Dataset Information

Guidelines for systematic reporting of sequence alignments.

ABSTRACT: Bioinformatics methods are increasingly needed and used to analyze and interpret extensive datasets many of which are produced by diverse high-throughput technologies. Unfortunately, it is quite common that published articles do not contain sufficient information to allow the reader to fully comprehend and repeat computational and other studies. Guidelines were developed for reporting studies and results from sequence alignment. Brief and concise checklist of required data items was compiled making it easy to provide necessary details. Implementation of the guidelines requires similar meticulous attitude toward details as other parts of publications. If the journal does not allow reporting full details in the main article, it can be provided in supplementary material. It is important to make the alignments available. Systematic and detailed description of bioinformatics analyses adds to the value of papers and makes it easier for the scientific community to evaluate, understand, verify, and extend the published articles and their results.

SUBMITTER: Vihinen M

PROVIDER: S-EPMC6994045 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Guidelines for systematic reporting of sequence alignments.

Vihinen Mauno M

Biology methods & protocols 20200130 1

Bioinformatics methods are increasingly needed and used to analyze and interpret extensive datasets many of which are produced by diverse high-throughput technologies. Unfortunately, it is quite common that published articles do not contain sufficient information to allow the reader to fully comprehend and repeat computational and other studies. Guidelines were developed for reporting studies and results from sequence alignment. Brief and concise checklist of required data items was compiled mak ...[more]

PMID: 32161811

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Project description:ObjectiveTo assess whether the completeness of reporting of health research is related to journals' endorsement of reporting guidelines.DesignSystematic review.Data sourcesReporting guidelines from a published systematic review and the EQUATOR Network (October 2011). Studies assessing the completeness of reporting by using an included reporting guideline (termed "evaluations") (1990 to October 2011; addendum searches in January 2012) from searches of either Medline, Embase, and the Cochrane Methodology Register or Scopus, depending on reporting guideline name.Study selectionEnglish language reporting guidelines that provided explicit guidance for reporting, described the guidance development process, and indicated use of a consensus development process were included. The CONSORT statement was excluded, as evaluations of adherence to CONSORT had previously been reviewed. English or French language evaluations of included reporting guidelines were eligible if they assessed the completeness of reporting of studies as a primary intent and those included studies enabled the comparisons of interest (that is, after versus before journal endorsement and/or endorsing versus non-endorsing journals).Data extractionPotentially eligible evaluations of included guidelines were screened initially by title and abstract and then as full text reports. If eligibility was unclear, authors of evaluations were contacted; journals' websites were consulted for endorsement information where needed. The completeness of reporting of reporting guidelines was analyzed in relation to endorsement by item and, where consistent with the authors' analysis, a mean summed score.Results101 reporting guidelines were included. Of 15,249 records retrieved from the search for evaluations, 26 evaluations that assessed completeness of reporting in relation to endorsement for nine reporting guidelines were identified. Of those, 13 evaluations assessing seven reporting guidelines (BMJ economic checklist, CONSORT for harms, PRISMA, QUOROM, STARD, STRICTA, and STROBE) could be analyzed. Reporting guideline items were assessed by few evaluations.ConclusionsThe completeness of reporting of only nine of 101 health research reporting guidelines (excluding CONSORT) has been evaluated in relation to journals' endorsement. Items from seven reporting guidelines were quantitatively analyzed, by few evaluations each. Insufficient evidence exists to determine the relation between journals' endorsement of reporting guidelines and the completeness of reporting of published health research reports. Journal editors and researchers should consider collaborative prospectively designed, controlled studies to provide more robust evidence.Systematic review registrationNot registered; no known register currently accepts protocols for methodology systematic reviews.

Project description:BackgroundPrevious reviews show that reporting guidelines have improved the quality of trial reports in medicine, yet existing guidelines may not be fully suited for social and psychological intervention trials.Objective/designWe conducted a two-part study that reviewed (1) reporting guidelines for and (2) the reporting quality of social and psychological intervention trials.Data sources(1) To identify reporting guidelines, we systematically searched multiple electronic databases and reporting guideline registries. (2) To identify trials, we hand-searched 40 journals with the 10 highest impact factors in clinical psychology, criminology, education, and social work. ELIGIBILITY: (1) Reporting guidelines consisted of articles introducing a checklist of reporting standards relevant to social and psychological intervention trials. (2) Trials reported randomised experiments of complex interventions with psychological, social, or health outcomes.Results(1) We identified 19 reporting guidelines that yielded 147 reporting standards relevant to social and psychological interventions. Social and behavioural science guidelines included 89 standards not found in CONSORT guidelines. However, CONSORT guidelines used more recommended techniques for development and dissemination compared to other guidelines. (2) Our review of trials (n = 239) revealed that many standards were poorly reported, such as identification as a randomised trial in titles (20% reported the information) and abstracts (55%); information about blinding (15%), sequence generation (23%), and allocation concealment (17%); and details about actual delivery of experimental (43%) and control interventions (34%), participant uptake (25%), and service environment (28%). Only 11 of 40 journals referenced reporting guidelines in "Instructions to Authors."ConclusionExisting reporting guidelines have important limitations in content, development, and/or dissemination. Important details are routinely missing from trial publications; most leading journals in social and behavioural sciences do not ask authors to follow reporting standards. Findings demonstrate a need to develop a CONSORT extension with updated standards for social and psychological intervention trials.

Project description:BackgroundReporting of health research is often inadequate and incomplete. Complete and transparent reporting is imperative to enable readers to assess the validity of research findings for use in healthcare and policy decision-making. To this end, many guidelines, aimed at improving the quality of health research reports, have been developed for reporting a variety of research types. Despite efforts, many reporting guidelines are underused. In order to increase their uptake, evidence of their effectiveness is important and will provide authors, peer reviewers and editors with an important resource for use and implementation of pertinent guidance. The objective of this study was to assess whether endorsement of reporting guidelines by journals influences the completeness of reporting of health studies.MethodsGuidelines providing a minimum set of items to guide authors in reporting a specific type of research, developed with explicit methodology, and using a consensus process will be identified from an earlier systematic review and from the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) Network's reporting guidelines library. MEDLINE, EMBASE, the Cochrane Methodology Register and Scopus will be searched for evaluations of those reporting guidelines; relevant evaluations from the recently conducted CONSORT systematic review will also be included. Single data extraction with 10% verification of study characteristics, 20% of outcomes and complete verification of aspects of study validity will be carried out. We will include evaluations of reporting guidelines that assess the completeness of reporting: (1) before and after journal endorsement, and/or (2) between endorsing and non-endorsing journals. For a given guideline, analyses will be conducted for individual and the total sum of items. When possible, standard, pooled effects with 99% confidence intervals using random effects models will be calculated.DiscussionEvidence on which guidelines have been evaluated and which are associated with improved completeness of reporting is important for various stakeholders, including editors who consider which guidelines to endorse in their journal editorial policies.

Dataset Information

Guidelines for systematic reporting of sequence alignments.

Publications

Guidelines for systematic reporting of sequence alignments.

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