Use Cases

Use cases for SPARQL Builder

We here introduce some use cases for SPARQL Builder.

1. Adding full forms of abbreviated names to your data

Because abbreviations of terms such as gene names and protein names often have many variations, if your data includes abbreviations, it may be very difficult to understand what they are and to search related information using them.  Adding full forms  makes them easy for you to read, understand, and use your data.

How to do

1. select the SPARQL endpoint of the Allie database whose URI is http://data.allie.dbcls.jp/sparql

2. select “ShortForm” as a start class.

3. select “LongForm” as an end class.

4. select a path of “ShortForm”-(hasShortFormOf)->”EachPair”-(hasLongFormOf)->”LongForm”.

5. download result and join to your data. If you need, change “limit 100” to another number or delete it before downloading.

2. Adding information of proteins and binding sites to chemical data

How to do

1. select the SPARQL endpoint of the ChEMBL database whose URI is http://www.ebi.ac.uk/rdf/services/chembl/sparql

2. select “SmallMolecule” as a start class.

3. select “BindingSite” as an end class.

4. select a path of “SmallMolecule”-(hasMolecule)->”Mechanism”-(hasTarget)->”SingleProtein”->”Mechanism”-(hasTarget)->”BindingSite”.

5. download result and join to your data. If you need, change “limit 100” to another number or delete it before downloading.