Enable curating broad/narrow

biopragmatics · Sep 23, 2023 · 4a3166e · 4a3166e
1 parent 038670d
commit 4a3166e
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Showing 2 changed files with 31 additions and 2 deletions.
diff --git a/src/biomappings/templates/home.html b/src/biomappings/templates/home.html
@@ -66,7 +66,9 @@ <h5 class="card-header text-center">
                         {% endif %}
                         <th scope="col">Target</th>
                         <th scope="col">Target Name</th>
-                        <th scope="col">Confidence</th>
+                        <th scope="col">Conf.</th>
+                        <th scope="col"></th>
+                        <th scope="col"></th>
                         <th scope="col"></th>
                         <th scope="col"></th>
                         <th scope="col"></th>
@@ -111,6 +113,20 @@ <h5 class="card-header text-center">
                                     <i class="far fa-thumbs-up"></i>
                                 </a>
                             </td>
+                            <td>
+                                <a data-toggle="tooltip"
+                                   title="{{ p['source name'] }} is broader than {{ p['target name'] }}."
+                                   href="{{ url_for_state('.mark', state, line=line, value='broad') }}">
+                                    -B-
+                                </a>
+                            </td>
+                            <td>
+                                <a data-toggle="tooltip"
+                                   title="{{ p['source name'] }} is narrower than {{ p['target name'] }}."
+                                   href="{{ url_for_state('.mark', state, line=line, value='narrow') }}">
+                                    -N-
+                                </a>
+                            </td>
                             <td>
                                 <a data-toggle="tooltip"
                                    title="These two entities do not have the {{ p['relation'] }} relationship. You should still click this even if you think there could be a different relationship."

diff --git a/src/biomappings/wsgi.py b/src/biomappings/wsgi.py
@@ -398,7 +398,7 @@ def mark(self, line: int, value: str) -> None:
         """
         if line not in self._marked:
             self.total_curated += 1
-        if value not in {"correct", "incorrect", "unsure"}:
+        if value not in {"correct", "incorrect", "unsure", "broad", "narrow"}:
             raise ValueError
         self._marked[line] = value
 
@@ -459,6 +459,15 @@ def persist(self):
             prediction["prediction_confidence"] = prediction.pop("confidence")
             prediction["source"] = _manual_source()
             prediction["type"] = "semapv:ManualMappingCuration"
+
+            # note these go backwards because of the way they are read
+            if value == "broad":
+                value = "correct"
+                prediction['relation'] = "skos:narrowMatch"
+            elif value == "narrow":
+                value = "correct"
+                prediction['relation'] = "skos:broadMatch"
+
             entries[value].append(prediction)
 
         append_true_mappings(entries["correct"], path=self.positives_path)
@@ -581,6 +590,10 @@ def _normalize_mark(value: str) -> str:
         return "incorrect"
     elif value in UNSURE:
         return "unsure"
+    elif value in {"broader", "broad"}:
+        return "broad"
+    elif value in {"narrow", "narrower"}:
+        return "narrow"
     else:
         raise ValueError