Table 4 Queries making use of external resources. Queries are available at https://smartprotocols.github.io/ queries/
From: Using semantics for representing experimental protocols
| Competency question | Was the question answered? | Other Information Resources | SPARQL | Comment |
|---|---|---|---|---|
| Retrieve all the protocols that use mouse as a sample | Yes. Could there be a short description about the organism and also, mouse is too specific, I may also be interested in rats and other rodents. | The DBPEDIA property dbo:order of includes individuals that belong to the order rodents, e.g. rats, hamsters, squirrels, etc. DBPEDIA also has dbo:abstract, this property allows us to retrieve information about rodents. | Query#1. Retrieve all the protocols with samples that belong to the Rodent order and also retrieve information for these samples | Additional information was useful but basic |
| Retrieve all the reagents used in the protocols | Yes. It is also useful to know where to buy these products. | PubChem has a list of vendors for some reagents. For instance, for sodium chloride it has more than ten vendors. Also, we are resolving the entities against the websites of the manufacturers. | Query #4.Retrieve all the reagents along with the different web sites to buy them and all the different manufacturers registered for every reagent | Additional information was useful |
| Retrieve the protocols in which Bromophenol blue is used | Yes. Could the applications for the reagent be included in the answer? | ChEBI is an external resource that has the applications for some reagents. | Query #23 Retrieve the protocols in which Bromophenol blue is used and tell me about the application of Bromophenol blue | Additional information was useful |
| Retrieve the steps that have CAUTIONS as alert messages from the protocol “X” | Yes. I would also like to have the diseases caused by this reagent | In this case we are making use of Bioportal and SNOMED (causative_agent_of). | Query #14. Retrieve all the diseases caused by the reagents in the protocol “Extraction of total RNA from fresh/frozen tissue (FT)” | Additional information was useful |