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Updated HumanCyc and Drugbank cleaner classes; minor polish in the in…
…dex and tests.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,27 +1,65 @@ | ||
| package cpath.cleaner; | ||
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| import cpath.service.api.Cleaner; | ||
| import org.biopax.paxtools.io.SimpleIOHandler; | ||
| import org.biopax.paxtools.model.BioPAXLevel; | ||
| import org.biopax.paxtools.model.Model; | ||
| import org.biopax.paxtools.model.level3.Xref; | ||
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| import java.io.InputStream; | ||
| import java.io.OutputStream; | ||
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| public class DrugbankCleaner implements Cleaner { | ||
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| /* | ||
| * drugbank biopax data uses the following values in xref.db properties, | ||
| * which biopax validator reports as "Unknown"; | ||
| * so we need to replace with the corresponding standard prefix/name from bioregistry.io (or identifiers.org): | ||
| GenBank Gene Database -> "genbank" | ||
| GenBank Protein Database -> "genbank" (numeric IDs, not like it's in ncbiprotein) | ||
| Therapeutic Targets Database -> | ||
| Guide to Pharmacology -> | ||
| HUGO Gene Nomenclature Committee (HGNC) -> "hgnc.symbol" (or "HGNC Symbol") | ||
| IUPHAR -> | ||
| Drugs Product Database (DPD) -> | ||
| */ | ||
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| * drugbank biopax data uses the following weird values in xref.db properties | ||
| * (which biopax validator reports as "Unknown"; so we need to map to standard names from bioregistry.io) | ||
| * - GenBank Gene Database -> "genbank" | ||
| * - GenBank Protein Database -> "genbank" (numeric IDs, not like it's in ncbiprotein) | ||
| * - Therapeutic Targets Database -> ttd.drug | ||
| * - HUGO Gene Nomenclature Committee (HGNC) -> "hgnc" (e.g. HGNC:1111) | ||
| * - Drugs Product Database (DPD) -> cdpd | ||
| * - IUPHAR -> iuphar.family or iuphar.ligand or iuphar.receptor? | ||
| * - Guide to Pharmacology -> likely same as IUPHAR (but which of the three collections?) | ||
| */ | ||
| @Override | ||
| public void clean(InputStream data, OutputStream cleanedData) { | ||
| //TODO: implement | ||
| try | ||
| { | ||
| SimpleIOHandler simpleReader = new SimpleIOHandler(BioPAXLevel.L3); | ||
| Model model = simpleReader.convertFromOWL(data); | ||
| cleanXrefDBName(model); | ||
| simpleReader.convertToOWL(model, cleanedData); | ||
| } catch (Exception e) { | ||
| throw new RuntimeException("HumanCycCleaner failed", e); | ||
| } | ||
| } | ||
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| protected void cleanXrefDBName(Model model) | ||
| { | ||
| for (Xref xr : model.getObjects(Xref.class)) | ||
| { | ||
| if(xr.getDb() == null) { | ||
| //skip | ||
| } | ||
| else if(xr.getDb().equalsIgnoreCase("GenBank Gene Database")) { | ||
| xr.setDb("genbank"); | ||
| } | ||
| else if(xr.getDb().equalsIgnoreCase("GenBank Protein Database")) { | ||
| xr.setDb("genbank"); | ||
| } | ||
| else if(xr.getDb().equalsIgnoreCase("Therapeutic Targets Database")) { | ||
| xr.setDb("ttd.drug"); | ||
| xr.addComment("Therapeutic Targets Database"); | ||
| } | ||
| else if(xr.getDb().equalsIgnoreCase("HUGO Gene Nomenclature Committee (HGNC)")) { //HGNC:1234 ids | ||
| xr.setDb("hgnc"); | ||
| } | ||
| else if(xr.getDb().equalsIgnoreCase("Drugs Product Database (DPD)")) { | ||
| xr.setDb("cdpd"); | ||
| xr.addComment("Drugs Product Database (DPD)"); | ||
| } | ||
| } | ||
| } | ||
|
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| } |
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