Table 4 Queries making use of external resources. Queries are available at https://smartprotocols.github.io/ queries/

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