A guideline for reporting experimental protocols in life sciences

Authors : Olga Giraldo​, Alexander Garcia, Oscar Corcho

Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements.

This article presents a guideline for describing key content for reporting experimental protocols in the domain of life sciences, together with the methodology followed in order to develop such guideline.

As part of our work, we propose a checklist that contains 17 data elements that we consider fundamental to facilitate the execution of the protocol. These data elements are formally described in the SMART Protocols ontology.

By providing guidance for the key content to be reported, we aim (1) to make it easier for authors to report experimental protocols with necessary and sufficient information that allow others to reproduce an experiment, (2) to promote consistency across laboratories by delivering an adaptable set of data elements, and (3) to make it easier for reviewers and editors to measure the quality of submitted manuscripts against an established criteria.

Our checklist focuses on the content, what should be included. Rather than advocating a specific format for protocols in life sciences, the checklist includes a full description of the key data elements that facilitate the execution of the protocol.

URL : A guideline for reporting experimental protocols in life sciences

DOI : https://doi.org/10.7717/peerj.4795

Biotea: semantics for Pubmed Central

Authors : Alexander Garcia​, Federico Lopez, Leyla Garcia, Olga Giraldo, Victor Bucheli, Michel Dumontier

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies.

In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology.

We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language.

We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.

URL : Biotea: semantics for Pubmed Central

DOI : https://doi.org/10.7717/peerj.4201