An 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, etc. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers see 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 criterion with respect to the syntactic structure and the semantics for representing experimental protocols. In this project we present “SMART Protocols”, a semantic and NLP-based infrastructure for representing experimental protocols. Our contribution is twofold; SMART Protocols delivers a semantic layer that represents the knowledge encoded in experimental protocols; our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. It also builds the groundwork for making use of such semantics within a NLP framework. We are reporting on the semantic and NLP components, namely the SMART Protocols (SP) Ontology, the Sample Instrument Reagent Objective (SIRO) model, the linked data representation for protocols and, the text mining integrative architecture built upon GATE. The SIRO model defines an extended layer of metadata for experimental protocols; SIRO is also a Minimal Information (MI) model conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine.

Ontology Files
Sample queries
Checklist 0.2
Checklist 1.0
Protocols as RDF
SPARQL Endpoint
F1 score, Precision and Recall for the Gold Standard Corpus