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".
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" |