Using semantics for representing experimental protocols

Abstract

BackgroundAn experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols.ResultsIn this paper we present “SMART Protocols ontology”, an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample.ConclusionImproving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/.

A guideline for reporting experimental protocols in life sciences

“…During our development process, we considered the SMART Protocols ontology ( Giraldo et al, 2017 ); it reuses terminology from OBI, IAO, EXACT, ChEBI, NCBI taxonomy, and other ontologies. Our metadata elements have been mapped to the SMART Protocols ontology; the metadata elements in our guideline could also be mapped to resources on the web such as PubChem ( Kim et al, 2016 ) ( Wang et al, 2017 ) and the Taxonomy database from UniProt ( UniProt, 2017 ).…”

“…Experimental protocols are fundamental information structures that support the description of the processes by means of which results are generated in experimental research ( Giraldo et al, 2017 ; Freedman, Venugopalan & Wisman, 2017 ). Experimental protocols, often as part of “Materials and Methods” in scientific publications, are central for reproducibility; they should include all the necessary information for obtaining consistent results ( Casadevall & Fang, 2010 ; Festing & Altman, 2002 ).…”

“…In a similar manner, The Minimum Information about a Cellular Assay (MIACA) ( MIACA, 2017 ), The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) ( Lee et al, 2008 ) and many other “minimal information” efforts deliver minimal data elements describing specific types of experiments. Soldatova et al (2008) and Soldatova et al (2014) proposes the EXACT ontology for representing experimental actions in experimental protocols; similarly, Giraldo et al (2017) proposes the S e MA ntic R epresen T ation of Protocols ontology (henceforth SMART Protocols Ontology) an ontology for reporting experimental protocols and the corresponding workflows. These approaches are not minimal; they aim to be comprehensive in the description of the workflow, parameters, sample, instruments, reagents, hints, troubleshooting, and all the data elements that help to reproduce an experiment and describe experimental actions.…”

Peer Review #2 of "A guideline for reporting experimental protocols in life sciences (v0.1)"

“…Experimental protocols are fundamental information structures that support the description of the processes by means of which results are generated in experimental research (Giraldo et al, 2017;Freedman et al, 2017). Experimental protocols, often as part of "Materials and Methods" in scientific publications, are central for reproducibility; they should include all the necessary information for obtaining consistent results (Casadevall and Fang, 2010;Festing and Altman, 2002).…”

“…In a similar manner, The Minimum Information about a Cellular Assay (MIACA) (MIACA, 2017), The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) (Lee et al, 2008) and many other "minimal information" efforts deliver minimal data elements describing specific types of experiments. Soldatova et al, (Soldatova et al, 2008(Soldatova et al, , 2014 proposes the EXACT ontology for representing experimental actions in experimental protocols; similarly, Giraldo et al, (Giraldo et al, 2017) proposes the SeMAntic RepresenTation of Protocols ontology (henceforth SMART Protocols Ontology) an ontology for reporting experimental protocols and the corresponding workflows. These approaches are not minimal, they aim to be comprehensive in the description of the workflow, parameters, sample, instruments, reagents, hints, troubleshooting, and all the data elements that help to reproduce an experiment and describe experimental actions.…”