@[toc](Resources for Implementing TOP) ## TOP Checklists ## - Checklists for an editor verifying an author submission ([level 1][1]; [mixed levels][2]) - Checklist for an author submitting to a TOP signatory journal ([level 1][3]) - [Suggested tools and checklists][4] in ecology and evolution. ## Data Reproducibility Policies ## Dozens of journals implement computational reproducibility checks prior to publication. See "Level 3" policies for [data][5] or [code][6] on TOP Factor for an up-to-date listing. ## Data Sharing: Practices and Repositories ## - [Data Authorship as an Incentive to Data Sharing][7] - De-Identification - [De-identification Guidelines for Structured Data][8] - [Anonymisation Decision-making Framework][9] - Data Repositories - [COPDESS][10] Directory of Data Repositories - [Re3Data][11] Registry of Research Data Repositories - [Data-PASS][12] - [Dryad][13] - [Figshare][14] - [OAD][15] (Open Access Data Repositories) - [OSF][16] - Nature Scientific Data, recommended [repositories][17] ## Reporting Guidelines ## - See the [Open Science Literature][18] for research on the effectiveness of reporting guidelines. Our recommended best practice is to include items deemed essential into the article submission process. - See the [Equator Network][19] for a large, searchable collection of reporting guidelines. ### Community Created Guidelines ### - [CONSORT][20] (Consolidated Standards of Reporting Trials) - For meta-analysis: [PRISMA][21] or [AMSTAR][22] - [NIH Reporting Guidelines By Organization][23] - Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups [COREQ][24] - STrengthening the Reporting of OBservational studies in Epidemiology ([STROBE][25]) - An Updated List of Essential Items for Reporting Diagnostic Accuracy Studies ([STARD][26]) - [Experimental design and analysis and their reporting: new guidance for publication in BJP][27] - [ARRIVE][28] (Animal Research: Reporting of In Vivo Experiments) - [TIDieR-PHP: a reporting guideline for population health and policy interventions][29] - [Standardization in Metabolomics Experiments][30] - Minimum Information for reporting: - Proteomics Experiments ([MIAPE][31]) - Genotyping Experiments ([MIGen][32]) - Flow Cytometry Experiments ([MIFlowCyt][33]) - Minimal Information About T cell Assays ([MIATA][34] project) - Quantitative Real-Time PCR Experiments ([MIQE][35]) - RNAi Experiment ([MIARE][36]) - [BRISQ][37] (Biospecimen reporting for improved study quality) - [Citation of Bioresources in Journal Articles (CoBRA)][38] ### Journal and Society Created Guidelines ### - From Cell Press: Structured, Transparent, Accessible Reporting (STAR) guidelines from Cell Press: [Website][39], [Methods Guide][40], and the [Key Resources Table][41] - American Psychological Association: Journal Article Reporting Standards ([JARS][42] 2018 Update; [JARS][43] 2008) - BioMedCentral's [Minimum Standards of Reporting Checklist][44] - [Guidelines for Reporting Quantitative Methods and Results in Primary Research][45] at Language Learning - [Reporting Guidelines for Experimental Research: A Report from the Experimental Research Section Standards Committee][46] of the American Political Science Association - Association for Psycholgical Science's [reporting guidelines][47] - Journal of Experimental Social Psychology [reporting guidelines][48] - Journal of Neuroscience [Policy on Reporting Experimental Design and Statistical Analysis][49] - [Reporting Checklist for Life Sciences Articles][50] at Nature Publishing Group - [eLife's Transparent Reporting form][51] - Biophysical Journal's [Guidelines for the Reproducibility of Biophysics Research][52] - [A checklist for writing up research reports][53] in the journal Addiction - PLOS One's [Reporting Guidelines for Specific Study Types][54] ## Registries ## - [American Economics Association RCT Registry][55] - [ClinicalTrials.gov][56] - [EGAP][57] (Evidence in Governance and Politics) - [OSF][58] - [PROSPERO][59] International prospective register of systematic reviews - [Research Registry][60] - [RIDIE][61] (Registry for International Development Impact Evaluations) - [Registry of Efficacy and Effectiveness Studies][62] in education ## Editorials announcing TOP ## - [Association for Psychological Society][63] - [Ecology Letters][64] - [Experimental Psychology][65] - [International Journal of Primatology][66] - Journal of Research in Personality ([preprint][67]) - [Nature][68] - [Royal Society Open Science][69] - [Science][70] - [Survey Research Methods][71] ## Examples of author guidelines using TOP ## - [Science][72] | AAAS - [Brain and Behavior][73] | Wiley - [Collabra][74] | UC Press - [Cultural Diversity & Ethnic Minority Psychology][75] | APA - [Journal of Cognition][76] | Ubiquity Press - [Nicotine & Tobacco Research][77] | Oxford University Press - [Evolution and Human Behavior][78] | Elsevier ---------- ## Disclosure Statements ## ### Data, Materials, and Code Disclosures ### | 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]. | ---------- Other examples of data disclosure statements - [The Impact on Authors and Editors of Introducing Data Availability Statements at Nature Journals][79] - [Nature Research][80] - [American Geophysical Union][81] ---------- ### Preregistration of Study or Analysis Plan Disclosure ### | 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. | ---------- ## Persistent Identifiers ## - [ARK][82] (Archival Resource Key) - [DOI][83] (Digitial Object Identifier) - [IGSN][84] (International Geo Sample Number) - [RRIDs][85] (Research Resource Identifiers) - [PURL][86] (Persistent Uniform Resource Locators) Please contact us if you would like to add to this list: contact@cos.io [1]: https://osf.io/hcnme/ [2]: https://osf.io/87v93/ [3]: https://osf.io/55eu7/ [4]: https://osf.io/y8aqx/ [5]: https://topfactor.org/journals?factor=Data%20Transparency&perPage=50 [6]: https://topfactor.org/journals?factor=Analysis%20Code%20Transparency&perPage=50 [7]: http://www.nejm.org/doi/full/10.1056/NEJMsb1616595 [8]: https://www.ipc.on.ca/resource/de-identification-guidelines-for-structured-data/ [9]: http://ukanon.net/ukan-resources/ukan-decision-making-framework/ [10]: https://copdessdirectory.osf.io/ [11]: http://www.re3data.org/ [12]: http://www.data-pass.org/ [13]: http://datadryad.org/ [14]: https://figshare.com/ [15]: http://oad.simmons.edu/oadwiki/Data_repositories [16]: https://osf.io [17]: http://www.nature.com/sdata/policies/repositories [18]: https://osf.io/kgnva/wiki/Open%20Science%20Literature/ [19]: http://www.equator-network.org/ [20]: http://www.consort-statement.org/ [21]: http://prisma-statement.org/PRISMAStatement/Checklist.aspx [22]: https://amstar.ca/Amstar_Checklist.php [23]: https://www.nlm.nih.gov/services/research_report_guide.html [24]: https://academic.oup.com/intqhc/article/19/6/349/1791966/Consolidated-criteria-for-reporting-qualitative [25]: https://www.strobe-statement.org/index.php?id=strobe-home [26]: http://www.stard-statement.org/ [27]: http://onlinelibrary.wiley.com/doi/10.1111/bph.12856/full [28]: https://www.nc3rs.org.uk/arrive-guidelines [29]: https://www.bmj.com/content/361/bmj.k1079 [30]: http://metabolomicssociety.org/index.php/resources/metabolomics-standards [31]: http://www.psidev.info/index.php?q=node/91 [32]: https://osf.io/4nryf/ [33]: https://osf.io/edwhp/ [34]: http://miataproject.org/ [35]: https://osf.io/kjqtf/ [36]: http://miare.sourceforge.net/HomePage [37]: http://onlinelibrary.wiley.com/doi/10.1002/cncy.20147/abstract [38]: http://www.equator-network.org/reporting-guidelines/cobra/ [39]: http://www.cell.com/star-methods [40]: http://www.cell.com/pb-assets/journals/research/cell/methods/Methods%20Guide_general.pdf [41]: https://www.star-methods.com/key-resources/webform/els_key_resources_table [42]: http://www.apa.org/pubs/journals/releases/amp-amp0000191.pdf [43]: http://www.apastyle.org/manual/related/apa-jars-2008.pdf [44]: http://resource-cms.springer.com/springer-cms/rest/v1/content/7117202/data/v2/Minimum+standards+of+reporting+checklist [45]: http://onlinelibrary.wiley.com/doi/10.1111/lang.12104/full [46]: 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 [47]: http://www.psychologicalscience.org/publications/psychological_science/ps-submissions#DISC [48]: https://www.journals.elsevier.com/journal-of-experimental-social-psychology/news/jesp-editorial-guidelines/ [49]: http://www.jneurosci.org/content/general-information#policies [50]: https://www.nature.com/authors/policies/ReportingSummary-flat.pdf [51]: https://submit.elifesciences.org/html/transparent_reporting.pdf [52]: http://www.cell.com/pb/assets/raw/journals/society/biophysj/PDFs/reproducibility-guidelines.pdf [53]: http://onlinelibrary.wiley.com/doi/10.1046/j.1360-0443.2000.951217594.x/epdf [54]: http://journals.plos.org/plosone/s/submission-guidelines#loc-guidelines-for-specific-study-types [55]: https://www.socialscienceregistry.org/ [56]: https://clinicaltrials.gov/ [57]: http://egap.org/ [58]: https://osf.io [59]: https://www.crd.york.ac.uk/prospero/ [60]: http://www.researchregistry.com/ [61]: http://ridie.3ieimpact.org/ [62]: https://sreereg.icpsr.umich.edu/ [63]: http://www.psychologicalscience.org/publications/observer/obsonline/aps-commits-to-promoting-transparent-science.html#.WG-9ObYrJBw [64]: http://onlinelibrary.wiley.com/doi/10.1111/ele.12611/full [65]: http://econtent.hogrefe.com/doi/10.1027/1618-3169/a000317 [66]: http://link.springer.com/article/10.1007/s10764-016-9925-x [67]: https://osf.io/preprints/psyarxiv/ay59f [68]: http://www.nature.com/news/announcement-transparency-upgrade-for-nature-journals-1.21627 [69]: http://rsos.royalsocietypublishing.org/content/royopensci/4/1/160979.full.pdf [70]: http://science.sciencemag.org/content/352/6290/1147 [71]: https://ojs.ub.uni-konstanz.de/srm/article/view/6256/5679 [72]: http://science.sciencemag.org/content/sci/suppl/2016/06/01/352.6290.1147.DC1/aag2359-editorial.McNutt.SM.pdf [73]: http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%292157-9032/homepage/ForAuthors.html [74]: http://www.collabra.org/about/editorialpolicies/ [75]: http://www.apa.org/pubs/journals/cdp/?tab=4 [76]: https://www.journalofcognition.org/about/editorialpolicies/ [77]: https://www.oxfordjournals.org/our_journals/nictob/for_authors/ntr%20top%20guidelines.pdf [78]: https://www.elsevier.com/journals/evolution-and-human-behavior/1090-5138/transparency-and-openness [79]: http://www.ijdc.net/article/view/614 [80]: http://www.nature.com/authors/policies/data/data-availability-statements-data-citations.pdf [81]: http://publications.agu.org/author-resource-center/publication-policies/data-policy/data-policy-faq/ [82]: https://confluence.ucop.edu/display/Curation/ARK [83]: https://www.doi.org/ [84]: http://www.geosamples.org/ [85]: https://scicrunch.org/resources [86]: https://www.isoc.org/inet96/proceedings/a4/a4_1.htm