diff --git a/frontend/public/schemas/20251121/linkml/manifest.json b/frontend/public/schemas/20251121/linkml/manifest.json
index 287b1eb18c..ca5c32814a 100644
--- a/frontend/public/schemas/20251121/linkml/manifest.json
+++ b/frontend/public/schemas/20251121/linkml/manifest.json
@@ -1,5 +1,5 @@
 {
-  "generated": "2026-01-13T19:29:48.201Z",
+  "generated": "2026-01-13T19:37:31.837Z",
   "schemaRoot": "/schemas/20251121/linkml",
   "totalFiles": 2894,
   "categoryCounts": {
diff --git a/frontend/src/components/ontology/OntologyTermPopup.tsx b/frontend/src/components/ontology/OntologyTermPopup.tsx
index db2e2ad6b6..c22ad66ec6 100644
--- a/frontend/src/components/ontology/OntologyTermPopup.tsx
+++ b/frontend/src/components/ontology/OntologyTermPopup.tsx
@@ -12,7 +12,7 @@
  * - Falls back to Wikidata API for wd: prefixed terms
  */
 
-import React, { useEffect, useState, useRef, useCallback } from 'react';
+import React, { useEffect, useLayoutEffect, useState, useRef, useCallback } from 'react';
 import DOMPurify from 'dompurify';
 import { 
   loadOntology, 
@@ -660,6 +660,7 @@ export const OntologyTermPopup: React.FC<OntologyTermPopupProps> = ({
   
   // Draggable state
   const [position, setPosition] = useState<Position | null>(initialPosition || null);
+  const [isPositioned, setIsPositioned] = useState(!!initialPosition); // Track if we've calculated position
   const [isDragging, setIsDragging] = useState(false);
   const dragStartRef = useRef<{ x: number; y: number; posX: number; posY: number } | null>(null);
   const panelRef = useRef<HTMLDivElement>(null);
@@ -705,13 +706,15 @@ export const OntologyTermPopup: React.FC<OntologyTermPopupProps> = ({
   }, [curie]);
 
   // Center the popup on initial load if no position provided
-  useEffect(() => {
+  // Using useLayoutEffect to calculate position before browser paints (prevents flash)
+  useLayoutEffect(() => {
     if (!initialPosition && panelRef.current && !position) {
       const rect = panelRef.current.getBoundingClientRect();
       setPosition({
         x: (window.innerWidth - rect.width) / 2,
         y: (window.innerHeight - rect.height) / 3,
       });
+      setIsPositioned(true);
     }
   }, [initialPosition, position]);
 
@@ -927,6 +930,8 @@ export const OntologyTermPopup: React.FC<OntologyTermPopupProps> = ({
   const panelStyle: React.CSSProperties = {
     width: size.width,
     height: isMinimized ? 'auto' : size.height,
+    // Hide until position is calculated to prevent flash
+    visibility: isPositioned ? 'visible' : 'hidden',
     ...(position && {
       position: 'fixed',
       left: position.x,