Fixing a problem with annotations in the PSI OBO for PSM scores

julianu · Jul 12, 2024 · a568536 · a568536
1 parent 0be2a0d
commit a568536
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Showing 2 changed files with 22 additions and 12 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
 	<groupId>de.mpc.pia</groupId>
 	<artifactId>pia</artifactId>
-	<version>1.5.3</version>
+	<version>1.5.4</version>
 	<name>PIA - Protein Inference Algorithms</name>
 	<url>https://github.com/mpc-bioinformatics/pia</url>
 

diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/MzIdentMLFileParser.java
@@ -6,6 +6,7 @@
 import de.mpc.pia.intermediate.PeptideSpectrumMatch;
 import de.mpc.pia.intermediate.compiler.PIACompiler;
 import de.mpc.pia.modeller.score.ScoreModel;
+import de.mpc.pia.modeller.score.ScoreModelEnum;
 import de.mpc.pia.tools.MzIdentMLTools;
 import de.mpc.pia.tools.OntologyConstants;
 import de.mpc.pia.tools.obo.AbstractOBOMapper;
@@ -854,21 +855,30 @@ private ScoreModel parseOBOTermAsScore(Term oboTerm, String value) {
         ScoreModel score = null;
 
         if (oboTerm != null) {
-            // the score is in the OBO file, get the relations etc.
-            Set<Triple> tripleSet = compiler.getOBOMapper().getTriples(oboTerm, null, null);
-
-            for (Triple triple : tripleSet) {
-                if (triple.getPredicate().getName().equals(AbstractOBOMapper.OBO_IS_A) &&
-                        triple.getObject().getName().equals(OntologyConstants.SEARCH_ENGINE_PSM_SCORE.getPsiAccession())) {
-                    // subject is a "search engine specific score for PSM"
-                    double doubleValue = Double.parseDouble(value);
-                    score = new ScoreModel(doubleValue,
-                            StringEscapeUtils.unescapeJava(oboTerm.getName()),
-                            StringEscapeUtils.unescapeJava(oboTerm.getDescription()));
+            ScoreModelEnum scEnum = ScoreModelEnum.getModelByAccession(oboTerm.getName());
+            if ((scEnum != null) && !scEnum.equals(ScoreModelEnum.UNKNOWN_SCORE)) {
+                // the term is a recognized / hard coded score
+                double doubleValue = Double.parseDouble(value);
+                score = new ScoreModel(doubleValue, scEnum);
+            } else {
+                // the score is in the OBO file, try to get the relations etc.
+                Set<Triple> tripleSet = compiler.getOBOMapper().getTriples(oboTerm, null, null);
+
+                for (Triple triple : tripleSet) {
+                    if (triple.getPredicate().getName().equals(AbstractOBOMapper.OBO_IS_A) &&
+                            triple.getObject().getName().equals(OntologyConstants.SEARCH_ENGINE_PSM_SCORE.getPsiAccession())) {
+                        // subject is a "search engine specific score for PSM"
+                        double doubleValue = Double.parseDouble(value);
+                        score = new ScoreModel(doubleValue,
+                                StringEscapeUtils.unescapeJava(oboTerm.getName()),
+                                StringEscapeUtils.unescapeJava(oboTerm.getDescription()));
+                    }
                 }
             }
         }
 
+        LOGGER.debug("parsing term {} -> {}", oboTerm, score);
+
         return score;
     }