partially address #1290

Since biological sex is a common one, we can at least be consistent.
PavlidisLab · Nov 15, 2024 · 728f829 · 728f829
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commit 728f829
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diff --git a/gemma-core/src/main/java/ubic/gemma/core/analysis/expression/diff/BaselineSelection.java b/gemma-core/src/main/java/ubic/gemma/core/analysis/expression/diff/BaselineSelection.java
@@ -55,7 +55,8 @@ public class BaselineSelection {
             "untreated",
             "wild type control",
             "wild type genotype",
-            "wild type"
+            "wild type",
+            "female" // alphabetically before male.
     );
     /**
      * Ontology terms we treat as baseline. Checked: 2024-08-12
@@ -73,7 +74,8 @@ public class BaselineSelection {
             "http://purl.org/nbirn/birnlex/ontology/BIRNLex-Investigation.owl#birnlex_2201", // control group, old
             "http://mged.sourceforge.net/ontologies/MGEDOntology.owl#wild_type", // retired
             "http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2001", // normal control_group (retired)
-            "http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2201" // control_group, new version (retired)
+            "http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2201", // control_group, new version (retired)
+            "http://purl.obolibrary.org/obo/PATO_0000383" // female
     );
 
     /**

diff --git a/...re/src/main/java/ubic/gemma/core/datastructure/matrix/ExpressionDataMatrixColumnSort.java b/...re/src/main/java/ubic/gemma/core/datastructure/matrix/ExpressionDataMatrixColumnSort.java
@@ -155,6 +155,8 @@ public static Map<ExperimentalFactor, FactorValue> getBaselineLevels( List<BioMa
                                 for ( FactorValue bfv : bm.getFactorValues() ) {
                                     if ( fv.equals( bfv ) ) {
                                         arbitraryBaselineFV = fv;
+                                        // FIXME: consider gathering up all of the eligible factorvalues,
+                                        // and choosing one in a deterministic way i.e. alphabetically or some other convention.
                                         break;
                                     }
                                 }