SMART Protocols Ontology: Document Module: Description back to ToC

The document module of SMART Protocols is compatible with other formalisms in order to facilitate interoperability. The class iao:information content entity and its subclasses iao:document, iao:document part, iao:textual entity and iao:data set were imported from the Information Artifact Ontology (IAO). This module also represents metadata such as sp:title of the protocol, sp:purpose of the protocol, sp:application of the protocol, sp:reagent list, sp:equipment and supplies list, sp:manufacturer, sp:catalog number and sp:storage conditions. Our running example, "Extraction of total RNA from fresh/frozen tissue (FT)", is illustrated as an SMART Protocol. The application of the SMART Protocols-Document module is presented in (Table 2) and (Figure 1); metadata elements are organized in SP-Document as "information content entities".

Table 2: Metadata represented in SP-Document
Bibliographic metadata
sp:title of the protocol "Extraction of total RNA from fresh/frozen tissue (FT)"
sp:author name "Kim M. Linton"
"Yvonne Hey"
"Sian Dibben"
"Crispin J. Miller"
"Anthony J. Freemont"
"John A. Radford"
"Stuart D. Pepper"
sp:protocol identifier "DOI:10.2144/000113260"
Descriptive metadata
sp:application of the protocol "Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays"
sp:provenance of the protocol "The extraction method (steps 2 - 21) is taken from the method supplied with TRIzol reagent (Invitrogen, Paisley, UK)."
Metadata about the input
sp:specimen name "tumor tissue"
Metadata about the materials
sp:reagent name "TRIzol"
"Chloroform"
"Ethyl alcohol"
"Isopropyl alcohol"
sp:manufacturer name "Invitrogen"
"Sigma-Aldrich"
"Sigma-Aldrich"
"Sigma-Aldrich"
sp:equipment or supplies name "Tissue storage container"
"Homogenizer blades"
"Forceps"
"Scalpel"
"Scalpel holder"
Figure 1: SP-Document module. This diagram illustrates the metadata elements described in table 2. The classes, properties and individuals are represented by their respective labels.