<p>@<a href="Resources for Implementing TOP" rel="nofollow">toc</a></p> <h2>TOP Checklists</h2> <ul> <li>Checklists for an editor verifying an author submission (<a href="https://osf.io/hcnme/" rel="nofollow">level 1</a>; <a href="https://osf.io/87v93/" rel="nofollow">mixed levels</a>)</li> <li>Checklist for an author submitting to a TOP signatory journal (<a href="https://osf.io/55eu7/" rel="nofollow">level 1</a>)</li> <li><a href="https://osf.io/y8aqx/" rel="nofollow">Suggested tools and checklists</a> in ecology and evolution.</li> </ul> <h2>Data Reproducibility Policies</h2> <p>The following journals use shared data and code to reproduce the computational findings reported in articles prior to publication. <strong>This represents level 3 of the TOP Guidelines for Data, Materials, and Code.</strong> </p> <ul> <li><a href="https://ajps.org/ajps-replication-policy/" rel="nofollow">American Journal of Political Science</a></li> <li><a href="https://academic.oup.com/biostatistics/pages/General_Instructions" rel="nofollow">Biostatistics</a> </li> <li><a href="https://www.cambridge.org/core/journals/journal-of-experimental-political-science/information/instructions-contributors" rel="nofollow">Journal of Experimental Political Science</a></li> <li><a href="https://www.prio.org/JPR/Datasets/" rel="nofollow">Journal of Peace Research</a></li> <li><a href="https://open.lnu.se/index.php/metapsychology/about" rel="nofollow">Meta-Psychology</a></li> <li><a href="http://www.nowpublishers.com/Journal/AuthorInstructions/QJPS" rel="nofollow">Quarterly Journal of Political Science</a></li> </ul> <h2>Data Sharing: Practices and Repositories</h2> <ul> <li><a href="http://www.nejm.org/doi/full/10.1056/NEJMsb1616595" rel="nofollow">Data Authorship as an Incentive to Data Sharing</a></li> <li>De-Identification</li> <li><a href="https://www.ipc.on.ca/resource/de-identification-guidelines-for-structured-data/" rel="nofollow">De-identification Guidelines for Structured Data</a></li> <li><a href="http://ukanon.net/ukan-resources/ukan-decision-making-framework/" rel="nofollow">Anonymisation Decision-making Framework</a></li> <li>Data Repositories</li> <li><a href="https://copdessdirectory.osf.io/" rel="nofollow">COPDESS</a> Directory of Data Repositories </li> <li><a href="http://www.re3data.org/" rel="nofollow">Re3Data</a> Registry of Research Data Repositories </li> <li><a href="http://www.data-pass.org/" rel="nofollow">Data-PASS</a> </li> <li><a href="http://datadryad.org/" rel="nofollow">Dryad</a></li> <li><a href="https://figshare.com/" rel="nofollow">Figshare</a></li> <li><a href="http://oad.simmons.edu/oadwiki/Data_repositories" rel="nofollow">OAD</a> (Open Access Data Repositories)</li> <li><a href="https://osf.io" rel="nofollow">OSF</a> </li> <li>Nature Scientific Data, recommended <a href="http://www.nature.com/sdata/policies/repositories" rel="nofollow">repositories</a></li> </ul> <h2>Funder Policies</h2> <p>The following polices from public and private funding agencies include language about data, materials, or code sharing, reporting guidelines, preregistration, or replication. | Funder | Type of Policy | | ------ | ---------- | | Cancer Research UK | <a href="https://academic.oup.com/ntr/article/19/7/773/3106460" rel="nofollow">Partnership with Nicotine and Tobacco Research for Registered Reports</a> | | Global Research Awards for Nicotine Dependence | <a href="http://www.grandawardsprogram.org/news/news-and-announcements.html" rel="nofollow">Partnership with Nicotine and Tobacco Research for Registered Reports</a> | | Children’s Tumor Foundation (CTF) | <a href="http://blogs.plos.org/everyone/2017/09/26/registered-reports-with-ctf/" rel="nofollow">Partnership with PLOS ONE for Registered Reports</a> | | The Laura and John Arnold Foundation | <a href="http://www.arnoldfoundation.org/wp-content/uploads/Guidelines-for-Investments-in-Research.pdf" rel="nofollow">Open data, materials, code, and preregistration requirements</a> | | The National Institutes of Health | <a href="https://grants.nih.gov/reproducibility/index.htm" rel="nofollow">Guidelines on Rigor and Reproducibility</a> and <a href="https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-050.html" rel="nofollow">reporting preprints and preregistrations as interim research outputs</a> | | National Science Foundation | <a href="https://www.nsf.gov/bfa/dias/policy/dmp.jsp" rel="nofollow">Data sharing guidelines</a>, <a href="https://www.nsf.gov/pubs/2018/nsf18053/nsf18053.jsp" rel="nofollow">Replication studies for the Social, Behavioral and Economic Sciences (SBE) Directorate</a> | | The Netherlands Organisation for Scientific Research (NWO) | <a href="https://www.nwo.nl/en/news-and-events/news/2016/nwo-makes-3-million-available-for-replication-studies-pilot.html" rel="nofollow">Funding for direct replications</a> | | Agency for Healthcare Research and Quality | <a href="https://www.ahrq.gov/funding/policies/publicaccess/index.html" rel="nofollow">Data sharing requirements</a> |Patient-Centered Outcomes Research Institute (PCORI) | <a href="http://www.pcori.org/funding-opportunities/awardee-resources" rel="nofollow">Data sharing and preregistration requirements</a> | |The Howard Hughes Medical Institute | <a href="https://www.hhmi.org/about/policies" rel="nofollow">Data sharing and open access requirements</a> | | The Engineering and Physical Sciences Research Council | <a href="https://www.epsrc.ac.uk/about/standards/researchdata/expectations/" rel="nofollow">Data sharing disclosure requirements</a> | | Wellcome Trust |<a href="https://wellcome.ac.uk/what-we-do/topics/data-sharing" rel="nofollow">Data sharing requirements</a> | |Research Councils UK | <a href="http://www.rcuk.ac.uk/research/datapolicy/" rel="nofollow">Recommendations for data sharing</a> | | FWF (Austrian Science Foundation) | <a href="https://www.fwf.ac.at/en/research-funding/open-access-policy/" rel="nofollow">Open data and open access requirements</a> | | Canadian government | <a href="http://open.canada.ca/en/content/canadas-action-plan-open-government-2014-16#ch4-3" rel="nofollow">Principles of open data in research and government</a> | | The Bill and Melinda Gates Foundation | <a href="http://www.gatesfoundation.org/how-we-work/general-information/open-access-policy" rel="nofollow">Data sharing mandate and funded open access mandate</a> | | Belmont Forum | <a href="http://www.belmontforum.org/about/open-data-policy-and-principles/" rel="nofollow">Open Data Policy</a>: Findable, Accessible, Understandable, and Manageable |</p> <h2>Reporting Guidelines</h2> <ul> <li>See the <a href="https://osf.io/kgnva/wiki/Open%20Science%20Literature/" rel="nofollow">Open Science Literature</a> for research on the effectiveness of reporting guidelines. Our recommended best practice is to include items deemed essential into the article submission process.</li> <li>See the <a href="http://www.equator-network.org/" rel="nofollow">Equator Network</a> for a large, searchable collection of reporting guidelines. </li> </ul> <h3>Community Created Guidelines</h3> <ul> <li><a href="http://www.consort-statement.org/" rel="nofollow">CONSORT</a> (Consolidated Standards of Reporting Trials)</li> <li>For meta-analysis: <a href="http://prisma-statement.org/PRISMAStatement/Checklist.aspx" rel="nofollow">PRISMA</a> or <a href="https://amstar.ca/Amstar_Checklist.php" rel="nofollow">AMSTAR</a></li> <li><a href="https://www.nlm.nih.gov/services/research_report_guide.html" rel="nofollow">NIH Reporting Guidelines By Organization</a></li> <li>Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups <a href="https://academic.oup.com/intqhc/article/19/6/349/1791966/Consolidated-criteria-for-reporting-qualitative" rel="nofollow">COREQ</a></li> <li>STrengthening the Reporting of OBservational studies in Epidemiology (<a href="https://www.strobe-statement.org/index.php?id=strobe-home" rel="nofollow">STROBE</a>)</li> <li>An Updated List of Essential Items for Reporting Diagnostic Accuracy Studies (<a href="http://www.stard-statement.org/" rel="nofollow">STARD</a>)</li> <li><a href="http://onlinelibrary.wiley.com/doi/10.1111/bph.12856/full" rel="nofollow">Experimental design and analysis and their reporting: new guidance for publication in BJP</a></li> <li><a href="https://www.nc3rs.org.uk/arrive-guidelines" rel="nofollow">ARRIVE</a> (Animal Research: Reporting of In Vivo Experiments)</li> <li><a href="https://www.bmj.com/content/361/bmj.k1079" rel="nofollow">TIDieR-PHP: a reporting guideline for population health and policy interventions</a></li> <li><a href="http://metabolomicssociety.org/index.php/resources/metabolomics-standards" rel="nofollow">Standardization in Metabolomics Experiments</a></li> <li>Minimum Information for reporting:<ul> <li>Proteomics Experiments (<a href="http://www.psidev.info/index.php?q=node/91" rel="nofollow">MIAPE</a>)</li> <li>Genotyping Experiments (<a href="https://osf.io/4nryf/" rel="nofollow">MIGen</a>)</li> <li>Flow Cytometry Experiments (<a href="https://osf.io/edwhp/" rel="nofollow">MIFlowCyt</a>)</li> <li>Minimal Information About T cell Assays (<a href="http://miataproject.org/" rel="nofollow">MIATA</a> project)</li> <li>Quantitative Real-Time PCR Experiments (<a href="https://osf.io/kjqtf/" rel="nofollow">MIQE</a>)</li> <li>RNAi Experiment (<a href="http://miare.sourceforge.net/HomePage" rel="nofollow">MIARE</a>)</li> </ul> </li> <li><a href="http://onlinelibrary.wiley.com/doi/10.1002/cncy.20147/abstract" rel="nofollow">BRISQ</a> (Biospecimen reporting for improved study quality)</li> </ul> <h3>Journal Created Guidelines</h3> <ul> <li>From Cell Press: Structured, Transparent, Accessible Reporting (STAR) guidelines from Cell Press: <a href="http://www.cell.com/star-methods" rel="nofollow">Website</a>, <a href="http://www.cell.com/pb-assets/journals/research/cell/methods/Methods%20Guide_general.pdf" rel="nofollow">Methods Guide</a>, and the <a href="https://www.star-methods.com/key-resources/webform/els_key_resources_table" rel="nofollow">Key Resources Table</a> </li> <li>American Psychological Association: Journal Article Reporting Standards (<a href="http://www.apa.org/pubs/journals/releases/amp-amp0000191.pdf" rel="nofollow">JARS</a> 2018 Update; <a href="http://www.apastyle.org/manual/related/apa-jars-2008.pdf" rel="nofollow">JARS</a> 2008)</li> <li>BioMedCentral's <a href="http://resource-cms.springer.com/springer-cms/rest/v1/content/7117202/data/v2/Minimum+standards+of+reporting+checklist" rel="nofollow">Minimum Standards of Reporting Checklist</a></li> <li><a href="http://onlinelibrary.wiley.com/doi/10.1111/lang.12104/full" rel="nofollow">Guidelines for Reporting Quantitative Methods and Results in Primary Research</a> at Language Learning</li> <li><a href="https://www.cambridge.org/core/journals/journal-of-experimental-political-science/article/reporting-guidelines-for-experimental-research-a-report-from-the-experimental-research-section-standards-committee/F09D4BEC6E9F493DC7E048BB252366F2" rel="nofollow">Reporting Guidelines for Experimental Research: A Report from the Experimental Research Section Standards Committee</a> of the American Political Science Association</li> <li>Association for Psycholgical Science's <a href="http://www.psychologicalscience.org/publications/psychological_science/ps-submissions#DISC" rel="nofollow">reporting guidelines</a></li> <li>Journal of Experimental Social Psychology <a href="https://www.journals.elsevier.com/journal-of-experimental-social-psychology/news/jesp-editorial-guidelines/" rel="nofollow">reporting guidelines</a> </li> <li>Journal of Neuroscience <a href="http://www.jneurosci.org/content/general-information#policies" rel="nofollow">Policy on Reporting Experimental Design and Statistical Analysis</a> </li> <li><a href="https://www.nature.com/authors/policies/ReportingSummary-flat.pdf" rel="nofollow">Reporting Checklist for Life Sciences Articles</a> at Nature Publishing Group</li> <li><a href="https://submit.elifesciences.org/html/transparent_reporting.pdf" rel="nofollow">eLife's Transparent Reporting form</a></li> <li>Biophysical Journal's <a href="http://www.cell.com/pb/assets/raw/journals/society/biophysj/PDFs/reproducibility-guidelines.pdf" rel="nofollow">Guidelines for the Reproducibility of Biophysics Research</a></li> <li><a href="http://onlinelibrary.wiley.com/doi/10.1046/j.1360-0443.2000.951217594.x/epdf" rel="nofollow">A checklist for writing up research reports</a> in the journal Addiction</li> <li>PLOS One's <a href="http://journals.plos.org/plosone/s/submission-guidelines#loc-guidelines-for-specific-study-types" rel="nofollow">Reporting Guidelines for Specific Study Types</a></li> </ul> <h2>Registries</h2> <ul> <li><a href="https://www.socialscienceregistry.org/" rel="nofollow">American Economics Association RCT Registry</a></li> <li><a href="https://clinicaltrials.gov/" rel="nofollow">ClinicalTrials.gov</a> </li> <li><a href="http://egap.org/" rel="nofollow">EGAP</a> (Evidence in Governance and Politics)</li> <li><a href="https://osf.io" rel="nofollow">OSF</a> </li> <li><a href="https://www.crd.york.ac.uk/prospero/" rel="nofollow">PROSPERO</a> International prospective register of systematic reviews</li> <li><a href="http://www.researchregistry.com/" rel="nofollow">Research Registry</a></li> <li><a href="http://ridie.3ieimpact.org/" rel="nofollow">RIDIE</a> (Registry for International Development Impact Evaluations)</li> </ul> <h2>Editorials announcing TOP</h2> <ul> <li><a href="http://www.psychologicalscience.org/publications/observer/obsonline/aps-commits-to-promoting-transparent-science.html#.WG-9ObYrJBw" rel="nofollow">Association for Psychological Society</a></li> <li><a href="http://onlinelibrary.wiley.com/doi/10.1111/ele.12611/full" rel="nofollow">Ecology Letters</a></li> <li><a href="http://econtent.hogrefe.com/doi/10.1027/1618-3169/a000317" rel="nofollow">Experimental Psychology</a></li> <li><a href="http://link.springer.com/article/10.1007/s10764-016-9925-x" rel="nofollow">International Journal of Primatology</a></li> <li>Journal of Research in Personality (<a href="https://osf.io/preprints/psyarxiv/ay59f" rel="nofollow">preprint</a>)</li> <li><a href="http://www.nature.com/news/announcement-transparency-upgrade-for-nature-journals-1.21627" rel="nofollow">Nature</a></li> <li><a href="http://rsos.royalsocietypublishing.org/content/royopensci/4/1/160979.full.pdf" rel="nofollow">Royal Society Open Science</a></li> <li><a href="http://science.sciencemag.org/content/352/6290/1147" rel="nofollow">Science</a></li> <li><a href="https://ojs.ub.uni-konstanz.de/srm/article/view/6256/5679" rel="nofollow">Survey Research Methods</a></li> </ul> <h2>Examples of author guidelines using TOP ##</h2> <ul> <li><a href="http://science.sciencemag.org/content/sci/suppl/2016/06/01/352.6290.1147.DC1/aag2359-editorial.McNutt.SM.pdf" rel="nofollow">Science</a> | AAAS</li> <li><a href="http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292157-9032/homepage/ForAuthors.html" rel="nofollow">Brain and Behavior</a> | Wiley</li> <li><a href="http://www.collabra.org/about/editorialpolicies/" rel="nofollow">Collabra</a> | UC Press</li> <li><a href="http://www.apa.org/pubs/journals/cdp/?tab=4" rel="nofollow">Cultural Diversity & Ethnic Minority Psychology</a> | APA</li> <li><a href="https://www.journalofcognition.org/about/editorialpolicies/" rel="nofollow">Journal of Cognition</a> | Ubiquity Press</li> <li><a href="https://www.oxfordjournals.org/our_journals/nictob/for_authors/ntr%20top%20guidelines.pdf" rel="nofollow">Nicotine & Tobacco Research</a> | Oxford University Press</li> <li><a href="https://www.elsevier.com/journals/evolution-and-human-behavior/1090-5138/transparency-and-openness" rel="nofollow">Evolution and Human Behavior</a> | Elsevier</li> </ul> <hr> <h2>Disclosure Statements</h2> <h3>Data, Materials, and Code Disclosures</h3> <p>| Type of Disclosure | Example Language | | ------ | ---------- | | Data created for the study are available in a persistent repository. | All data and materials have been made publicly available at the [repository name] and can be accessed at [persistent URL or DOI] | | Anonymized data created for the study are available in a persistent repository. | Anonymized data and materials have been made publicly available at the [repository name] and can be accessed at [persistent URL or DOI] | | Some data available | In order to minimize the possibility of unintentionally sharing information that can be used to re-identify private information, a subset of the data generated for this study are available at [repository name] and can be accessed at [persistent URL or DOI] | | Data available upon request from a third party | Because of the sensitive nature of the data collected for this study, requests to access the dataset from qualified researchers trained in human subject confidentiality protocols may be sent to [name of organization] at [contact information]. |</p> <hr> <p>Other examples of data disclosure statements</p> <ul> <li><a href="http://www.nature.com/authors/policies/data/data-availability-statements-data-citations.pdf" rel="nofollow">Nature Research</a></li> <li><a href="http://publications.agu.org/author-resource-center/publication-policies/data-policy/data-policy-faq/" rel="nofollow">American Geophysical Union</a></li> </ul> <hr> <h3>Preregistration of Study or Analysis Plan Disclosure</h3> <p>| Type of Disclosure | Example Language | | ------ | ---------- | | Both the study and analysis plan were preregistered | This paper reports the results of [N] preregistered studies with complete analysis plans. The preregistration(s) can be accessed at [persistent URL]. We certify that the results of all preregistered analyses are reported, and that any unregistered analyses are clearly indicated as being [unregistered, exploratory, hypothesis-generating]. | | The study was preregistered without an analysis plan | This paper reports the results of [N] preregistered studies, which can be accessed at [name of repository] here [persistent URL or DOI]. | | No preregistration | No preregistration exists for the reported studies reported in this article. |</p> <hr> <h2>Persistent Identifiers</h2> <ul> <li><a href="https://confluence.ucop.edu/display/Curation/ARK" rel="nofollow">ARK</a> (Archival Resource Key)</li> <li><a href="https://www.doi.org/" rel="nofollow">DOI</a> (Digitial Object Identifier)</li> <li><a href="http://www.geosamples.org/" rel="nofollow">IGSN</a> (International Geo Sample Number)</li> <li><a href="https://scicrunch.org/resources" rel="nofollow">RRIDs</a> (Research Resource Identifiers)</li> <li><a href="https://www.isoc.org/inet96/proceedings/a4/a4_1.htm" rel="nofollow">PURL</a> (Persistent Uniform Resource Locators)</li> </ul> <p>Please contact us if you would like to add to this list: contact@cos.io</p>