Difference between revisions of "Pharmacoracle"
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The Pharmacoracle contains OWL ontologies that are based on CPIC recommendations provided by PharmGKB, and which have been further curated to fit the needs of the Department of Pharmacology at Oslo University Hospital. | The Pharmacoracle contains OWL ontologies that are based on CPIC recommendations provided by PharmGKB, and which have been further curated to fit the needs of the Department of Pharmacology at Oslo University Hospital. | ||
| − | Queries to Pharmacoracle can be performed in the Manchester syntax. | + | Queries to Pharmacoracle can be performed in the Manchester syntax. For each query we add a code word to indicate the relationship between our query and the desired answer (cf. the DL Query tab in the desktop version of Stanford's Protégé) |
| + | |||
| + | {| class="wikitable" | ||
| + | |- | ||
| + | ! Code word !! Relationship | ||
| + | |- | ||
| + | | SubClasses || Get elements that contain the query (but not equivalent) | ||
| + | |- | ||
| + | | DirectSubClasses || Get only the SubClasses that are closest to the query | ||
| + | |- | ||
| + | | EquivalentClasses || Get only elements equivalent to the query | ||
| + | |- | ||
| + | | SuperClasses || Get elements that contain parts of the query (but not the entire query and not equivalent) | ||
| + | |- | ||
| + | | DirectSuperClasses || Get only the SuperClasses that are closest to the query | ||
| + | |} | ||
===Examples of use=== | ===Examples of use=== | ||
Find the PGx alleles that contain the variant snpC>T at chr6:18139228 | Find the PGx alleles that contain the variant snpC>T at chr6:18139228 | ||
| − | <pre>curl https://www.pgx.no/api/pharmacoracle -d " | + | <pre>curl https://www.pgx.no/api/pharmacoracle -d "query=SubClasses:snpCtoT_at some chr6_18139228"</pre> |
| + | |||
| + | Find the PGx allele that is identical to the variants snpC>T at chr6:18139228 and snpT>C at chr6:18130918 | ||
| + | <pre>curl https://www.pgx.no/api/pharmacoracle -d "query=EquivalentClasses:(snpCtoT_at some chr6_18139228) and (snpTtoC_at some chr6_18130918)"</pre> | ||
| + | |||
| + | Find the PGx alleles that contain either snpC>T at chr6:18139228 or snpT>C at chr6:18130918 | ||
| + | <pre>curl https://www.pgx.no/api/pharmacoracle -d "query=DirectSuperClasses:(snpCtoT_at some chr6_18139228) and (snpTtoC_at some chr6_18130918)"</pre> | ||
Find the Azathioprine TPMT functional status of the TPMT*3B allele: | Find the Azathioprine TPMT functional status of the TPMT*3B allele: | ||
<pre>curl https://www.pgx.no/api/pharmacoracle -d "drugs=azathioprine&query=SuperClasses:has_haplotype some TPMTstar3B"</pre> | <pre>curl https://www.pgx.no/api/pharmacoracle -d "drugs=azathioprine&query=SuperClasses:has_haplotype some TPMTstar3B"</pre> | ||
Revision as of 14:04, 13 July 2018
Pharmacoracle - a REST API based on the OWLAPI
The Pharmacoracle contains OWL ontologies that are based on CPIC recommendations provided by PharmGKB, and which have been further curated to fit the needs of the Department of Pharmacology at Oslo University Hospital.
Queries to Pharmacoracle can be performed in the Manchester syntax. For each query we add a code word to indicate the relationship between our query and the desired answer (cf. the DL Query tab in the desktop version of Stanford's Protégé)
| Code word | Relationship |
|---|---|
| SubClasses | Get elements that contain the query (but not equivalent) |
| DirectSubClasses | Get only the SubClasses that are closest to the query |
| EquivalentClasses | Get only elements equivalent to the query |
| SuperClasses | Get elements that contain parts of the query (but not the entire query and not equivalent) |
| DirectSuperClasses | Get only the SuperClasses that are closest to the query |
Examples of use
Find the PGx alleles that contain the variant snpC>T at chr6:18139228
curl https://www.pgx.no/api/pharmacoracle -d "query=SubClasses:snpCtoT_at some chr6_18139228"
Find the PGx allele that is identical to the variants snpC>T at chr6:18139228 and snpT>C at chr6:18130918
curl https://www.pgx.no/api/pharmacoracle -d "query=EquivalentClasses:(snpCtoT_at some chr6_18139228) and (snpTtoC_at some chr6_18130918)"
Find the PGx alleles that contain either snpC>T at chr6:18139228 or snpT>C at chr6:18130918
curl https://www.pgx.no/api/pharmacoracle -d "query=DirectSuperClasses:(snpCtoT_at some chr6_18139228) and (snpTtoC_at some chr6_18130918)"
Find the Azathioprine TPMT functional status of the TPMT*3B allele:
curl https://www.pgx.no/api/pharmacoracle -d "drugs=azathioprine&query=SuperClasses:has_haplotype some TPMTstar3B"
