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<h1>About</h1>
<p>
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.
</p>

<a href="/ontology">Ontology Files</a>
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<a href="/queries">Sample queries</a>
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<a href="/files/annex/Annex1_Checklist.pdf">Checklist 0.2</a>
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<a href="/checklist1.0">Checklist 1.0</a>
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<a href="/protocolsrdf">Protocols as RDF</a>
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<a href="http://smartprotocols.linkeddata.es/sparql" target="_blank">SPARQL Endpoint</a>
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<a href="https://smartprotocols.github.io/sp_ontology_v4.0/sp-indexV4.0.htm" target="_blank">Documentation</a>
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<a href="/gold-standard">F1 score, Precision and Recall for the Gold Standard Corpus</a>
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