and approved the final version of the manuscript. Authors should adhere to the practices of their research field and the guidelines of the International Committee of Medical Journal Editors (<a data-link-id="81e0d18b-cff3-448d-af3a-8f42102c825f" href="http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html">ICMJE</a>).</p> <p>Authors should not list AI and AI-assisted technologies as an author or co-author, nor cite AI as an author or credit them as a contributor in the Acknowledgements. Each author is fully accountable for ensuring the accuracy or integrity of their manuscript, including those parts produced by an AI tool.</p> <p>Please see the <a data-link-id="0391bb97-4894-42da-a27e-f32d53956945" href="https://credit.niso.org/">CRediT Contributor Roles Taxonomy</a> for instructions on how to declare, describe and format authorship details in the manuscript. This information is collected during the submission process and will be included as part of the published article.</p> <p>The corresponding author is the individual who takes primary responsibility for communication with the journal during the manuscript submission, peer review, and publication process, and typically ensure that all the journal's administrative requirements, such as providing details of authorship, ethics committee approval, clinical trial registration documentation, and gathering conflict of interest forms and statements, are properly completed. The corresponding author should be available throughout the submission and peer review process to respond to editorial queries in a timely way, as well as after publication should questions about the paper arise. <em>GigaScience</em> allows a maximum of two corresponding authors, and these must be responsive with these administrative tasks and responsibility. If an author is too senior for this role then please ensure it is handled by someone able to handle it in a timely manner. We also allow and recognise joint-authorship of up to three authors as well as senior authorship, and can highlight this on the paper.</p> <p>The involvement of scientific (medical) writers or anyone else who assisted with the preparation of the manuscript content should be acknowledged, along with their source of funding, as described in the <a data-link-id="ca7d50d6-7ade-4dae-a24a-a6af8e19fc12" href="https://www.emwa.org/documents/about_us/EMWAguidelines.pdf">European Medical Writers Association (EMWA) guidelines</a>.</p> <p>Other than in exceptional circumstances the Journal does not allow addition or removal of author names after submission without a detailed explanation provided in writing. More detailed guidelines are available from our <a data-link-id="f2734b6b-c884-45e9-bd2b-5a304c08cedd" href="https://academic.oup.com/gigascience/pages/authorship_guidelines">Authorship Guidelines page</a>.</p> <h3>Use of AI Tools and Technologies in Writing</h3> <p>Use of generative AI-writing tools such as ChatGPT is allowed as long as it is disclosed in a transparent manner and does not negatively affect empirical data and conclusions. AI-writing tools must be highlighted wherever necessary with in-text citations and mentioned among references. A summary of use (particularly in the introduction or among methods) needs to be included at the end of the paper, and the outputs should also be included as a supplementary file hosted in GigaDB or other open repositories. Authors should not list AI-writing tools and other AI-assisted technologies as an author or co-author. All authors should acknowledge that they are fully responsible for text generated or refined by AI-writing tools.</p> <h3>Acknowledgments</h3> <p>All contributors who do not meet the above criteria for authorship should be listed in the ‘Acknowledgements’. Examples of those who might be acknowledged include a person who provided purely technical or writing assistance, or a department or institutional head who provided only general support.</p> <h3>Text recycling</h3> <p>Authors should be aware that replication of text from their own previous publications is text recycling (also referred to as self-plagiarism), and in some cases is considered unacceptable. Where overlap of text with authors’ own previous publication is necessary or unavoidable, duplication must always be reported transparently and be properly attributed and compliant with copyright requirements. If a manuscript contains text that has been published elsewhere, authors should notify the Editor of this on submission. One method to make it easier to avoid self-plagiarism of commonly used methods is to submit them to <a data-link-id="c8e999db-5196-4db2-b150-129ef47e892e" href="https://www.protocols.io/">protocols.io</a>. Again, authors making their manuscripts available in this way must clearly note this in their submission.</p> <p>Once the manuscript has been accepted with authors must acknowledge that the article has been accepted for publication as follows:</p> <p>"This article has been accepted for publication in [Journal Title] ©: [year][owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved."</p> <p>Please read the <a data-link-id="0a7d5f5c-9886-4a1a-880e-29ce739c7745" href="https://academic.oup.com/pages/self_archiving_policy_b">full policy on self-archiving</a>.</p> <h3>Confidentiality</h3> <p>Editors will treat all manuscripts submitted to all <em>GigaScience</em> in confidence, adhering to COPE’s <a data-link-id="e2f2a52a-a424-454e-9842-197e0a26764c" href="http://publicationethics.org/files/Peer%20review%20guidelines_0.pdf">Ethical Guidelines for Peer Reviewers</a>. Any manuscript sent for peer review is a confidential document and should remain so until it is formally published. Exceptions to the above confidentiality agreement can ONLY occur in cases where the manuscript is publicly available on a preprint server AND the authors have clearly stated they are happy to have open discussion of their work prior to publication.</p> <p>If reviewers wish to involve a colleague in the review process, because we use an open and transparent review process, please co-sign and include the names of any individuals who assisted in the review process when the report is returned. <em>GigaScience</em> will not share manuscripts with third parties except in cases of suspected misconduct.</p> <h3>Conflicts of Interest</h3> <p>At the point of submission, <em>GigaScience</em> policy requires that each author reveal any financial interests or connections, direct or indirect, or other situations that might raise the question of bias in the work reported or the conclusions, implications, or opinions states — including pertinent commercial or other sources of funding for the individual author(s) or for the associated department(s), personal relationships, or direct academic competition. Authors from pharmaceutical companies, or other commercial organizations that sponsor clinical trials, should adhere to the <a data-link-id="117d97cd-f0cd-4721-b5e5-486ff1d69a03" href="http://www.ismpp.org/gpp3">Good Publication Practice guidelines for pharmaceutical companies</a>(GPP3). When considering whether you should declare a conflicting interest or connection please consider the conflict of interest test: Is there any arrangement that would embarrass you or any of your co-authors if it was to emerge after publication and you had not declared it?</p> <p>All submitted manuscripts must include a ‘competing interests’ section at the end of the manuscript listing all competing interests (financial and non-financial). Where authors have no competing interests, the statement should read “The author(s) declare(s) that they have no competing interests”. The Editor may ask for further information relating to competing interests.</p> <p>As we use open and transparent peer review, reviewers are also required to declare any competing interests and may be excluded from the peer review process if a competing interest exists.</p> <p><em>GigaScience</em> promotes full transparency and openness: We carry out named open peer review and ask for all potential financial and non-financial conflicts to be declared to reduce potential bias and Conflicts of Interest (COI). It is extremely difficult to completely remove all biases, thus, we cannot consider manuscripts in cases where research studies are funded by groups that have a COI where the work presents conclusions that support products with known serious health risks to humans or the environment. Studies presenting large-scale datasets in a more neutral manner may be considered.</p> <h3>Ethics and consent</h3> <p>Please see the <a data-link-id="2b922d97-c70e-4a0c-92cd-547d77141b7f" href="https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript/ethics">OUP Statement on Publication Ethics</a>. Research involving human subjects, human material, or human data, must have been performed in accordance with the <a data-link-id="fcde1663-b578-49df-aabb-92fde71cbe94" href="https://doi.org/10.1001/jama.2013.281053">Declaration of Helsinki</a> and must have been approved by an entire ethics committee. A statement detailing this, including the name of the ethics committee and the reference number where appropriate, must appear in all manuscripts reporting such research. If a study has been granted an exemption from requiring ethics approval, this should also be detailed in the manuscript (including the name of the ethics committee that granted the exemption). Further information and documentation to support this should be made available to the Editor on request. Manuscripts may be rejected if the Editor considers that the research has not been carried out within an appropriate ethical framework. In rare cases, the Editor may contact the ethics committee for further information.</p> <p>For all research involving human subjects, informed consent to participate in the study should be obtained from participants (or their parent or legal guardian in the case of children under 16) and a statement to this effect should appear in the manuscript. Please also confirm you have followed national guidelines on data collection and release in the place the research was carried out (for example: confirming you have acquired the most up-to-date Ministry of Science and Technology (MOST) approval in China). Please also state the year in which approval was granted.</p> <h3>Research involving animals</h3> <p>Please see the <a data-link-id="2d4ed4fa-0669-4ccd-ba8a-1d9c28c7264e" href="https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript/ethics">OUP Statement on Publication Ethics</a>. Where animals are used in research, we expect them to have been treated in a humane manner and in line with the <a data-link-id="d1f58f9a-06f7-482e-9300-6adb76112c29" href="http://www.nc3rs.org.uk/arrive-guidelines">ARRIVE</a> guidelines. The International Council for Laboratory Animal Science has published guidelines specifically for editors and reviewers on how to handle submission involving animal research. OUP supports these guidelines and, wherever possible, encourages editors and society partners to adopt them. A statement detailing compliance with relevant guidelines (e.g. <a data-link-id="54a34e9b-1f1c-44b3-8313-206558e7ba5c" href="http://www.legislation.gov.uk/ukpga/1986/14/contents">the revised Animals (Scientific Procedures) Act 1986</a> in the UK and<a data-link-id="da9bf848-cef9-4697-b8c6-e2d60080c0b9" href="http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2010:276:0033:0079:EN:PDF"> Directive 2010/63/EU in Europe</a>) and/or ethical approval (including the name of the ethics committee and the reference number where appropriate) must be included in the manuscript. Authors may be required to provide evidence that they obtained ethical and/or legal approval prior to conducting the research. We also recommend that authors comply with the <a data-link-id="f163523b-6b37-45a2-a388-3babb6c569a7" href="https://cites.org/">Convention on the Trade in Endangered Species of Wild Fauna and Flora</a> and the <a data-link-id="e56df387-66aa-4231-ade3-95c384cf90ac" href="https://portals.iucn.org/library/efiles/documents/PP-003-En.pdf">IUCN Policy Statement on Research Involving Species at Risk of Extinction</a>. The Editor will take account of animal welfare issues and reserves the right to reject a manuscript, especially if the research involves protocols that are inconsistent with commonly accepted norms of animal research.</p> <h3>Research involving plants</h3> <p>Experimental research on plants and plant materials must comply with institutional, national, or international guidelines. Field studies should be conducted in accordance with local legislation, and the manuscript should include a statement specifying the appropriate permissions and/or licenses. We recommend that authors comply with the <a data-link-id="daf0cb53-1449-4f54-829e-9fe1bb0b83d7" href="https://cites.org/">Convention on the Trade in Endangered Species of Wild Fauna and Flora</a>. Voucher specimens must be deposited in a public herbarium or other public collection providing access to deposited material, and any relevant reference or accession numbers for germplasm must be included in the manuscript.</p> <h3>Trial registration</h3> <p><em>GigaScience</em> supports initiatives to improve reporting of clinical trials. Please see the <a data-link-id="c82faeee-d729-45b5-9aac-5645a7e69ba4" href="https://academic.oup.com/pages/authoring/journals/preparing_your_manuscript/ethics">OUP Statement on Publication Ethics</a> for more information.</p> <h3>Acceptance</h3> <p>When accepted by the editors, authors may be asked to send the files of the final manuscript to the editorial office. These files are used for typesetting and should be either Word or LaTex files.</p> <p>Because accepted manuscripts are published online following acceptance, it is important that the final version of the manuscript supplied by the author contains no information regarding the citation information (volume, issue, year) or a copyright line as this will mislead readers.</p> <h3>Scientific Misconducts</h3> <p>When dealing with potential cases of misconduct the journal follows the guidelines provided by the Committee on Publication Ethics (COPE).</p> <h3>Peer Review</h3> <p>All submissions are assessed by an Editor, who will decide whether they are suitable for peer review by at least two independent peer reviewers. <em>GigaScience</em> operates an open peer review process as standard, the reviewers' names are included on the peer review reports. In addition, if the manuscript is published, the name reports are published online alongside the article as part of a 'pre-publication history'. See our <a data-link-id="a9f3af02-1353-497a-a955-b817c8618f27" href="https://academic.oup.com/gigascience/pages/reviewer_guidelines">reviewer guidelines</a> for more.</p> <h3>Open Science</h3> <p><em>GigaScience</em> endorses and promotes more rapid “open science” mechanisms for disseminating research, using the <a data-link-id="38decda1-4718-4efc-82f8-166e7e393236" href="https://doi.org/10.54677/MNMH8546">UNESCO Recommendation on Open Science</a> as a framework for action (see <a data-link-id="f9feda97-adb2-4f30-b68e-cd57b7a01612" href="https://doi.org/10.1093/gigascience/giac067">our Editorial</a>). Our in-house Editorial and Curation teams provide a single unified service to provide hands-on assistance to our authors to meet new global standards and policies for sharing research outputs. Specifically, we feel that the <a data-link-id="013a66d3-ab2f-4584-bcf7-598d13e31fc3" href="http://www.nejm.org/doi/full/10.1056/NEJM198110013051408#t=article">Ingelfinger Rule</a>, which discourages discussion of manuscripts ahead of normal formal publication, hinders scientific discourse and slows the pace of discovery. Prior to formal publication, authors are encouraged to present their findings and data to their peers, including at meetings and conferences; to deposit copies of their manuscript in open-access repositories, or to make the manuscript available via their website; and to blog and discuss their findings on social media, wikis and electronic lab notebooks. As long as it is clear what is and isn't peer-reviewed, and copyright and attribution norms are followed, none of these activities will affect consideration of a manuscript by <em>GigaScience</em>.</p> <p>Making scientific datasets, protocols and code publicly available as early as possible before associated manuscripts are submitted is strongly recommended, particularly as we require reviewer access before the manuscript can be sent out to peer review. These should be considered legitimate, citable products of research, and accorded the same importance in the scholarly record as citations of other research objects, such as publications. Therefore we follow the guidelines of the <a data-link-id="69cfb629-a39b-46c7-b147-48e3db21f0f2" href="https://www.force11.org/group/joint-declaration-data-citation-principles-final">Data Citation</a> and <a data-link-id="04b9d398-8954-4584-af9b-650d215574ef" href="https://doi.org/10.7717/peerj-cs.86">Software Citation Principles</a>. The DOIs cited in the relevant parts of the text, and alongside any accession numbers summarised in the Data Availability section of the paper. See the <a data-link-id="124155b7-e67a-4bf9-a9e3-b193f4b6d5d3" href="https://f1000research.com/articles/9-1257/v2">Software Citation Guide</a> for details on how to cite more dynamic and granular research objects such as software.</p> <p>Preprint availability reduces the delay between discovery and dissemination of results, and we strongly recommend the use of community preprint servers such as <a data-link-id="455494f6-64e3-410b-8100-77832d55c428" href="https://arxiv.org/">arXiv</a>, <a data-link-id="161748fd-9c3d-4f16-b619-b3557d61f1fb" href="http://biorxiv.org/">bioRxiv</a>, <a data-link-id="3f08249c-c06b-4860-902b-f50fa615474a" href="https://www.medrxiv.org/">medRxiv</a>, and <a data-link-id="02cfb693-547f-493d-9c0b-1d3d0eacd785" href="https://osf.io/preprints/">OSF Preprints</a>. When published our openly licensed open peer reviews can then be linked to the preprint via the bioRxiv TRiP (Transparent Review in Preprints) functionality (<a data-link-id="360ef52e-a57f-481e-9914-84bf5dfe715b" href="https://connect.biorxiv.org/eval/?platform=x6WjqQay&subject=all">see examples</a>). And also aggregated in the<a data-link-id="78ece415-2e90-477d-aca0-2f9dac26d46e" href="https://sciety.org/groups/gigascience/about"> Sciety preprint evaluation platform</a>. We encourage the citation of preprints where appropriate in the reference list, and will not consider them in the evaluation of the conceptual advance of a manuscript submitted for publication. We also offer direct transfer from bioRxiv (B2J), saving author’s time in submitting papers. See <a data-link-id="460a14b6-75a8-406d-95c5-b77c9c5833d5" href="http://biorxiv.org/submit-a-manuscript">this page</a> for more information.</p> <h2><a data-link-id="0ca03910-170f-485c-9230-cfb2b78e1a48" id="Availability of Data and Materials" name="Availability of Data and Materials"></a>Availability of Data and Materials</h2> <h3>Software</h3> <p>Any previously unreported software application or custom code described in the manuscript should be available for testing by reviewers, and also include test data. Users must have the right to examine, compile, run and modify the code for any purpose. This needs to be under an <a data-link-id="cc0dcea9-f4ba-4155-b326-69f6d0754ea5" href="https://opensource.org/licenses">Open Source Initiative</a> approved license where practicable compiled running software is made available. The manuscript should include a description of how the reviewers can access the unreported software application or custom code in a trusted code repository. This should include a link to the most recent version of your software or code (e.g. <a data-link-id="525054d5-34db-4638-8862-7f8da87c32ac" href="https://github.com/">GitHub</a> or <a data-link-id="cf3ecc8a-599f-42b5-baae-3cf5b3c694a2" href="https://about.gitlab.com/">GitLab</a>) as well as a link to the archived version referenced in the manuscript. Documentation is expected to be consistent with best practice for the language and/or discipline, and highlighted in the paper. The software or code should be archived in an appropriate repository with a DOI or other unique identifier. For software in GitHub, we recommend using <a data-link-id="72140363-f1f0-4471-af56-f5b867bda44b" href="http://gigadb.org/site/guide">GigaDB</a>, <a data-link-id="61b4bc46-0d8c-47a6-be35-176551046212" href="https://www.softwareheritage.org/">Software Heritage</a> or <a data-link-id="a4d062d9-69a5-4b12-ae75-4032ff1350a5" href="https://guides.github.com/activities/citable-code/">Zenodo</a> or we can take snapshots in our GigaDB server. Computational workflows should also be registered in workflowhub.eu and the DOIs cited in the relevant places in the manuscript. A “Data availability“ statement is also required, and the code snapshots should be cited here. <em>GigaScience</em> follows the <a data-link-id="385e278b-30b5-4fa5-82a0-65deced7df69" href="https://f1000research.com/articles/9-1257/v2">recommendations of the FORCE11 Software Citation Implementation Working Group</a>, and software should be cited in the references following the <a data-link-id="25901d33-f04f-4f45-883a-520c767ae6d9" href="https://doi.org/10.12688/f1000research.26932.2">software citation principles</a>. If an article exists that describes the software, it should be cited as an additional reference, as well as citing the software itself.</p> <h3>Machine Learning</h3> <p>For papers utilising machine learning (ML) approaches, we ask authors to follow <a data-link-id="ce5dfbb3-7d27-4300-b141-7da245e9f152" href="https://www.nature.com/articles/s41592-021-01256-7">best practice</a> and the <a data-link-id="26c031ad-7028-4f1c-a71f-b5788284e37b" href="https://dome-ml.org/">DOME-ML</a> (Data, Optimization, Model and Evaluation in Machine Learning) guidelines. To do this please include the model and all information to re-run it, such as computational resources (including data size & distribution) and time taken to train it. Authors should at the very least ensure that the ML analysis is reproducible and includes open optimization and evaluation data for transparent benchmarking and testing. To do this we recommend the use of literate programming outputs, such as Jupyter notebooks, and/or publishing environments, such as <a data-link-id="24398211-42e7-459f-a275-eeee3f239ed4" href="https://codeocean.com/">Code Ocean</a>. To ensure reproducibility of ML analysis, authors should try to include at least one Open Data use case example. If the study additionally utilises Controlled Access Data, we invite the authors to provide details on how a researcher would obtain access to this Restricted Data.</p> <h3>Open Hardware</h3> <p>Submissions including Open Hardware need to utilise appropriate licenses for the hardware components. These include CC0, the <a data-link-id="d4d562aa-b6bf-4197-92b2-9097363eaad5" href="https://www.gnu.org/licenses/gpl-3.0.en.html">GNU General Public License (GPL)</a> and other copyleft licenses specifically designed for hardware such as the <a data-link-id="664a7508-499f-4a86-8481-fbca04299278" href="https://ohwr.org/cernohl">CERN Open Hardware License (OHL)</a> and <a data-link-id="0267b64f-028f-4857-8ca1-2c5b6fb1f799" href="https://tapr.org/the-tapr-open-hardware-license/">TAPR Open Hardware License (OHL)</a>. The hardware must also be released with documentation (design files, etc.), and must allow modification and distribution of these as well. Hardware and documentation files can be deposited in a suitable repository such as GigaDB or <a data-link-id="6ead3002-bdac-4fe9-9d97-124670387bf4" href="http://docubricks.com/">Docubricks</a>. See the <a data-link-id="9c2a3d3f-0308-427b-bab1-3111db4cd5ea" href="https://www.oshwa.org/definition/">Open Source Hardware definition</a> for more.</p> <h3>Supporting Data</h3> <p>All data on which the conclusions given in the publication are based should be available to readers, either in our <em>Giga</em>DB repository, or in a trusted community established repository where available and appropriate (for examples see below). The DOIs cited in the relevant parts of the text, and alongside any accession numbers summarized in the Data Availability section of the paper. The peer reviewers also needing to be able to scrutinise all described data and results before publication. <em>GigaScience</em> fully supports the recommendations of the National Academies regarding data sharing (see <a data-link-id="26043a46-4d8a-4f37-996b-41583132e9a4" href="https://doi.org/10.17226/10613">Board on Life Sciences, Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences</a>).</p> <p>Authors using unpublished genomic data are expected to abide by the guidelines of the <a data-link-id="c0f46642-e09a-452b-9bd8-f9cdca58f285" href="https://www.genome.gov/Pages/Research/WellcomeReport0303.pdf">Fort Lauderdale</a> and <a data-link-id="fb0534ee-a332-43cf-95c3-47b89589da5e" href="https://doi.org/10.1038/461168a">Toronto</a> agreements. Based on broadly accepted scientific community standards, the key requirement of third parties using genomic data is to contact the owners of unpublished data (i.e. the principal investigator and sequencing center) prior to undertaking their research, to advise them about their planned analyses.</p> <p>Should the manuscript be approved for publication, the accompanying datasets must be accessible by any researcher wishing to use them under a <a data-link-id="932935f4-6f01-4d68-b5d1-98baa62611b9" href="http://creativecommons.org/about/cc0">Creative Commons CC0</a> waiver, without restrictions, such as the need for a material transfer agreement. Exceptions to the use of a Creative Commons CC0 waiver for data are made for data that has specific legal restrictions for open sharing, but these must be submitted to a persistent, but restricted database for other researchers to submit a request for use form.</p> <p>To drive the maximum re-use and utility of published research, we expect authors to comply with available field-specific standards for the preparation and recording of data, materials and methods. Please see the <a data-link-id="17e974cf-a09d-48ec-8246-d3ca33b6ec5f" href="https://fairsharing.org/standards/">FAIRSharing</a> website for information on field-specific data standards. Authors must comply with best practice in their field for sharing of data, with particular attention to maintaining <a data-link-id="b7931a40-b5e5-4da9-8119-69b55f5693b9" href="http://www.trialsjournal.com/content/11/1/9">patient confidentiality</a>. A list of recommended repositories by subject area and data type can be found on the <a data-link-id="5caf5548-2750-42d8-bb9b-b622efa3b3cc" href="http://service.re3data.org/">Re3data (Registry of Research Data Repositories) registry</a> and ELIXIR has a <a data-link-id="230323d8-c8ab-4dbe-8b3b-2dd3c98b15b0" href="https://www.elixir-europe.org/platforms/data/core-data-resources">list of Core Data Resources</a>. Additional information is also available from our <a data-link-id="d9fecb33-cd68-4229-a79b-de281d84312e" href="https://fairsharing.org/recommendation/GigaScience">FAIRsharing page</a>.</p> <div class='tableContainer'><table> <tbody> <tr> <td> <p>DNA and RNA sequences</p> </td> <td> <p>INSDC databases:</p> <p><a data-link-id="474f4bf3-eadc-4e62-addb-7a895935643a" href="http://www.ddbj.nig.ac.jp/">DNA DataBank of Japan (DDBJ)</a></p> <p><a data-link-id="f396a682-a877-4d02-8ee2-4e3bb2a6e544" href="http://www.ebi.ac.uk/ena">European Nucleotide Archive (EBI)</a></p> <p><a data-link-id="dc9bfc61-448a-4dee-9426-b31efdcf78d9" href="http://www.ncbi.nlm.nih.gov/genbank/">Genbank (NCBI)</a></p> <p><a data-link-id="13fa39c6-9962-4c30-ab91-6bec61cf03a8" href="https://www.ebi.ac.uk/ega/">The European Genome-phenome Archive (EGA)</a>*</p> <p><a data-link-id="8125c21e-22ae-48d7-af29-09389188e451" href="https://www.ncbi.nlm.nih.gov/gap">dbGAP</a>*</p> <p><a data-link-id="b890e1ea-c038-4718-abb4-d2101341d895" href="https://www.ddbj.nig.ac.jp/jga/index-e.html">JGA</a>*</p> <p>*for restricted access (human) data/sequences.</p> <p><a data-link-id="b47d4926-b64e-4167-80bf-aeb10658eac0" href="https://www.ncbi.nlm.nih.gov/sra">NCBI Sequence Read Archive (NCBI-SRA)</a></p> </td> </tr> <tr> <td> </td> <td> <p><a data-link-id="1fc8c087-9701-4b87-a56e-74b20a2ef920" href="http://www.ebi.ac.uk/ena">EBI European Nucleotide Archive (EBI-ENA)</a></p> <p><a data-link-id="594d8c46-3f03-4dad-9ddb-492fa0624122" href="https://www.ddbj.nig.ac.jp/dra/index-e.html">DDBJ Sequence Read Archive (DDBJ-SRA)</a></p> </td> </tr> <tr> <td> <p>Genetic polymorphisms</p> </td> <td> <p><a data-link-id="4a5084d1-27c6-4469-922f-599a28b4387b" href="http://www.ncbi.nlm.nih.gov/snp">dbSNP</a></p> <p><a data-link-id="98a4f865-95c7-4987-a1f3-82054b74aa67" href="http://www.ncbi.nlm.nih.gov/dbvar/">dbVar</a></p> <p><a data-link-id="948c93c4-a088-43c6-8bd0-318e4a65e2f6" href="http://www.ebi.ac.uk/EVA">European Variation Archive (EVA)</a></p> </td> </tr> <tr> <td> <p>Linked genotype and phenotype data</p> </td> <td> <p><a data-link-id="3602e982-957e-4708-bcd2-03d220b336d0" href="http://www.ncbi.nlm.nih.gov/gap">dbGAP</a></p> <p><a data-link-id="32d38b57-163e-4b0b-96a9-d1aaca420a08" href="http://www.ebi.ac.uk/ega/">The European Genome-phenome Archive (EGA)</a>*</p> <p><a data-link-id="7ccff617-f883-4c42-aad8-eabd4f944b0c" href="https://www.ddbj.nig.ac.jp/jga/index-e.html">JGA</a></p> <p>*Note that dbGAP and the EGA only accept clinical data.</p> </td> </tr> <tr> <td> <p>Protein sequences</p> </td> <td> <p><a data-link-id="bceb0b76-c60f-4a8b-a282-57036c80f7f5" href="http://www.ebi.ac.uk/uniprot">Uniprot</a></p> </td> </tr> <tr> <td> <p>Macromolecular structure</p> </td> <td> <p><a data-link-id="c406a9d0-08f4-4fc0-9135-636c4466341b" href="http://wwpdb.org/">Worldwide Protein Data Bank (wwPDB)</a></p> <p><a data-link-id="a371f61d-2402-4060-b75d-bcad7ac2c369" href="http://www.bmrb.wisc.edu/">Biological Magnetic Resonance Data Bank (BMRB)</a></p> <p><a data-link-id="3bd58417-c989-4048-917a-a6e2aff2fa6c" href="https://thebiogrid.org/">BioGrid: Biological General Repository For Interaction Datasets</a></p> <p><a data-link-id="06c90adc-29e6-4200-a4c7-48bfaf1f812a" href="https://data.sbgrid.org/">Structural Biology Data Grid</a></p> </td> </tr> <tr> <td> <p>Metabolomics</p> </td> <td> <p><a data-link-id="1dcfdfec-2550-4523-abc8-6a9b02c2cfbe" href="http://www.ebi.ac.uk/metabolights/">MetaboLights</a></p> <p><a data-link-id="728eded7-d522-4900-9d0c-2c6d5fa2370b" href="http://www.metabolomexchange.org/site/">MetabolomeXchange</a> (and any databases linked from Metabolome Exchange, including<a data-link-id="cf9afe8c-f660-4713-9858-ed3495f34226" href="https://www.metabolomicsworkbench.org/"> NIH Metabolomics Workbench</a> & <a data-link-id="47f33d21-b368-4da6-9d58-91b00cd1b2be" href="http://www.ebi.ac.uk/metabolights/">MetaboLights</a>)</p> </td> </tr> <tr> <td> <p>Proteomics</p> </td> <td> <p><a data-link-id="36d0c454-ba3c-4b2e-85c2-5d2212a6e7ae" href="http://www.proteomexchange.org/">Proteome Exchange</a>* (and any databases linked from Proteome Exchange, including <a data-link-id="e5337d2f-c62c-4ce1-8131-c1c120ebfd4d" href="http://www.ebi.ac.uk/pride/archive/">PRIDE Archive</a> and <a data-link-id="784f9920-ad90-4ab7-9b98-7b65b4ae190c" href="http://www.peptideatlas.org/">Peptide Atlas</a>)</p> <p>*This is a curated resource and may not accept direct submission of data. Please contact the database directly for further information.</p> </td> </tr> <tr> <td> <p>Flow Cytometry</p> </td> <td> <p><a data-link-id="9ebfa86c-18df-4552-b115-37afd93086bc" href="https://flowrepository.org/">FlowRepository</a></p> </td> </tr> <tr> <td> <p>Imaging</p> </td> <td> <p><a data-link-id="9d717e5c-3570-4cdc-9a56-36bbcd0496ce" href="https://www.ebi.ac.uk/bioimage-archive/">BioImage Archive</a> (includes <a data-link-id="8713d5c9-60c1-4786-b04f-e72c8aa297e9" href="https://www.ebi.ac.uk/empiar/">EMPIAR</a> and <a data-link-id="b4ba2b87-380e-4f9e-aef8-3d35155a2dac" href="https://idr.openmicroscopy.org/">Image Data Resource</a>)</p> <p><a data-link-id="0464f6e9-e0a7-48e9-80e6-9107caa5321d" href="https://www.cancerimagingarchive.net/">Cancer Imaging Archive</a></p> <p><a data-link-id="129c0497-8cbe-4f69-9fac-a34056b68517" href="http://www.cellimagelibrary.org/home">Cell Image Library</a></p> </td> </tr> <tr> <td> <p>Chemistry</p> </td> <td> <p><a data-link-id="da42b182-03c9-4cd9-afe1-838c755b414d" href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></p> <p><a data-link-id="6903d944-5309-49b3-add5-117016e7d80f" href="https://www.crystallography.net/cod/">Crystallography Open Database</a></p> <p><a data-link-id="ba94f0a5-f1fa-4806-8d2e-fd00817af04b" href="https://earthchem.org">EarthChem</a></p> </td> </tr> <tr> <td> <p>Neuroscience</p> </td> <td> <p><a data-link-id="32224e2e-4b11-4c7c-bb62-6fb617ea5377" href="https://openneuro.org/">OpenNeuro</a></p> <p><a data-link-id="f922be68-2b66-46eb-8d24-9a76b3883100" href="https://neurovault.org/">Neurovault</a></p> <p><a data-link-id="590a40af-61cc-40f5-827a-4dfa65df1601" href="http://neuromorpho.org/">Neuromorpho</a></p> <p><a data-link-id="d878ce74-3623-4fb7-99b3-cb23d191cf62" href="https://www.nitrc.org/">Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)</a></p> <p><a data-link-id="b8aea124-cd08-40a4-a223-e07dd3815355" href="http://fcon_1000.projects.nitrc.org/indi/abide/">Autism Brain Imaging Data Exchange (ABIDE)</a></p> <p><a data-link-id="5fde8a60-84af-40e5-9016-2546c7806e14" href="https://openneuro.org/">International Neuroimaging Data-Sharing Initiative (INDI) OpenNEURO*</a></p> <p>*Please note human-subject data submitted to OpenNEURO must be de-identified, whilst INDI can take clinical data</p> </td> </tr> <tr> <td> <p>Plant</p> </td> <td> <p><a data-link-id="6856904d-8149-4392-8909-b4645c105939" href="http://edal.ipk-gatersleben.de/repos/pgp/">Plant Genomics and Phenomics Research Data Repository (PGP)</a></p> <p>**Please note that authors must choose a CC0 license for their data when submitted to the PGP</p> </td> </tr> <tr> <td> <p>Taxonomy</p> </td> <td> <p><a data-link-id="bd62b5c1-e252-4892-9f33-cff88f53d470" href="http://www.gbif.org/">Global Biodiversity Information Facility (GBIF)</a></p> <p><a data-link-id="1f0b3c45-04dd-4b16-a0bd-cceb7b368681" href="https://www.itis.gov/">Integrated Taxonomic Information System (ITIS)</a></p> <p><a data-link-id="5120e77a-0fcc-4287-a114-43f1a8838397" href="https://www.ncbi.nlm.nih.gov/taxonomy">NCBI Taxonomy*</a></p> <p><a data-link-id="0e3c5e81-1233-4b51-95b2-1a5e0056f6e9" href="http://www.morphobank.org/">Morphobank.org</a></p> <p>*NCBI Taxonomy is the preferred choice for sequencing data</p> </td> </tr> </tbody> </table></div> <p>Other (If alternative licensing options are offered please ensure CC0 is selected)</p> <p><a data-link-id="2693765d-b0d1-40aa-a9bd-89fba9224c78" href="http://gigadb.org/">GigaDB</a></p> <p><a data-link-id="a16a2d98-625b-413b-826a-915257100fd7" href="https://www.ebi.ac.uk/biostudies/">Biostudies</a></p> <p><a data-link-id="42525e09-e4f9-4db9-8a7b-6f5871645827" href="https://dataverse.org/">Dataverse</a></p> <p><a data-link-id="dc56208e-71fa-4892-b4fd-22b98d2f7165" href="http://datadryad.org/">Dryad</a></p> <p><a data-link-id="36659d93-895b-4a1e-af5d-987816c4e68c" href="https://figshare.com/">FigShare</a></p> <p><a data-link-id="58d6550f-8ae3-460c-ad32-86c0a77433ab" href="https://data.nal.usda.gov/about-ag-data-commons">Ag Data Commons</a> (for USDA funded research)</p> <p><a data-link-id="fdc0334f-41c6-42d5-b11f-9b9bf5278762" href="https://qdr.syr.edu/">Qualitative Data Repository</a></p> <p><a data-link-id="3bdd48e7-8ca8-449d-a30d-b558228eb083" href="https://www.synapse.org/">Synapse</a></p> <p><a data-link-id="91a29c31-ed22-489a-bcba-73477920434c" href="https://zenodo.org/">Zenodo</a></p> <p>National and Institutional repository(s)*</p> <p>*If there are not geographic restrictions to access and under a CC0 license.</p> <h3>QTL/GWAS mapping</h3> <p>If the manuscript includes QTL analyses, GWAS, or similar methods linking genotypes and phenotypes, all data and code to reproduce the results from raw data must be shared. This includes genotypes (usually in Variant Call Format), individual-level phenotype data, as well as any other necessary information such as custom scripts, SNP positions or linkage maps. Data availability via a controlled access database is acceptable if necessary to protect the anonymity of human subjects. Manuscripts based on proprietary genotype and / or phenotype data cannot be considered.</p> <h3>Models</h3> <p>If your manuscript describes a three-dimensional model of a protein that has been manually built, you should deposit it <u><a data-link-id="7f93cbb7-09c0-4470-ae31-a33737a4bc2a" href="http://srv00.recas.ba.infn.it/PMDB/">in the PMDB database,</a></u> see also <a data-link-id="d009deff-316f-4676-9452-3a77cd3cc232" href="https://doi.org/10.1093/nar/gkj105">NAR 34, 306-309</a>. The database will return a unique identifier which you can include in your manuscript, thereby allowing readers to have access to your model. Curated models can also be hosted with <a data-link-id="92deb26b-03b8-48f3-9c6a-606cb51dcffd" href="http://jjj.mib.ac.uk/">JWS Online</a> and the <a data-link-id="662ccd5e-bf52-4d12-a645-007576a5b6ce" href="http://www.ebi.ac.uk/biomodels-main/">BioModels</a> databases, and should follow <a data-link-id="4de87de4-d80e-4102-904c-818381319a29" href="http://co.mbine.org/">COMBINE Computational Modeling Standards</a>. </p> <h3>Materials </h3> <p>If reproducible materials are generated as a result of the research (for example plasmids, cell lines, and model organisms), these need to be made publicly available and a statement on their availability should be included. Like data, materials need to be openly shared with no restrictions to meet our Open Science policies. </p> <h3>Supplementary Files</h3> <p>In addition to the larger datasets hosted in our GigaDB or other public repositories, smaller (less than 20MB in size) supporting materials and Appendices which are not essential for inclusion in the full text can also be published as online-only Supplementary Data. Supplementary Data should be submitted for review, in a separate file or files from the manuscript. Authors should make sure that all additional text, figures and tables are presented in a single file to minimise the number of files. Authors should ensure that the Supplementary Data is referred to in the main manuscript at an appropriate point in the text. It cannot be altered or replaced after the paper has been accepted for publication. For the purpose of long-term preservation of this information, we require supplementary material to be published and stored on our journal website or in our GigaDB repository. It is acceptable for authors to post supplementary material on their own website in addition to this, but not in place of this.</p> <h3>Data Availability statement</h3> <p>As noted, all authors must include a “Data Availability” statement in the end matter of their manuscript detailing where the data supporting their findings can be found. Commentaries and Reviews should just state "not applicable" in the Data Availability section if no data needs to be declared. <em>GigaScience</em> endorses and implements the <a data-link-id="a248a332-8868-4029-96f4-a230a2616d10" href="https://www.force11.org/datacitationprinciples">Force 11 Data Citation Principles</a> and requires that all publicly available datasets be fully referenced in the reference list with an accession number or unique identifier such as a digital object identifier (DOI). Data and supplemental information deposited in GigaDB will automatically be given DOIs allowing the data to be cited.</p> <h3>Publication of clinical datasets</h3> <p>For datasets containing clinical data, authors have an ethical and legal responsibility to respect participants’ rights to privacy and to protect their identity. Ideally, authors should gain informed consent for publication of the dataset from participants at the point of recruitment. Or if this is not possible, authors must demonstrate that publication of such data does not compromise anonymity or confidentiality or breach local data protection laws, for the dataset to be considered for publication. For example confirming you have Ministry of Science and Technology (MOST) approval in China. Authors must consider whether the dataset contains any direct or indirect identifiers and consult their local ethics committee or other appropriate body before submission if there is any possibility that participants will not be fully anonymous. Authors must state in their manuscript on submission whether informed consent was obtained for publication of patient data, and copies of unsigned consent forms may be required for inspection upon submission. If informed consent was not obtained, authors must state the reason for this, and which body was consulted in the preparation of the dataset. </p> <h2><a data-link-id="a6892005-7193-49e6-8b97-fcd44c0d0ddc" id="Reporting Standards" name="Reporting Standards"></a>Reporting Standards</h2> <p><em>GigaScience</em> advocates complete and transparent reporting of biomedical and biological research. Please refer to the <a data-link-id="99d06dc6-1ced-4584-b281-b9e0fc0a509a" href="https://academic.oup.com/gigascience/pages/Minimum_Standards_of_Reporting_Checklist">Minimum standards of reporting checklist</a> when reporting your research (read the <em>GigaScience</em> <a data-link-id="42ee7155-e59f-496e-af0a-2f68f3e1e120" href="https://academic.oup.com/gigascience/article/4/1/1/2707571/Better-reporting-for-better-research-a-checklist?searchresult=1">editorial</a> for more information). We also ask that authors refer to the minimum reporting guidelines for health research hosted by the <a data-link-id="a17e368f-4a0a-49cd-87cf-944a61d619a1" href="http://www.equator-network.org/">EQUATOR Network</a> when preparing their manuscript, and the <a data-link-id="e3a79381-5987-444e-9b1b-efa4bdd5fd72" href="https://fairsharing.org/">FAIRsharing Portal</a> for reporting checklists for biological and biomedical research, where applicable. Authors should adhere to these guidelines when drafting their manuscript, and reviewers will be asked to refer to these checklists when evaluating such studies. Checklists are available for a number of study designs, including randomized controlled trials (<a data-link-id="118863b8-cc40-4bd5-ad75-bf6f7a5c5401" href="http://www.consort-statement.org/downloads">CONSORT</a>), systematic reviews and meta-analyses (<a data-link-id="f2be5b09-c560-41a0-a000-cb5f44e100a9" href="http://www.prisma-statement.org/">PRISMA</a>), observational studies (<a data-link-id="5fe33791-e712-48a6-955f-8f9f491c2948" href="http://www.strobe-statement.org/">STROBE</a>), diagnostic/prognostic studies (<a data-link-id="6084b7f9-a341-439f-9a7e-dfdd99282448" href="https://www.equator-network.org/reporting-guidelines/stard/">STARD</a>/<a data-link-id="9177dee5-6cd8-4991-9d0f-68762d9ca8a2" href="http://www.tripod-statement.org/TRIPOD/TRIPOD-Checklists/TRIPOD-Checklist-Prediction-Model-Development-and-Validation">TRIPOD</a>), and pre-clinical animal studies (<a data-link-id="3b7be06e-a709-4c9f-a1e7-e5adbf3ff904" href="http://www.nc3rs.org.uk/arrive-guidelines">ARRIVE</a>). At manuscript submission, authors must confirm that they reviewed the standards, report whether any standards were relevant for the research application, and confirm that they followed those standards in the manuscript. The editors and reviewers will then verify that the appropriate standards were adopted and followed. We have found that it is useful to have the conducted research pre-registered prior to conducting the research with an analysis plan in an independent, institutional registry (e.g. the <a data-link-id="1d180395-5807-4129-b48f-7950901f78e5" href="https://osf.io/">Open Science Framework</a>), this should then be shared in the review process, and cited in the paper as it provides extensive support for collaboration and organizing all components of your research.</p> <h3>Trial registration</h3> <p><em>GigaScience</em> supports initiatives to improve reporting of clinical trials. Please see the <a data-link-id="301f7a82-4dc8-4bed-92e3-d67c10e7f43e" href="http://oxfordjournals.org/en/authors/ethics.html">OUP Statement on Publication Ethics</a> for more information. </p> <h3>Statistical methods</h3> <p>Authors should include full information on the statistical methods and measures used in their research, including justification of the appropriateness of the statistical test used (see the <a data-link-id="3ca49412-ec2e-445e-930e-b3bf2b9d5456" href="http://www.equator-network.org/reporting-guidelines/sampl/">SAMPL guidelines</a> for more information). Reviewers will be asked to check the statistical methods, and the manuscript may be sent for an additional specialist statistical review if considered necessary.</p> <h3>Resource identification</h3> <p>To enable effective tracking of the key resources used to produce the scientific findings reported in the biomedical literature, authors are expected to include a full description of all resources with enough information to allow them to be uniquely identified. In support of the <a data-link-id="946887c8-17a9-4007-a060-bcf43d3af077" href="https://www.force11.org/node/4463">Resource Identification Initiative</a> (RII), we encourage authors to use unique <a data-link-id="153ba34d-e007-4f16-a03e-74b146528851" href="https://scicrunch.org/resources">Resource Identifiers</a> (RRIDs) within their manuscript to identify their model organisms, antibodies, or tools. If your resource is not found, we encourage you to <a data-link-id="90692d6f-9734-4c0b-bb80-ac7aaf25a537" href="https://scicrunch.org/resources/about/resource">add your resource to the registry</a>. We also have put together a list of common bioinformatics RRIDs for easy reference.</p> <p>Cell line authentication If human cell lines are used, authors are strongly encouraged to include the following information in their manuscript:</p> <ul> <li>The source of the cell line, including when and from where it was obtained</li> <li>Whether the cell line has recently been authenticated and by what method</li> <li>Whether the cell line has recently been tested for mycoplasma contamination</li> </ul> <p>If the cell line has an RRID<a data-link-id="3ec31414-d31b-40c2-be90-19bd2cdb290e" href="https://scicrunch.org/resources"> Resource Identifier</a> please also include that. Further information is available from the <a data-link-id="22ec490b-0756-4495-8035-32226d5b71f6" href="https://www.atcc.org/about-us/what-we-do/standards">International Cell Line Authentication Committee</a> (ICLAC). We recommend that authors check the <a data-link-id="e68b537a-db8f-4c82-a7e8-ee78f8e69a5d" href="http://www.ncbi.nlm.nih.gov/biosample/?term=cell%20line%20status%20misidentified%5bAttribute%5d">NCBI database</a> for misidentification and contamination of human cell lines. Cell line authentication and distribution services are also offered by <a data-link-id="dc9bf2e0-49b2-45c4-bc43-6d9e71efb3f4" href="https://www.atcc.org/services/cell-authentication">ATCC</a> and others. It is also recommended that bioinformatics tools are registered in the ELIXIR <a data-link-id="707888f8-fa24-4703-b173-d1753bd08316" href="https://bio.tools">bio.tools</a> repository and their identifiers are also included in the paper.</p> <h3>Gene nomenclature</h3> <p>Standardized gene nomenclature should be used throughout. Human gene symbols and names can be found in the <a data-link-id="05b1eb27-1e21-4f65-842b-28cacf7d81ef" href="https://www.genenames.org/about/">HUGO Gene Nomenclature Committee</a> (HGNC) database; <a data-link-id="b8ac808d-f879-4250-8323-b0c24edaa478" href="https://www.genenames.org/contact/request/">requests for new gene symbols should be submitted</a> and any enquiries about gene nomenclature can be directed to them. Alternative gene aliases that are commonly used may also be reported, but should not be used alone in place of the HGNC symbol. See the <a data-link-id="fe63452d-825f-4a56-b948-c390986cf9fc" href="https://vertebrate.genenames.org/">Vertebrate Gene Nomenclature Committee (VGNC)</a> for other species.</p> <h3>Reporting of sequence variants</h3> <p><em>GigaScience</em> endorses the recommendations of the Human Variome Project Consortium for describing sequence variants (<a data-link-id="3537902a-5cc4-49c9-96ae-a01b4f8fd94a" href="http://www.hgvs.org/mutnomen/">Human Genome Variation Society</a>) and phenotypes (<a data-link-id="43548c6e-baf8-4e49-898e-6b4ed768045a" href="http://www.human-phenotype-ontology.org/">Human Phenotype Ontology</a>). We recommend that authors should submit all variants described in a manuscript to the relevant public gene/disease specific database (LSDB): <a data-link-id="ce52a0d6-a02b-4fc6-b0f8-2585906ad55a" href="http://grenada.lumc.nl/LSDB_list/lsdbs">a list is available</a>. The database URL and the unique identifier should be reported in the manuscript.</p> <h3>Describing new taxa guidelines set by the International Code of Nomenclature for algae, fungi, and plants.</h3> <p>Authors describing new fungal taxa should register the names with a recognized repository, such as <a data-link-id="395bb1bd-5183-48f7-b0c3-aa8e1b9a484f" href="http://mycobank.org/">Mycobank</a>, and request a unique digital identifier which should be included in the published article. Manuscripts containing new taxon names for animals must follow the <a data-link-id="13e576db-4fca-443d-963e-30609a22cc1a" href="http://iczn.org/content/iczn-amendment-electronic-publication">guidelines</a> set by the International Commission on Zoological Nomenclature. We require the new taxon name and the article it is published in to be registered with ZooBank, and the unique <a data-link-id="83dafba2-e075-484e-91ba-082fc359ae3d" href="http://www.zoobank.org/">Zoobank</a> identifier should be included in the published article. For bacterial species, authors must comply with rules of the International Committee on Systematics of Prokaryotes (<a data-link-id="acccdd4c-d586-4107-9c68-983ca6976e76" href="https://doi.org/10.1099/ijs.0.2008/005082-0">ICSP</a> for valid <a data-link-id="66c1370d-69b4-41fa-9d7c-36f0fed86d5a" href="https://doi.org/10.1099/ijs.0.64780-0">publication</a><u>)</u>. The proposal of new virus names must follow the guidelines established by the International Committee on Taxonomy of Viruses (ICTV) in the <a data-link-id="c6463274-2abb-4905-b04c-b79699d7ca38" href="https://ictv.global/about/code">International Code of Virus Classification and Nomenclature</a>.</p> <h3>Data</h3> <p>To drive the maximum re-use and utility of published research, we expect authors to comply with available field-specific standards for the preparation and recording of data. Please see the <a data-link-id="dfbac5ac-72dd-4b48-b5d6-731769860c22" href="https://fairsharing.org/">FAIRharing</a> website for information on field-specific data standards. Authors must comply with best practice in their field for sharing of data, with particular attention to maintaining <a data-link-id="adc541d5-5c53-4984-86ce-81186c65f264" href="http://www.trialsjournal.com/content/11/1/9">patient confidentiality</a>.</p> <p>Authors using unpublished genomic data are expected to abide by the guidelines of the <a data-link-id="cb339b1d-58c8-44d6-b2ae-c7c39b78a57c" href="https://www.genome.gov/Pages/Research/WellcomeReport0303.pdf">Fort Lauderdale</a> and <a data-link-id="006ecce2-c766-4dcb-877d-2e6f0a346606" href="http://www.nature.com/nature/journal/v461/n7261/full/461168a.html">Toronto</a> agreements. Based on broadly accepted scientific community standards, the key requirement of third parties using genomic data is to contact the owners of unpublished data (i.e. the principal investigator and sequencing center) prior to undertaking their research, to advise them about their planned analyses.</p> <p>Sequence information should be deposited following the <a data-link-id="45092ced-8799-4b56-b8f1-fa9df52e2616" href="http://www.ebi.ac.uk/ena/submit/mixs-checklists">MIxS guidelines</a> (consisting of MIGS, MIMS and MIMARKS standards depending on the type of sequencing experiment).</p> <p>To facilitate complete and concise reporting and standardization across interdisciplinary microbiome studies and improve data reporting for Human microbiome data, GigaByte requires authors of metagenomics papers to add and follow the <a data-link-id="7e64942a-6a56-4ec7-87ab-ab8c39313bbc" href="https://doi.org/10.1038/s41591-021-01552-x">STORMS checklist</a> and to add it in their supplementary material with their submitted manuscript. Authors preparing Human microbiome papers to be submitted to the journal can download the STORMS versioned spreadsheet from <a data-link-id="a29e35c0-8c7a-4d14-bb01-543b7f867241" href="https://docs.google.com/spreadsheets/d/10uJpBUm-143T2B8DZR9EdiQntR3ERxoK8D3c9pEQifs/edit#gid=64430838">http://storms.waldronlab.io/</a></p> <p>Microarray data should be submitted to one of the recognized public repositories in a <a data-link-id="652ab3aa-614c-42aa-b9ca-1d0c33d6ca6e" href="https://www.fged.org/projects/miame">MIAME</a> compliant way and sequencing based functional genomics data needs to follow the <a data-link-id="b1c0e6df-4974-4c17-98ba-97593293ddb8" href="https://www.fged.org/projects/minseqe">MINSEQE</a> guidelines (for more <a data-link-id="b658d953-1241-4faf-9d59-be725b74dc18" href="https://doi.org/10.1371/journal.pbio.0020317">see this page</a>).</p> <p>Mass spectrometry data should be supplied in the mzML format recommended by the <a data-link-id="17100e67-4378-48e5-90cf-18e4c6339b3a" href="http://www.psidev.info/index.php?q=node/80">HUPO Protein Standards Initiative</a> Mass Spectrometry Standards Working Group.</p> <p>In any event, all data should be made available to the journal for the purpose of peer review.</p> <h2><a data-link-id="a7622cec-d610-4a5a-bc47-595cb7dd06ad" id="Misconduct" name="Misconduct"></a>Misconduct</h2> <p><em>GigaScience</em> takes seriously all allegations of potential misconduct. All research involving humans (including human data and human material) and animals must have been carried out within an appropriate ethical framework. As members of <a data-link-id="bdd25914-6eb7-4487-a3eb-4b7dd9e82145" href="http://publicationethics.org/">COPE</a>, <em>GigaScience</em> will follow the <a data-link-id="ef342a30-3dbe-4e34-8dc8-7eb38d7d243a" href="http://publicationethics.org/">COPE</a> guidelines outlining how to deal with cases of suspected misconduct. In cases of suspected research or publication misconduct, it may be necessary for the Editor to contact and share manuscripts with third parties, for example, author(s)’ institution(s) and ethics committee(s). <em>GigaScience</em> may also seek advice from <a data-link-id="da6d0cda-536f-42bc-a53e-a8bdf155f9fa" href="http://publicationethics.org/">COPE</a> and discuss anonymized cases in the COPE Forum. In cases of proven research misconduct involving published articles, or where the scientific integrity of the article is significantly undermined, articles may be retracted.</p> <h3>Image manipulation</h3> <p>If any questions are raised at any time, these will be referred to the Editor. The use of generative AI tools must not be used to alter figures, particularly in any manner that adds, removes, alters, highlights, or modifies the relationship of individual elements within the image. The authors must be able to supply the original data, which will then be compared to the prepared figures. If the original data are not provided, the manuscript may be rejected during peer review, or retracted if published. If image manipulation effects in any way the interpretation of the data, the work will be rejected or retracted. If misconduct is suspected, this will be reported to the author(s)’ institution(s). ALL authors of the work will be held accountable.</p> <h3>Plagiarism</h3> <p><em>GigaScience</em> is a member of <a data-link-id="7b6a389f-70a5-41dc-b4d0-90a3ae78b0a2" href="http://www.crossref.org/crosscheck/index.html">CrossCheck</a>’s plagiarism detection initiative and uses plagiarism detection software. If plagiarism is identified, the <a data-link-id="631b54ad-ccaa-4ca4-bf7d-da84ceb05779" href="http://publicationethics.org/files/u2/02A_Plagiarism_Submitted.pdf">COPE guidelines</a> on plagiarism will be followed.</p> <h3>Misuse of AI-assisted technologies</h3> <p>Authors must follow <em>GigaScience</em> and COPE guidelines on use of generative AI-assisted technologies. Authors hold responsibility for fact-checking and validity of any material generated using these technologies. <em>GigaScence</em> may use tools to detect undeclared or misuse of AI.</p> <h3>Corrections and retractions</h3> <p>Rarely, it may be necessary for <em>GigaScience</em> to publish corrections to, or retractions of, articles published, so as to maintain the integrity of the academic record. Changes to published articles that affect the interpretation and conclusion of the article, but do not fully invalidate the article, will, at the Editor(s)’ discretion, be corrected via publication of an correction notice that is indexed and linked to the original article. On rare occasions, when the scientific information in an article is substantially undermined, it may be necessary for published articles to be retracted. <em>GigaScience</em> will follow the <a data-link-id="c5c6e6a8-9613-4058-933b-389e8704806e" href="http://publicationethics.org/files/retraction%20guidelines.pdf">COPE guidelines</a> in such cases.</p> <h3>Appeals and complaints</h3> <p><em>GigaScience</em> adheres to <a data-link-id="702aeb9f-06b2-4e1b-b599-ad195e339e7e" href="http://publicationethics.org/files/2008%20Code%20of%20Conduct.pdf">COPE guidelines</a> regarding appeals to editorial decisions and complaints.</p> <script type="text/javascript"> $(".expandableSection").hide(); $(".expandableSectionToggle").click(function() { var y = $(this).attr("trigger-for");$('#' + y).toggle(); }) </script></div></div><div class="right"> <div class="ad"> <div class="widget widget-AdBlockDynamic widget-instance-SecondaryTemplate_RightRailB0SelfServeTopSidebar"> <div class="js-adBlock-parent-wrap"> <div class="adBlockMainBodyTop-wrap js-adBlockMainBodyTop hide"> <div id="adBlockMainBodyTop" class="js-adblock" style=" " data-lazy-load-margin="150"> <script> googletag.cmd.push(function () { googletag.display('adBlockMainBodyTop'); 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