#Exercise 4 Build a SPARQL query to find: * **Proteins with a lipidation site having a variant on it** ## Procedure * Select query sample 99 (NXQ_00099) The query shows a single constraint on the PTM annotation: its start position. We need to add a second constraint on it to select lipidation sites only. So we first have to make the PTM annotation an explicit variable (i.e. ?ptm): * Remove the line: ``` ?iso :ptm /:start ?varpos. ``` * Add the lines: ``` ?iso :ptm ?ptm . ?ptm :start ?varpos . ``` The modified version is equivalent to the original one, except that now we have a hook (the ?ptm variable) to set the PTM type * In the Help page, search for *Isoform* (CTRL-F) * Click on the Isoform link in the list of classes (left panel), then search *:ptm* in the page. You’ll see the list of PTM types in the right panel * Copy the :LipidationSite and add the following line to the query: ``` ?ptm a :LipidationSite . ``` * Run the query * Check the result you get by clicking one of the (neXtProt link) in the result: * see feature viewer in of Sequence TAB� * check that you find at least one variant at the position of a lipidation site **Optionally** To get non transmembrane proteins with a variant on a lipidation site: add the line: ``` filter not exists {?iso :transmembraneRegion ?_} ```
#Exercise 4
Build a SPARQL query to find:
- Proteins with a lipidation site having a variant on it
Procedure
- Select query sample 99 (NXQ_00099)
The query shows a single constraint on the PTM annotation: its start position. We need to add a second constraint on it to select lipidation sites only. So we first have to make the PTM annotation an explicit variable (i.e. ?ptm):
- Remove the line:
?iso :ptm /:start ?varpos.
- Add the lines:
?iso :ptm ?ptm .
?ptm :start ?varpos .
The modified version is equivalent to the original one, except that now we have a hook (the ?ptm variable) to set the PTM type
-
In the Help page, search for Isoform (CTRL-F)
-
Click on the Isoform link in the list of classes (left panel), then search :ptm in the page. You’ll see the list of PTM types in the right panel
-
Copy the :LipidationSite and add the following line to the query:
?ptm a :LipidationSite .
-
Run the query
-
Check the result you get by clicking one of the (neXtProt link) in the result:
- see feature viewer in of Sequence TAB�
- check that you find at least one variant at the position of a lipidation site
Optionally To get non transmembrane proteins with a variant on a lipidation site: add the line:
filter not exists {?iso :transmembraneRegion ?_}