SPARQL property path for identifying downstream targets of a directed interaction

[Matt Karikomi]

Hi,

First, I just want to say thanks for creating the wp RDF resource.  I think you have done a really  great job balancing the vocabulary of WP in terms of usability and level of detail!

I am attempting to get all "(ancestor,descendent)" pairs where "ancestor" is a source and "descendent" is a target of some arbitrary sequence of directed interactions.  Here is an example using WP3655 (the simplest one I could find):

Query 1:

```

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?pathway ?src ?tgt

WHERE {

   ?pathway a wp:Pathway .

   ?interaction dcterms:isPartOf ?pathway .

   ?interaction a wp:DirectedInteraction .

   ?interaction wp:source ?src .

   ?interaction wp:target ?tgt .

   ?src (wp:source/^wp:target)+ ?tgt .

   ?pathway dcterms:identifier "WP3655"^^xsd:string .

}

LIMIT 1000

```

From a brief inspection of WP 3655, Query 1 should return at least the following pair:

(<http://identifiers.org/ensembl/ENSG00000137203>,

<http://identifiers.org/ensembl/ENSG00000137962>)

Representing the path:

<http://identifiers.org/ensembl/ENSG00000137203> ->

<http://identifiers.org/ensembl/ENSG00000117595> ->

http://identifiers.org/ensembl/ENSG00000137962

However, I get no pairs from Query 1.

*Can this be refactored in some way?*

Best, Matt

[Matt Karikomi]

Ok I think there was a bug in the original query.

Replace original with the following property path:

"  ?src (^wp:source/wp:target)+ ?tgt . "

Which translates to:

("find ?directedInteraction that ?src is the source of" ->

"find ?tgt that is the target of ?directedInteraction")+

Query 2:

```

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?pathway ?src ?tgt

WHERE {

   ?pathway a wp:Pathway .

   ?interaction dcterms:isPartOf ?pathway .

   ?interaction a wp:DirectedInteraction .

   ?interaction wp:source ?src .

   ?interaction wp:target ?tgt .

   ?src (^wp:source/wp:target)+ ?tgt .

   ?pathway dcterms:identifier "WP3655"^^xsd:string .

    FILTER(?src != ?tgt)

}

LIMIT 10

```

I've also included "FILTER(?src != ?tgt)" in an attempt to include only simple paths (no loops).

Unfortunately even with only "LIMIT 10" records I'm getting a response that suggests something weird is going on:

"Virtuoso 42000 Error TN...: Exceeded 1000000000 bytes in transitive temp memory. use t_distinct, t_max or more T_MAX_memory options to limit the search or increase the pool"

Thanks, Matt