Dataset Information

Minimum information required for a DMET experiment reporting.

ABSTRACT: To provide pharmacogenomics reporting guidelines, the information and tools required for reporting to public omic databases.For effective DMET data interpretation, sharing, interoperability, reproducibility and reporting, we propose the Minimum Information required for a DMET Experiment (MIDE) reporting.MIDE provides reporting guidelines and describes the information required for reporting, data storage and data sharing in the form of XML.The MIDE guidelines will benefit the scientific community with pharmacogenomics experiments, including reporting pharmacogenomics data from other technology platforms, with the tools that will ease and automate the generation of such reports using the standardized MIDE XML schema, facilitating the sharing, dissemination, reanalysis of datasets through accessible and transparent pharmacogenomics data reporting.

SUBMITTER: Kumuthini J

PROVIDER: S-EPMC6123892 | biostudies-other | 2016 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Minimum information required for a DMET experiment reporting.

Kumuthini Judit J Mbiyavanga Mamana M Chimusa Emile R ER Pathak Jyotishman J Somervuo Panu P Van Schaik Ron Hn RH Dolzan Vita V Mizzi Clint C Kalideen Kusha K Ramesar Raj S RS Macek Milan M Patrinos George P GP Squassina Alessio A

Pharmacogenomics 20160822 14

<h4>Aim</h4>To provide pharmacogenomics reporting guidelines, the information and tools required for reporting to public omic databases.<h4>Material & methods</h4>For effective DMET data interpretation, sharing, interoperability, reproducibility and reporting, we propose the Minimum Information required for a DMET Experiment (MIDE) reporting.<h4>Results</h4>MIDE provides reporting guidelines and describes the information required for reporting, data storage and data sharing in the form of XML.<h ...[more]

PMID: 27548815

Similar Datasets

Project description:BACKGROUND:Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description reports. There appears to be, however, a high degree of variability in the content of these reports. Often, important details are omitted such that it is difficult to gain a sufficient understanding of the ontology, its content and method of creation. RESULTS:We propose the Minimum Information for Reporting an Ontology (MIRO) guidelines as a means to facilitate a higher degree of completeness and consistency between ontology documentation, including published papers, and ultimately a higher standard of report quality. A draft of the MIRO guidelines was circulated for public comment in the form of a questionnaire, and we subsequently collected 110 responses from ontology authors, developers, users and reviewers. We report on the feedback of this consultation, including comments on each guideline, and present our analysis on the relative importance of each MIRO information item. These results were used to update the MIRO guidelines, mainly by providing more detailed operational definitions of the individual items and assigning degrees of importance. Based on our revised version of MIRO, we conducted a review of 15 recently published ontology description reports from three important journals in the Semantic Web and Biomedical domain and analysed them for compliance with the MIRO guidelines. We found that only 41.38% of the information items were covered by the majority of the papers (and deemed important by the survey respondents) and a large number of important items are not covered at all, like those related to testing and versioning policies. CONCLUSIONS:We believe that the community-reviewed MIRO guidelines can contribute to improving significantly the quality of ontology description reports and other documentation, in particular by increasing consistent reporting of important ontology features that are otherwise often neglected.

Dataset Information

Minimum information required for a DMET experiment reporting.

Publications

Minimum information required for a DMET experiment reporting.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets