The workflow module delivers an extensible representation describing the sequence of activities in an experimental protocol. Our running example (see Figure 1 and Table 2), includes 3 laboratory procedures “Protocol overview” (indicating how to process the sample), “Prior to RNA extraction: cleaning process of equipment” and the “RNA extraction”. The first column in Table 2 includes the procedures from our running example. The second column includes subprocedures or instructions for each procedure. The “Protocol overview” (sp:lab procedure 1) has experimental input (sp:has experimental input) a tumor tissue (nci:tumor tissue) and has output (sp:has output) a homogenized tissue (sp:homogenized tissue). The laboratory procedure 1 includes 3 subprocedures (or steps/instructions) indicating how to manipulate and prepare the sample: sp:lab subprocedure1.1, sp:lab subprocedure 1.2 and sp:lab subprocedure 1.3. The order in which these subprocedures should be executed is represented by the BFO property “is preceded by” and “precedes”. The second lab procedure “Prior to RNA extraction: cleaning process of equipment" is a recipe describing how to clean the equipment to be used during the RNA extraction protocol. This recipe includes 3 steps, sp:lab subprocedure2.1, sp:lab subprocedure 2.2 and sp:lab subprocedure 2.3. The last procedure “RNA extraction" has as input the homogenized tissue (output from the lab procedure 1) and as output the chebi:RNA. It includes 20 subprocedures, these are not represented in the (Figure 1) due to lack of space. We propose the classes sp:laboratory procedure and sp:laboratory subprocedure for the representation of procedures and subprocedures. The property, sp:has procedure, is used to represent procedures in the protocol; the property sp:has subprocedure, is used to characterize the subprocedures that are part of a given procedure. For representing “instruments”, “reagents/chemical compounds”, “organisms" and “sample/specimen” we are reusing, amongst others, NCBI organismal classification (NCBI taxon), Cell Line Ontology (CLO), BioAssay Ontology (BAO), The Experimental Factor Ontology (EFO), eagle-i resource ontology (ERO) and Chemical Entities of Biological Interest (ChEBI).
Procedure | Subprocedure |
---|---|
Protocol overview (sp:lab procedure 1) | Recover tumor tissue at the time of surgery, trim into 1-cm3 fragments, and immerse immediately in TRIzol reagent prior to freezing at -80 C. |
Thaw and weigh tissue prior to RNA extraction, working quickly. | |
Use a tissue power homogenizer (or a mortar and pestle) to homogenize tissue by hand. | |
Prior to RNA extraction: cleaning process of equipment (sp:lab procedure 2) | Autoclave or wash equipment (i.e., tissue storage container, homogenizer blades, forceps, scalpel holder) in Neutracon solution for 2–4 h. |
Rinse equipment well in 1% SDS (prepared using DEPC-treated or other nuclease-free water). | |
Rinse in 100% ethanol and leave to air-dry. | |
RNA extraction (sp:lab procedure 3) | Homogenize sample using tissue homogenizer. |
Add 0.2 mL chloroform per 1 mL TRIzol and cap tube tightly. | |
Add 0.5 mL isopropyl alcohol per 1 mL TRIzol. | |
Add 1 mL 75% ethanol per 1 mL TRIzol and vortex for 10 s. |