gramene-search 2.0.7 → 2.0.9

package/dist/index.js

@@ -1458,8 +1458,8 @@ const $24971af0a229e0e3$var$grameneViews = {
                     shouldScroll: false
                 },
                 {
-                    id: 'gsea',
-                    name: 'Gene set enrichment',
+                    id: 'ontologyEnrichment',
+                    name: 'Ontology Enrichment',
                     show: 'off',
                     shouldScroll: false
                 },
@@ -1560,7 +1560,7 @@ const $24971af0a229e0e3$var$grameneViews = {
             'list',
             'export',
             'exprViz',
-            'gsea'
+            'ontologyEnrichment'
         ]);
         const autoDisable = numFound === 0 || !hasFilters;
         const hasFirebase = !!(config && config.firebaseConfig);
@@ -4451,23 +4451,24 @@ var $4f15cd8a7d970b18$export$2e2bcd8739ae039 = $4f15cd8a7d970b18$var$exprViz;
 
 
 
-// Gene Set Enrichment Analysis bundle.
+// Ontology over-representation analysis (clusterProfiler::enrichGO-style).
 //
 // For each species tab we run:
 //   foreground: q=<filters>&fq=taxon_id:<tid>&rows=0 + facet on six __ancestors fields
 //   background: q=taxon_id:<tid>&rows=0           + same facets (cached forever per tid)
 //
-// Per-ontology denominators (n_ont, N_ont) come from the root term's facet
-// count, since every annotated gene carries the root in __ancestors. Roots
-// are identified once ontology records are loaded by picking the ancestor
-// (or self) with the highest background facet count — this works for
-// multi-rooted GO (BP/MF/CC) and for the rice-rooted pathway tree.
-//
-// Enrichment uses the upper-tail Fisher exact (hypergeometric); p-values
-// are corrected per ontology with Benjamini–Hochberg. The "most-specific"
-// collapse is applied AFTER BH so a parent term that's significant on its
-// own is preserved even when none of its children clear the cutoff.
-const $0736cb5a41609896$var$ONTOLOGIES = [
+// For every ontology section we compute a single hypergeometric universe:
+//   N = # genes annotated to any term in this ontology section (= largest bg facet count)
+//   K = # input genes annotated to any term in this section    (= largest fg facet count)
+// and per term:
+//   M = bg facet count, count = fg facet count
+//   p = P(X >= count), X ~ Hypergeometric(N, M, K)
+// p-values are BH-adjusted across the tested terms in the section.
+// GO is split into its three sub-ontologies (BP/MF/CC) by namespace so each
+// gets its own (N, K) and BH correction, matching enrichGO. Terms with
+// fewer than `minGSSize` or more than `maxGSSize` annotated genes are
+// dropped before testing (enrichGO defaults: 10 / 500).
+const $d365d8c287ab0c94$var$ONTOLOGIES = [
     {
         key: 'GO',
         field: 'GO__ancestors',
@@ -4505,19 +4506,19 @@ const $0736cb5a41609896$var$ONTOLOGIES = [
         bucket: null
     }
 ];
-const $0736cb5a41609896$var$FACET_PARAMS = $0736cb5a41609896$var$ONTOLOGIES.map((o)=>`facet.field=${encodeURIComponent(`{!facet.limit=10000 facet.mincount=1 key=${o.key}}${o.field}`)}`).join('&');
-const $0736cb5a41609896$var$fgPending = {};
-const $0736cb5a41609896$var$bgPending = {};
-function $0736cb5a41609896$var$fgSig(q, taxon) {
+const $d365d8c287ab0c94$var$FACET_PARAMS = $d365d8c287ab0c94$var$ONTOLOGIES.map((o)=>`facet.field=${encodeURIComponent(`{!facet.limit=10000 facet.mincount=1 key=${o.key}}${o.field}`)}`).join('&');
+const $d365d8c287ab0c94$var$fgPending = {};
+const $d365d8c287ab0c94$var$bgPending = {};
+function $d365d8c287ab0c94$var$fgSig(q, taxon) {
     return `${q}|${taxon}`;
 }
-function $0736cb5a41609896$var$bgSig(taxon) {
+function $d365d8c287ab0c94$var$bgSig(taxon) {
     return `bg|${taxon}`;
 }
-function $0736cb5a41609896$var$parseFacets(json) {
+function $d365d8c287ab0c94$var$parseFacets(json) {
     const out = {};
     const ff = json && json.facet_counts && json.facet_counts.facet_fields || {};
-    for (const o of $0736cb5a41609896$var$ONTOLOGIES){
+    for (const o of $d365d8c287ab0c94$var$ONTOLOGIES){
         const arr = ff[o.key] || [];
         const map = {};
         for(let i = 0; i < arr.length; i += 2)map[+arr[i]] = +arr[i + 1];
@@ -4525,14 +4526,14 @@ function $0736cb5a41609896$var$parseFacets(json) {
     }
     return out;
 }
-const $0736cb5a41609896$var$gsea = {
-    name: 'gsea',
+const $d365d8c287ab0c94$var$ontologyEnrichment = {
+    name: 'ontologyEnrichment',
     // Background facet counts depend only on the species — they're invariant
     // across filter changes and across sessions, so we persist whenever a bg
     // fetch completes. Foreground state piggybacks on the same write but is
     // self-invalidated by the signature check in the reactor.
     persistActions: [
-        'GSEA_BG_SUCCEEDED'
+        'ONTOLOGY_ENRICHMENT_BG_SUCCEEDED'
     ],
     getReducer: ()=>{
         const initialState = {
@@ -4540,8 +4541,9 @@ const $0736cb5a41609896$var$gsea = {
             byTaxon: {},
             ui: {
                 pAdjCutoff: 0.05,
-                minK: 2,
-                mostSpecific: true,
+                minGSSize: 10,
+                maxGSSize: 500,
+                mostSpecific: false,
                 ontology: 'all',
                 search: ''
             }
@@ -4575,12 +4577,12 @@ const $0736cb5a41609896$var$gsea = {
         }
         return (state = initialState, { type: type, payload: payload })=>{
             switch(type){
-                case 'GSEA_ACTIVE_TAXON_SET':
+                case 'ONTOLOGY_ENRICHMENT_ACTIVE_TAXON_SET':
                     return {
                         ...ensureTaxon(state, payload),
                         activeTaxon: payload
                     };
-                case 'GSEA_UI_SET':
+                case 'ONTOLOGY_ENRICHMENT_UI_SET':
                     return {
                         ...state,
                         ui: {
@@ -4588,7 +4590,7 @@ const $0736cb5a41609896$var$gsea = {
                             ...payload || {}
                         }
                     };
-                case 'GSEA_FG_STARTED':
+                case 'ONTOLOGY_ENRICHMENT_FG_STARTED':
                     {
                         const next = ensureTaxon(state, payload.taxon);
                         const t = next.byTaxon[payload.taxon];
@@ -4610,7 +4612,7 @@ const $0736cb5a41609896$var$gsea = {
                             }
                         };
                     }
-                case 'GSEA_FG_SUCCEEDED':
+                case 'ONTOLOGY_ENRICHMENT_FG_SUCCEEDED':
                     {
                         const t = state.byTaxon[payload.taxon];
                         if (!t || payload.requestId !== t.fg.requestId) return state;
@@ -4630,7 +4632,7 @@ const $0736cb5a41609896$var$gsea = {
                             }
                         };
                     }
-                case 'GSEA_FG_FAILED':
+                case 'ONTOLOGY_ENRICHMENT_FG_FAILED':
                     {
                         const t = state.byTaxon[payload.taxon];
                         if (!t || payload.requestId !== t.fg.requestId) return state;
@@ -4649,7 +4651,7 @@ const $0736cb5a41609896$var$gsea = {
                             }
                         };
                     }
-                case 'GSEA_BG_STARTED':
+                case 'ONTOLOGY_ENRICHMENT_BG_STARTED':
                     {
                         const next = ensureTaxon(state, payload.taxon);
                         const t = next.byTaxon[payload.taxon];
@@ -4671,7 +4673,7 @@ const $0736cb5a41609896$var$gsea = {
                             }
                         };
                     }
-                case 'GSEA_BG_SUCCEEDED':
+                case 'ONTOLOGY_ENRICHMENT_BG_SUCCEEDED':
                     {
                         const t = state.byTaxon[payload.taxon];
                         if (!t || payload.requestId !== t.bg.requestId) return state;
@@ -4691,7 +4693,7 @@ const $0736cb5a41609896$var$gsea = {
                             }
                         };
                     }
-                case 'GSEA_BG_FAILED':
+                case 'ONTOLOGY_ENRICHMENT_BG_FAILED':
                     {
                         const t = state.byTaxon[payload.taxon];
                         if (!t || payload.requestId !== t.bg.requestId) return state;
@@ -4739,23 +4741,23 @@ const $0736cb5a41609896$var$gsea = {
             }
         };
     },
-    doSetGseaActiveTaxon: (tid)=>({ dispatch: dispatch })=>dispatch({
-                type: 'GSEA_ACTIVE_TAXON_SET',
+    doSetOntologyEnrichmentActiveTaxon: (tid)=>({ dispatch: dispatch })=>dispatch({
+                type: 'ONTOLOGY_ENRICHMENT_ACTIVE_TAXON_SET',
                 payload: tid
             }),
-    doSetGseaUI: (patch)=>({ dispatch: dispatch })=>dispatch({
-                type: 'GSEA_UI_SET',
+    doSetOntologyEnrichmentUI: (patch)=>({ dispatch: dispatch })=>dispatch({
+                type: 'ONTOLOGY_ENRICHMENT_UI_SET',
                 payload: patch
             }),
-    doFetchGseaForeground: (taxon)=>({ dispatch: dispatch, store: store })=>{
+    doFetchOntologyEnrichmentForeground: (taxon)=>({ dispatch: dispatch, store: store })=>{
             const q = store.selectGrameneFiltersQueryString();
-            const signature = $0736cb5a41609896$var$fgSig(q, taxon);
-            const state = store.selectGsea();
+            const signature = $d365d8c287ab0c94$var$fgSig(q, taxon);
+            const state = store.selectOntologyEnrichment();
             const t = state.byTaxon[taxon];
             if (t && t.fg.signature === signature && (t.fg.status === 'loading' || t.fg.status === 'ready')) return;
-            const requestId = $0736cb5a41609896$var$fgPending[taxon] = ($0736cb5a41609896$var$fgPending[taxon] || 0) + 1;
+            const requestId = $d365d8c287ab0c94$var$fgPending[taxon] = ($d365d8c287ab0c94$var$fgPending[taxon] || 0) + 1;
             dispatch({
-                type: 'GSEA_FG_STARTED',
+                type: 'ONTOLOGY_ENRICHMENT_FG_STARTED',
                 payload: {
                     taxon: taxon,
                     signature: signature,
@@ -4763,13 +4765,13 @@ const $0736cb5a41609896$var$gsea = {
                 }
             });
             const api = store.selectGrameneAPI();
-            const url = `${api}/search?q=${q}&fq=taxon_id:${taxon}&rows=0&facet=true&${$0736cb5a41609896$var$FACET_PARAMS}`;
+            const url = `${api}/search?q=${q}&fq=taxon_id:${taxon}&rows=0&facet=true&${$d365d8c287ab0c94$var$FACET_PARAMS}`;
             fetch(url).then((r)=>r.json()).then((json)=>{
-                if (requestId !== $0736cb5a41609896$var$fgPending[taxon]) return;
-                const terms = $0736cb5a41609896$var$parseFacets(json);
+                if (requestId !== $d365d8c287ab0c94$var$fgPending[taxon]) return;
+                const terms = $d365d8c287ab0c94$var$parseFacets(json);
                 const numFound = json && json.response && json.response.numFound || 0;
                 dispatch({
-                    type: 'GSEA_FG_SUCCEEDED',
+                    type: 'ONTOLOGY_ENRICHMENT_FG_SUCCEEDED',
                     payload: {
                         taxon: taxon,
                         requestId: requestId,
@@ -4777,11 +4779,11 @@ const $0736cb5a41609896$var$gsea = {
                         numFound: numFound
                     }
                 });
-                store.doEnsureGseaTermRecords(taxon);
+                store.doEnsureOntologyEnrichmentTermRecords(taxon);
             }).catch((err)=>{
-                if (requestId !== $0736cb5a41609896$var$fgPending[taxon]) return;
+                if (requestId !== $d365d8c287ab0c94$var$fgPending[taxon]) return;
                 dispatch({
-                    type: 'GSEA_FG_FAILED',
+                    type: 'ONTOLOGY_ENRICHMENT_FG_FAILED',
                     payload: {
                         taxon: taxon,
                         requestId: requestId,
@@ -4790,14 +4792,14 @@ const $0736cb5a41609896$var$gsea = {
                 });
             });
         },
-    doFetchGseaBackground: (taxon)=>({ dispatch: dispatch, store: store })=>{
-            const signature = $0736cb5a41609896$var$bgSig(taxon);
-            const state = store.selectGsea();
+    doFetchOntologyEnrichmentBackground: (taxon)=>({ dispatch: dispatch, store: store })=>{
+            const signature = $d365d8c287ab0c94$var$bgSig(taxon);
+            const state = store.selectOntologyEnrichment();
             const t = state.byTaxon[taxon];
             if (t && t.bg.signature === signature && (t.bg.status === 'loading' || t.bg.status === 'ready')) return;
-            const requestId = $0736cb5a41609896$var$bgPending[taxon] = ($0736cb5a41609896$var$bgPending[taxon] || 0) + 1;
+            const requestId = $d365d8c287ab0c94$var$bgPending[taxon] = ($d365d8c287ab0c94$var$bgPending[taxon] || 0) + 1;
             dispatch({
-                type: 'GSEA_BG_STARTED',
+                type: 'ONTOLOGY_ENRICHMENT_BG_STARTED',
                 payload: {
                     taxon: taxon,
                     signature: signature,
@@ -4805,13 +4807,13 @@ const $0736cb5a41609896$var$gsea = {
                 }
             });
             const api = store.selectGrameneAPI();
-            const url = `${api}/search?q=taxon_id:${taxon}&rows=0&facet=true&${$0736cb5a41609896$var$FACET_PARAMS}`;
+            const url = `${api}/search?q=taxon_id:${taxon}&rows=0&facet=true&${$d365d8c287ab0c94$var$FACET_PARAMS}`;
             fetch(url).then((r)=>r.json()).then((json)=>{
-                if (requestId !== $0736cb5a41609896$var$bgPending[taxon]) return;
-                const terms = $0736cb5a41609896$var$parseFacets(json);
+                if (requestId !== $d365d8c287ab0c94$var$bgPending[taxon]) return;
+                const terms = $d365d8c287ab0c94$var$parseFacets(json);
                 const numFound = json && json.response && json.response.numFound || 0;
                 dispatch({
-                    type: 'GSEA_BG_SUCCEEDED',
+                    type: 'ONTOLOGY_ENRICHMENT_BG_SUCCEEDED',
                     payload: {
                         taxon: taxon,
                         requestId: requestId,
@@ -4819,11 +4821,11 @@ const $0736cb5a41609896$var$gsea = {
                         numFound: numFound
                     }
                 });
-                store.doEnsureGseaTermRecords(taxon);
+                store.doEnsureOntologyEnrichmentTermRecords(taxon);
             }).catch((err)=>{
-                if (requestId !== $0736cb5a41609896$var$bgPending[taxon]) return;
+                if (requestId !== $d365d8c287ab0c94$var$bgPending[taxon]) return;
                 dispatch({
-                    type: 'GSEA_BG_FAILED',
+                    type: 'ONTOLOGY_ENRICHMENT_BG_FAILED',
                     payload: {
                         taxon: taxon,
                         requestId: requestId,
@@ -4832,165 +4834,175 @@ const $0736cb5a41609896$var$gsea = {
                 });
             });
         },
-    doEnsureGseaTermRecords: (taxon)=>({ store: store })=>{
-            const state = store.selectGsea();
+    doEnsureOntologyEnrichmentTermRecords: (taxon)=>({ store: store })=>{
+            const state = store.selectOntologyEnrichment();
             if (!state.byTaxon[taxon]) return;
             // The ontologies and pathways bundles bulk-load + persist on first
             // request; we just need to nudge each one once.
             const buckets = new Set();
-            for (const o of $0736cb5a41609896$var$ONTOLOGIES)if (o.bucket) buckets.add(o.bucket);
+            for (const o of $d365d8c287ab0c94$var$ONTOLOGIES)if (o.bucket) buckets.add(o.bucket);
             for (const k of buckets)store.doEnsureOntologyRecords(k);
             if (store.doRequestGramenePathways) store.doRequestGramenePathways();
         },
-    reactGseaFetch: (0, $gXNCa$reduxbundler.createSelector)('selectGsea', 'selectGrameneFiltersStatus', 'selectGrameneFiltersQueryString', 'selectGrameneViewsOn', (gs, fStatus, q, viewsOn)=>{
-        if (!viewsOn || !viewsOn.has('gsea')) return;
+    reactOntologyEnrichmentFetch: (0, $gXNCa$reduxbundler.createSelector)('selectOntologyEnrichment', 'selectGrameneFiltersStatus', 'selectGrameneFiltersQueryString', 'selectGrameneViewsOn', (gs, fStatus, q, viewsOn)=>{
+        if (!viewsOn || !viewsOn.has('ontologyEnrichment')) return;
         if (fStatus === 'init') return;
         const tid = gs.activeTaxon;
         if (!tid) return;
         const t = gs.byTaxon[tid];
         if (!t) return;
-        const sig = $0736cb5a41609896$var$fgSig(q, tid);
+        const sig = $d365d8c287ab0c94$var$fgSig(q, tid);
         // A 'loading' status from a rehydrated state with no live request is
         // treated as idle — otherwise we'd deadlock waiting on a fetch that
         // ended when the previous tab closed.
-        const fgInFlight = t.fg.status === 'loading' && ($0736cb5a41609896$var$fgPending[tid] || 0) === t.fg.requestId && t.fg.requestId > 0;
+        const fgInFlight = t.fg.status === 'loading' && ($d365d8c287ab0c94$var$fgPending[tid] || 0) === t.fg.requestId && t.fg.requestId > 0;
         if (t.fg.signature !== sig && !fgInFlight) return {
-            actionCreator: 'doFetchGseaForeground',
+            actionCreator: 'doFetchOntologyEnrichmentForeground',
             args: [
                 tid
             ]
         };
-        const bgInFlight = t.bg.status === 'loading' && ($0736cb5a41609896$var$bgPending[tid] || 0) === t.bg.requestId && t.bg.requestId > 0;
+        const bgInFlight = t.bg.status === 'loading' && ($d365d8c287ab0c94$var$bgPending[tid] || 0) === t.bg.requestId && t.bg.requestId > 0;
         if (t.bg.status !== 'ready' && !bgInFlight) return {
-            actionCreator: 'doFetchGseaBackground',
+            actionCreator: 'doFetchOntologyEnrichmentBackground',
             args: [
                 tid
             ]
         };
     }),
-    selectGsea: (state)=>state.gsea,
-    selectGseaUI: (state)=>state.gsea.ui,
-    selectGseaOntologyDefs: ()=>$0736cb5a41609896$var$ONTOLOGIES,
-    selectGseaResults: (0, $gXNCa$reduxbundler.createSelector)('selectGsea', 'selectOntologies', 'selectGramenePathways', (gs, ontoBuckets, pathwayDocs)=>{
+    selectOntologyEnrichment: (state)=>state.ontologyEnrichment,
+    selectOntologyEnrichmentUI: (state)=>state.ontologyEnrichment.ui,
+    selectOntologyEnrichmentOntologyDefs: ()=>$d365d8c287ab0c94$var$ONTOLOGIES,
+    selectOntologyEnrichmentResults: (0, $gXNCa$reduxbundler.createSelector)('selectOntologyEnrichment', 'selectOntologies', 'selectGramenePathways', (gs, ontoBuckets, pathwayDocs)=>{
         const tid = gs.activeTaxon;
         if (!tid) return null;
         const t = gs.byTaxon[tid];
         if (!t || !t.fg.terms || !t.bg.terms) return null;
         const ui = gs.ui;
         const out = {};
-        for (const o of $0736cb5a41609896$var$ONTOLOGIES){
+        for (const o of $d365d8c287ab0c94$var$ONTOLOGIES){
             const fg = t.fg.terms[o.key] || {};
             const bg = t.bg.terms[o.key] || {};
             const recs = o.key === 'pathways' ? pathwayDocs || {} : ontoBuckets && ontoBuckets[o.bucket] || {};
-            // Forest-fallback denominators: when a term is itself a forest root
-            // (no parents in `recs` — common for InterPro), root finding returns
-            // the term and we'd get fold=1 by construction. Use the maximum
-            // counts across the ontology as a proxy for "annotated in this
-            // ontology" instead. For ontologies with a true synthetic root,
-            // these maxima equal the root counts and the answer is unchanged.
-            let maxFg = 0, maxBg = 0;
-            for (const idStr of Object.keys(bg)){
-                const v = bg[idStr];
-                if (v > maxBg) maxBg = v;
-            }
-            for (const idStr of Object.keys(fg)){
-                const v = fg[idStr];
-                if (v > maxFg) maxFg = v;
-            }
-            const rootCache = {};
-            const rootOf = (id)=>{
-                if (rootCache.hasOwnProperty(id)) return rootCache[id];
-                const r = $0736cb5a41609896$var$findRoot(o.key, id, recs, bg);
-                rootCache[id] = r;
-                return r;
-            };
-            const rows = [];
-            for (const idStr of Object.keys(fg)){
-                const id = +idStr;
-                const k = fg[id];
-                const K = bg[id] || 0;
-                if (K < k) continue; // bg should always be >= fg
-                if (k < ui.minK) continue;
-                const termRec = recs && recs[id];
-                if (termRec && (termRec.is_obsolete || termRec.obsolete)) continue;
-                const root = rootOf(id);
-                // If the "root" is the term itself, the term is a forest root in
-                // this ontology — fall back to ontology-wide maxima.
-                const fellBack = +root === id;
-                const n = fellBack ? maxFg : root != null && fg[root] ? fg[root] : k;
-                const N = fellBack ? maxBg : root != null && bg[root] ? bg[root] : K;
-                if (n <= 0 || N <= 0) continue;
-                if (k > n || K > N) continue;
-                const fold = k / n / (K / N);
-                const p = $0736cb5a41609896$var$fisherUpperTail(k, n, K, N);
-                rows.push({
-                    ontology: o.key,
-                    ontology_label: o.label,
-                    term_id: id,
-                    field: o.field,
-                    k: k,
-                    n: n,
-                    K: K,
-                    N: N,
-                    fold: fold,
-                    p: p,
-                    pAdj: 1,
-                    root: root,
-                    denomFallback: fellBack
-                });
-            }
-            // GO is split into its three top-level namespaces (BP / MF / CC)
-            // and each is tested as its own ontology — both BH correction and
-            // most-specific collapse run within a namespace. We only split once
-            // ontology records have arrived and root finding has produced
-            // canonical roots; otherwise we'd see a swarm of singleton groups
-            // during the brief loading window between bg landing and records
-            // being fetched.
+            // GO is tested per sub-ontology (BP / MF / CC) so each gets its
+            // own universe size and BH correction, matching enrichGO. We can
+            // only split once ontology records have arrived and namespaces are
+            // known; until then, fall through to a single-section test.
             if (o.key === 'GO' && Object.keys(recs).length > 0) {
-                const byRoot = {};
-                for (const r of rows){
-                    const k = String(r.root);
-                    if (!byRoot[k]) byRoot[k] = [];
-                    byRoot[k].push(r);
+                const byNs = {
+                    biological_process: {
+                        fg: {},
+                        bg: {}
+                    },
+                    molecular_function: {
+                        fg: {},
+                        bg: {}
+                    },
+                    cellular_component: {
+                        fg: {},
+                        bg: {}
+                    }
+                };
+                for (const idStr of Object.keys(bg)){
+                    const id = +idStr;
+                    const ns = recs[id] && recs[id].namespace;
+                    if (!byNs[ns]) continue;
+                    byNs[ns].bg[id] = bg[id];
+                    if (fg[id] != null) byNs[ns].fg[id] = fg[id];
                 }
-                const rootKeys = Object.keys(byRoot).sort((a, b)=>{
-                    const na = $0736cb5a41609896$var$goRootName(recs[+a]) || a;
-                    const nb = $0736cb5a41609896$var$goRootName(recs[+b]) || b;
-                    return na.localeCompare(nb);
-                });
-                for (const rootKey of rootKeys){
-                    const rootRec = recs[+rootKey];
-                    const rootName = $0736cb5a41609896$var$goRootName(rootRec);
-                    const sectionKey = `GO:${rootKey}`;
-                    const sectionLabel = rootName ? `GO: ${$0736cb5a41609896$var$titleCase(rootName)}` : `GO: ${rootKey}`;
-                    out[sectionKey] = $0736cb5a41609896$var$finalizeBlock(byRoot[rootKey], o.key, o.field, recs, ui, sectionKey, sectionLabel);
+                for (const idStr of Object.keys(fg)){
+                    const id = +idStr;
+                    const ns = recs[id] && recs[id].namespace;
+                    if (!byNs[ns]) continue;
+                    if (byNs[ns].fg[id] == null) byNs[ns].fg[id] = fg[id];
+                }
+                for (const ns of Object.keys(byNs)){
+                    const sectionKey = `GO:${ns}`;
+                    const sectionLabel = `GO: ${$d365d8c287ab0c94$var$titleCase(ns)}`;
+                    out[sectionKey] = $d365d8c287ab0c94$var$enrichSection(byNs[ns].fg, byNs[ns].bg, recs, ui, o.key, o.field, o.label, sectionKey, sectionLabel);
                 }
-            } else out[o.key] = $0736cb5a41609896$var$finalizeBlock(rows, o.key, o.field, recs, ui, o.key, o.label);
+            } else out[o.key] = $d365d8c287ab0c94$var$enrichSection(fg, bg, recs, ui, o.key, o.field, o.label, o.key, o.label);
         }
         return out;
     })
 };
-function $0736cb5a41609896$var$goRootName(rec) {
-    if (!rec) return '';
-    return rec.name || rec.display_name || rec.namespace || '';
-}
-function $0736cb5a41609896$var$titleCase(s) {
+function $d365d8c287ab0c94$var$titleCase(s) {
     return String(s).split('_').map((w)=>w ? w[0].toUpperCase() + w.slice(1) : '').join(' ');
 }
-// BH correction + most-specific collapse + metadata + final sort, returning
-// the block descriptor consumed by the view layer.
-function $0736cb5a41609896$var$finalizeBlock(rows, ontKey, ontField, recs, ui, sectionKey, sectionLabel) {
-    rows.sort((a, b)=>a.p - b.p);
+// One ORA section: hypergeometric over a single (N, K) universe, BH-adjusted
+// across tested terms. Universe sizes come from the largest facet count in
+// the section — for an ontology with a synthetic root that's the root's
+// gene count (exact), and for forests it's the most populated top-level
+// term (a conservative approximation).
+function $d365d8c287ab0c94$var$enrichSection(fg, bg, recs, ui, ontKey, ontField, ontLabel, sectionKey, sectionLabel) {
+    let N = 0, K = 0;
+    for (const idStr of Object.keys(bg)){
+        const v = bg[idStr];
+        if (v > N) N = v;
+    }
+    for (const idStr of Object.keys(fg)){
+        const v = fg[idStr];
+        if (v > K) K = v;
+    }
+    const empty = {
+        ontology: sectionKey,
+        label: sectionLabel,
+        field: ontField,
+        tested: 0,
+        passing: 0,
+        rows: [],
+        universeSize: N,
+        deSize: K
+    };
+    if (N <= 0 || K <= 0) return empty;
+    const minGS = Math.max(1, +ui.minGSSize || 1);
+    const maxGS = Math.max(minGS, +ui.maxGSSize || N);
+    const rows = [];
+    for (const idStr of Object.keys(fg)){
+        const id = +idStr;
+        const count = fg[id];
+        const M = bg[id] || 0;
+        if (M < count) continue;
+        if (M < minGS || M > maxGS) continue;
+        const termRec = recs && recs[id];
+        if (termRec && (termRec.is_obsolete || termRec.obsolete)) continue;
+        if (count > K || M > N) continue;
+        const p = $d365d8c287ab0c94$var$fisherUpperTail(count, K, M, N);
+        const richFactor = M > 0 ? count / M : 0;
+        const foldEnrichment = M > 0 && K > 0 ? count / K / (M / N) : 0;
+        const mu = M * K / N;
+        const sigma2 = N > 1 ? mu * (N - K) * (N - M) / N / (N - 1) : 0;
+        const zScore = sigma2 > 0 ? (count - mu) / Math.sqrt(sigma2) : 0;
+        rows.push({
+            ontology: ontKey,
+            ontology_label: ontLabel,
+            term_id: id,
+            field: ontField,
+            Count: count,
+            DESize: K,
+            SetSize: M,
+            UniverseSize: N,
+            GeneRatio: `${count}/${K}`,
+            BgRatio: `${M}/${N}`,
+            RichFactor: richFactor,
+            FoldEnrichment: foldEnrichment,
+            zScore: zScore,
+            pvalue: p,
+            pAdjust: 1
+        });
+    }
+    // BH adjustment across all tested terms in this section.
+    rows.sort((a, b)=>a.pvalue - b.pvalue);
     const m = rows.length;
     let prev = 1;
     for(let i = m - 1; i >= 0; i--){
-        const adj = Math.min(prev, rows[i].p * m / (i + 1));
-        rows[i].pAdj = adj;
+        const adj = Math.min(prev, rows[i].pvalue * m / (i + 1));
+        rows[i].pAdjust = adj;
         prev = adj;
     }
-    const passing = rows.filter((r)=>r.pAdj <= ui.pAdjCutoff);
+    const passing = rows.filter((r)=>r.pAdjust <= ui.pAdjCutoff && r.pvalue <= ui.pAdjCutoff);
     let display = passing;
-    if (ui.mostSpecific) display = $0736cb5a41609896$var$collapseToMostSpecific(ontKey, passing, recs);
+    if (ui.mostSpecific) display = $d365d8c287ab0c94$var$collapseToMostSpecific(ontKey, passing, recs);
     for (const r of display){
         const rec = recs && recs[r.term_id];
         if (rec) {
@@ -5002,90 +5014,57 @@ function $0736cb5a41609896$var$finalizeBlock(rows, ontKey, ontField, recs, ui, s
             r.term_namespace = '';
             r.term_display_id = String(r.term_id);
         }
+        r.Description = r.term_name || r.term_display_id;
     }
-    display.sort((a, b)=>a.pAdj - b.pAdj || b.fold - a.fold);
+    display.sort((a, b)=>a.pAdjust - b.pAdjust || b.FoldEnrichment - a.FoldEnrichment);
     return {
         ontology: sectionKey,
         label: sectionLabel,
         field: ontField,
         tested: rows.length,
         passing: passing.length,
-        rows: display
+        rows: display,
+        universeSize: N,
+        deSize: K
     };
 }
 // ---------- math helpers ----------
-const $0736cb5a41609896$var$LF_CACHE = [
+const $d365d8c287ab0c94$var$LF_CACHE = [
     0,
     0
 ];
-function $0736cb5a41609896$var$logFactorial(n) {
-    if (n < $0736cb5a41609896$var$LF_CACHE.length) return $0736cb5a41609896$var$LF_CACHE[n];
-    let lf = $0736cb5a41609896$var$LF_CACHE[$0736cb5a41609896$var$LF_CACHE.length - 1];
-    for(let i = $0736cb5a41609896$var$LF_CACHE.length; i <= n; i++){
+function $d365d8c287ab0c94$var$logFactorial(n) {
+    if (n < $d365d8c287ab0c94$var$LF_CACHE.length) return $d365d8c287ab0c94$var$LF_CACHE[n];
+    let lf = $d365d8c287ab0c94$var$LF_CACHE[$d365d8c287ab0c94$var$LF_CACHE.length - 1];
+    for(let i = $d365d8c287ab0c94$var$LF_CACHE.length; i <= n; i++){
         lf += Math.log(i);
-        $0736cb5a41609896$var$LF_CACHE.push(lf);
+        $d365d8c287ab0c94$var$LF_CACHE.push(lf);
     }
-    return $0736cb5a41609896$var$LF_CACHE[n];
+    return $d365d8c287ab0c94$var$LF_CACHE[n];
 }
-function $0736cb5a41609896$var$logChoose(n, k) {
+function $d365d8c287ab0c94$var$logChoose(n, k) {
     if (k < 0 || k > n) return -Infinity;
-    return $0736cb5a41609896$var$logFactorial(n) - $0736cb5a41609896$var$logFactorial(k) - $0736cb5a41609896$var$logFactorial(n - k);
+    return $d365d8c287ab0c94$var$logFactorial(n) - $d365d8c287ab0c94$var$logFactorial(k) - $d365d8c287ab0c94$var$logFactorial(n - k);
 }
-function $0736cb5a41609896$var$logHypergeom(x, n, K, N) {
-    return $0736cb5a41609896$var$logChoose(K, x) + $0736cb5a41609896$var$logChoose(N - K, n - x) - $0736cb5a41609896$var$logChoose(N, n);
+function $d365d8c287ab0c94$var$logHypergeom(x, n, K, N) {
+    return $d365d8c287ab0c94$var$logChoose(K, x) + $d365d8c287ab0c94$var$logChoose(N - K, n - x) - $d365d8c287ab0c94$var$logChoose(N, n);
 }
-function $0736cb5a41609896$var$logSumExp(a, b) {
+function $d365d8c287ab0c94$var$logSumExp(a, b) {
     if (a === -Infinity) return b;
     if (b === -Infinity) return a;
     const m = Math.max(a, b);
     return m + Math.log(Math.exp(a - m) + Math.exp(b - m));
 }
-function $0736cb5a41609896$var$fisherUpperTail(k, n, K, N) {
+function $d365d8c287ab0c94$var$fisherUpperTail(k, n, K, N) {
     const upper = Math.min(n, K);
     let logP = -Infinity;
-    for(let x = k; x <= upper; x++)logP = $0736cb5a41609896$var$logSumExp(logP, $0736cb5a41609896$var$logHypergeom(x, n, K, N));
+    for(let x = k; x <= upper; x++)logP = $d365d8c287ab0c94$var$logSumExp(logP, $d365d8c287ab0c94$var$logHypergeom(x, n, K, N));
     const p = Math.exp(logP);
     if (!isFinite(p)) return 1;
     return Math.min(1, Math.max(0, p));
 }
 // ---------- ontology graph helpers ----------
-// Pick the "root" for a term as the ancestor (or self) with the highest
-// background facet count. The true root has every annotated gene under it,
-// so this selects BP/MF/CC for GO terms automatically and the rice root
-// for pathways without needing per-ontology hardcoded ids.
-function $0736cb5a41609896$var$findRoot(ontKey, id, recs, bgCounts) {
-    const rec = recs && recs[id];
-    const candidates = new Set([
-        +id
-    ]);
-    if (rec) {
-        if (ontKey === 'pathways') for (const k of Object.keys(rec)){
-            if (k.startsWith('ancestors_') && Array.isArray(rec[k])) for (const a of rec[k])candidates.add(+a);
-        }
-        else if (Array.isArray(rec.ancestors)) for (const a of rec.ancestors)candidates.add(+a);
-        else if (Array.isArray(rec.is_a)) {
-            const stack = rec.is_a.slice();
-            while(stack.length){
-                const cur = +stack.pop();
-                if (candidates.has(cur)) continue;
-                candidates.add(cur);
-                const r = recs[cur];
-                if (r && Array.isArray(r.is_a)) for (const p of r.is_a)stack.push(p);
-            }
-        }
-    }
-    let best = +id;
-    let bestCount = bgCounts[+id] || 0;
-    for (const c of candidates){
-        const cnt = bgCounts[c] || 0;
-        if (cnt > bestCount) {
-            bestCount = cnt;
-            best = c;
-        }
-    }
-    return best;
-}
-function $0736cb5a41609896$var$ancestorsOf(ontKey, id, recs) {
+function $d365d8c287ab0c94$var$ancestorsOf(ontKey, id, recs) {
     const out = new Set();
     const rec = recs && recs[id];
     if (!rec) return out;
@@ -5114,17 +5093,17 @@ function $0736cb5a41609896$var$ancestorsOf(ontKey, id, recs) {
 // Drop any term that is an ancestor of another term in the same passing set.
 // Applied AFTER BH so a parent term can survive when none of its children
 // pass the p_adj cutoff.
-function $0736cb5a41609896$var$collapseToMostSpecific(ontKey, rows, recs) {
+function $d365d8c287ab0c94$var$collapseToMostSpecific(ontKey, rows, recs) {
     if (!rows || rows.length <= 1) return rows;
     const inSet = new Set(rows.map((r)=>+r.term_id));
     const covered = new Set();
     for (const r of rows){
-        const ancs = $0736cb5a41609896$var$ancestorsOf(ontKey, +r.term_id, recs);
+        const ancs = $d365d8c287ab0c94$var$ancestorsOf(ontKey, +r.term_id, recs);
         for (const a of ancs)if (inSet.has(a)) covered.add(a);
     }
     return rows.filter((r)=>!covered.has(+r.term_id));
 }
-var $0736cb5a41609896$export$2e2bcd8739ae039 = $0736cb5a41609896$var$gsea;
+var $d365d8c287ab0c94$export$2e2bcd8739ae039 = $d365d8c287ab0c94$var$ontologyEnrichment;
 
 
 var $5df6c55c1bef3469$export$2e2bcd8739ae039 = [
@@ -5137,7 +5116,7 @@ var $5df6c55c1bef3469$export$2e2bcd8739ae039 = [
     (0, $1508f5a42be6e7b5$export$2e2bcd8739ae039),
     (0, $c921a0d2b34aadb6$export$2e2bcd8739ae039),
     (0, $4f15cd8a7d970b18$export$2e2bcd8739ae039),
-    (0, $0736cb5a41609896$export$2e2bcd8739ae039)
+    (0, $d365d8c287ab0c94$export$2e2bcd8739ae039)
 ];
 
 
@@ -13383,40 +13362,40 @@ var $1fd2507769d5bd00$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
-function $f511198465122338$var$speciesTaxonId(tid) {
+function $597fe213417ee6ca$var$speciesTaxonId(tid) {
     const n = +tid;
     return n > 1000000 ? Math.floor(n / 1000) : n;
 }
-function $f511198465122338$var$genomeName(grameneMaps, tid) {
+function $597fe213417ee6ca$var$genomeName(grameneMaps, tid) {
     if (!grameneMaps) return String(tid);
     const direct = grameneMaps[tid];
     if (direct && direct.display_name) return direct.display_name;
-    const sp = grameneMaps[$f511198465122338$var$speciesTaxonId(tid)];
+    const sp = grameneMaps[$597fe213417ee6ca$var$speciesTaxonId(tid)];
     if (sp && sp.display_name) return sp.display_name;
     return String(tid);
 }
-function $f511198465122338$var$fmtP(p) {
+function $597fe213417ee6ca$var$fmtP(p) {
     if (p == null) return '';
     if (p === 0) return '0';
     if (p < 1e-4) return p.toExponential(2);
     return p.toPrecision(3);
 }
-function $f511198465122338$var$fmtFold(f) {
+function $597fe213417ee6ca$var$fmtFold(f) {
     if (!isFinite(f)) return '';
     if (f >= 100) return f.toFixed(0);
     return f.toFixed(2);
 }
 // ---------- species tree helpers ----------
-function $f511198465122338$var$findRoots(tax) {
+function $597fe213417ee6ca$var$findRoots(tax) {
     return Object.values(tax).filter((n)=>!n.is_a || n.is_a.length === 0 || !n.is_a.some((p)=>tax[p]));
 }
 // Place each facet tid onto a taxonomy node id (fall back to species level
 // when the exact subspecies tid isn't in grameneTaxonomy).
-function $f511198465122338$var$placeTaxa(taxonomy, taxa) {
+function $597fe213417ee6ca$var$placeTaxa(taxonomy, taxa) {
     const placement = {};
     const byPlace = {};
     for (const { tid: tid, count: count } of taxa){
-        const place = taxonomy[tid] ? +tid : $f511198465122338$var$speciesTaxonId(tid);
+        const place = taxonomy[tid] ? +tid : $597fe213417ee6ca$var$speciesTaxonId(tid);
         placement[tid] = place;
         if (!byPlace[place]) byPlace[place] = [];
         byPlace[place].push({
@@ -13430,7 +13409,7 @@ function $f511198465122338$var$placeTaxa(taxonomy, taxa) {
     };
 }
 // Set of taxonomy node ids on the path from any placed leaf back to its root.
-function $f511198465122338$var$relevantNodeIds(taxonomy, byPlace) {
+function $597fe213417ee6ca$var$relevantNodeIds(taxonomy, byPlace) {
     const out = new Set();
     for (const placeId of Object.keys(byPlace)){
         let cur = taxonomy[placeId];
@@ -13444,18 +13423,18 @@ function $f511198465122338$var$relevantNodeIds(taxonomy, byPlace) {
     }
     return out;
 }
-function $f511198465122338$var$relevantChildren(node, taxonomy, relevant) {
+function $597fe213417ee6ca$var$relevantChildren(node, taxonomy, relevant) {
     return (node.children || []).map((cid)=>taxonomy[cid]).filter((c)=>c && relevant.has(+c._id));
 }
 // Walk down through single-relevant-child internal nodes to a branch / leaf.
-function $f511198465122338$var$compressChain(node, taxonomy, relevant, byPlace) {
+function $597fe213417ee6ca$var$compressChain(node, taxonomy, relevant, byPlace) {
     const chain = [
         node
     ];
     let cur = node;
     while(true){
         if (byPlace[cur._id]) break; // node itself is a placed leaf
-        const kids = $f511198465122338$var$relevantChildren(cur, taxonomy, relevant);
+        const kids = $597fe213417ee6ca$var$relevantChildren(cur, taxonomy, relevant);
         if (kids.length !== 1) break;
         cur = kids[0];
         chain.push(cur);
@@ -13465,10 +13444,10 @@ function $f511198465122338$var$compressChain(node, taxonomy, relevant, byPlace)
         terminal: cur
     };
 }
-const $f511198465122338$var$CHAIN_DISPLAY_MAX = 3;
-function $f511198465122338$var$renderChain(chain) {
+const $597fe213417ee6ca$var$CHAIN_DISPLAY_MAX = 3;
+function $597fe213417ee6ca$var$renderChain(chain) {
     const nameOf = (n)=>n.short_name || n.name || String(n._id);
-    if (chain.length <= $f511198465122338$var$CHAIN_DISPLAY_MAX) return chain.map((n, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, ($parcel$interopDefault($gXNCa$react))).Fragment, {
+    if (chain.length <= $597fe213417ee6ca$var$CHAIN_DISPLAY_MAX) return chain.map((n, i)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, ($parcel$interopDefault($gXNCa$react))).Fragment, {
             children: [
                 i > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
                     className: "tax-sep",
@@ -13518,21 +13497,21 @@ function $f511198465122338$var$renderChain(chain) {
         ]
     });
 }
-function $f511198465122338$var$dedupAdjacent(chain) {
+function $597fe213417ee6ca$var$dedupAdjacent(chain) {
     const out = [];
     for (const n of chain)if (out.length && out[out.length - 1].name === n.name) out[out.length - 1] = n;
     else out.push(n);
     return out;
 }
-const $f511198465122338$var$SpeciesTreeNode = ({ node: node, depth: depth, taxonomy: taxonomy, relevant: relevant, byPlace: byPlace, grameneMaps: grameneMaps, expanded: expanded, onToggleExpand: onToggleExpand, activeTaxon: activeTaxon, onSelect: onSelect })=>{
-    const { chain: rawChain, terminal: terminal } = $f511198465122338$var$compressChain(node, taxonomy, relevant, byPlace);
-    const chain = $f511198465122338$var$dedupAdjacent(rawChain);
+const $597fe213417ee6ca$var$SpeciesTreeNode = ({ node: node, depth: depth, taxonomy: taxonomy, relevant: relevant, byPlace: byPlace, grameneMaps: grameneMaps, expanded: expanded, onToggleExpand: onToggleExpand, activeTaxon: activeTaxon, onSelect: onSelect })=>{
+    const { chain: rawChain, terminal: terminal } = $597fe213417ee6ca$var$compressChain(node, taxonomy, relevant, byPlace);
+    const chain = $597fe213417ee6ca$var$dedupAdjacent(rawChain);
     const placed = byPlace[terminal._id] || [];
-    const kids = $f511198465122338$var$relevantChildren(terminal, taxonomy, relevant);
+    const kids = $597fe213417ee6ca$var$relevantChildren(terminal, taxonomy, relevant);
     const hasKids = kids.length > 0;
     const isOpen = expanded.has(+terminal._id);
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        className: "tax-node gsea-tree-node",
+        className: "tax-node oe-tree-node",
         children: [
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
                 className: "tax-row",
@@ -13549,14 +13528,14 @@ const $f511198465122338$var$SpeciesTreeNode = ({ node: node, depth: depth, taxon
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
                         className: hasKids ? 'tax-label tax-label-internal' : 'tax-label',
-                        children: $f511198465122338$var$renderChain(chain)
+                        children: $597fe213417ee6ca$var$renderChain(chain)
                     })
                 ]
             }),
             placed.map(({ tid: tid, count: count })=>{
                 const isActive = String(activeTaxon) === String(tid);
                 return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                    className: 'gsea-tree-leaf' + (isActive ? ' gsea-tree-leaf-active' : ''),
+                    className: 'oe-tree-leaf' + (isActive ? ' oe-tree-leaf-active' : ''),
                     style: {
                         paddingLeft: (depth + 1) * 7 + 18
                     },
@@ -13569,11 +13548,11 @@ const $f511198465122338$var$SpeciesTreeNode = ({ node: node, depth: depth, taxon
                             onChange: ()=>onSelect(tid)
                         }),
                         /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                            className: "gsea-tree-leaf-name",
-                            children: $f511198465122338$var$genomeName(grameneMaps, tid)
+                            className: "oe-tree-leaf-name",
+                            children: $597fe213417ee6ca$var$genomeName(grameneMaps, tid)
                         }),
                         /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                            className: "gsea-tree-leaf-count",
+                            className: "oe-tree-leaf-count",
                             children: count.toLocaleString()
                         })
                     ]
@@ -13581,7 +13560,7 @@ const $f511198465122338$var$SpeciesTreeNode = ({ node: node, depth: depth, taxon
             }),
             hasKids && isOpen && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
                 className: "tax-children",
-                children: kids.map((c)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SpeciesTreeNode, {
+                children: kids.map((c)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SpeciesTreeNode, {
                         node: c,
                         depth: depth + 1,
                         taxonomy: taxonomy,
@@ -13597,16 +13576,16 @@ const $f511198465122338$var$SpeciesTreeNode = ({ node: node, depth: depth, taxon
         ]
     });
 };
-const $f511198465122338$var$SpeciesTree = ({ taxonomy: taxonomy, grameneMaps: grameneMaps, taxa: taxa, activeTaxon: activeTaxon, onSelect: onSelect })=>{
-    const { placement: placement, byPlace: byPlace } = (0, $gXNCa$react.useMemo)(()=>$f511198465122338$var$placeTaxa(taxonomy, taxa), [
+const $597fe213417ee6ca$var$SpeciesTree = ({ taxonomy: taxonomy, grameneMaps: grameneMaps, taxa: taxa, activeTaxon: activeTaxon, onSelect: onSelect })=>{
+    const { placement: placement, byPlace: byPlace } = (0, $gXNCa$react.useMemo)(()=>$597fe213417ee6ca$var$placeTaxa(taxonomy, taxa), [
         taxonomy,
         taxa
     ]);
-    const relevant = (0, $gXNCa$react.useMemo)(()=>$f511198465122338$var$relevantNodeIds(taxonomy, byPlace), [
+    const relevant = (0, $gXNCa$react.useMemo)(()=>$597fe213417ee6ca$var$relevantNodeIds(taxonomy, byPlace), [
         taxonomy,
         byPlace
     ]);
-    const roots = (0, $gXNCa$react.useMemo)(()=>$f511198465122338$var$findRoots(taxonomy).filter((r)=>relevant.has(+r._id)), [
+    const roots = (0, $gXNCa$react.useMemo)(()=>$597fe213417ee6ca$var$findRoots(taxonomy).filter((r)=>relevant.has(+r._id)), [
         taxonomy,
         relevant
     ]);
@@ -13629,16 +13608,16 @@ const $f511198465122338$var$SpeciesTree = ({ taxonomy: taxonomy, grameneMaps: gr
     // itself a placed leaf, render from its child instead.
     const topLevel = [];
     for (const r of roots){
-        const { terminal: terminal } = $f511198465122338$var$compressChain(r, taxonomy, relevant, byPlace);
+        const { terminal: terminal } = $597fe213417ee6ca$var$compressChain(r, taxonomy, relevant, byPlace);
         if (byPlace[terminal._id]) topLevel.push(r);
         else {
-            const kids = $f511198465122338$var$relevantChildren(terminal, taxonomy, relevant);
+            const kids = $597fe213417ee6ca$var$relevantChildren(terminal, taxonomy, relevant);
             kids.forEach((k)=>topLevel.push(k));
         }
     }
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-tree",
-        children: topLevel.map((n)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SpeciesTreeNode, {
+        className: "oe-tree",
+        children: topLevel.map((n)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SpeciesTreeNode, {
                 node: n,
                 depth: 0,
                 taxonomy: taxonomy,
@@ -13653,14 +13632,35 @@ const $f511198465122338$var$SpeciesTree = ({ taxonomy: taxonomy, grameneMaps: gr
     });
 };
 // ---------- enrichment panel ----------
-const $f511198465122338$var$ControlsBar = ({ ui: ui, onChange: onChange })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        className: "gsea-controls",
+const $597fe213417ee6ca$var$HelpIcon = ({ text: text })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.OverlayTrigger), {
+        placement: "top",
+        overlay: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tooltip), {
+            children: text
+        }),
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+            className: "oe-help",
+            tabIndex: 0,
+            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reacticonsbs.BsInfoCircle), {})
+        })
+    });
+const $597fe213417ee6ca$var$LabeledHelp = ({ label: label, help: help })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Label, {
+        children: [
+            label,
+            " ",
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$HelpIcon, {
+                text: help
+            })
+        ]
+    });
+const $597fe213417ee6ca$var$ControlsBar = ({ ui: ui, onChange: onChange })=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        className: "oe-controls",
         children: [
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
-                className: "gsea-control",
+                className: "oe-control",
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
-                        children: "p_adj \u2264"
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$LabeledHelp, {
+                        label: "p.adjust \u2264",
+                        help: "Adjusted p-value cutoff (Benjamini\u2013Hochberg). Terms with p.adjust above this are not reported as significant."
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
                         type: "number",
@@ -13675,37 +13675,64 @@ const $f511198465122338$var$ControlsBar = ({ ui: ui, onChange: onChange })=>/*#_
                 ]
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
-                className: "gsea-control",
+                className: "oe-control",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$LabeledHelp, {
+                        label: "minGSSize",
+                        help: "Minimum gene set size: a term must have at least this many annotated genes in the universe to be tested. Filters out terms too small to give reliable enrichment statistics. clusterProfiler default: 10."
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
+                        type: "number",
+                        step: "1",
+                        min: "1",
+                        value: ui.minGSSize,
+                        onChange: (e)=>onChange({
+                                minGSSize: Math.max(1, +e.target.value)
+                            })
+                    })
+                ]
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
+                className: "oe-control",
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
-                        children: "min k"
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$LabeledHelp, {
+                        label: "maxGSSize",
+                        help: "Maximum gene set size: terms with more than this many annotated genes are excluded. Drops the very general top-level terms (e.g. GO root) which carry little biological signal. clusterProfiler default: 500."
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
                         type: "number",
                         step: "1",
                         min: "1",
-                        value: ui.minK,
+                        value: ui.maxGSSize,
                         onChange: (e)=>onChange({
-                                minK: Math.max(1, +e.target.value)
+                                maxGSSize: Math.max(1, +e.target.value)
                             })
                     })
                 ]
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Check, {
-                className: "gsea-control",
-                type: "switch",
-                id: "gsea-most-specific",
-                label: "Most-specific only",
-                checked: !!ui.mostSpecific,
-                onChange: (e)=>onChange({
-                        mostSpecific: e.target.checked
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                className: "oe-control oe-switch",
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Check, {
+                        type: "switch",
+                        id: "oe-most-specific",
+                        label: "Drop ancestor terms",
+                        checked: !!ui.mostSpecific,
+                        onChange: (e)=>onChange({
+                                mostSpecific: e.target.checked
+                            })
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$HelpIcon, {
+                        text: "If a passing term has a more specific descendant that also passes, hide the ancestor \u2014 keeps only the most-specific significant term in each branch. Applied after BH correction. Analogous to clusterProfiler's simplify() (off by default in enrichGO)."
                     })
+                ]
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Form).Group, {
-                className: "gsea-control gsea-control-grow",
+                className: "oe-control oe-control-grow",
                 children: [
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Label, {
-                        children: "Filter terms"
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$LabeledHelp, {
+                        label: "Filter terms",
+                        help: "Live text filter on the result table \u2014 matches term ID or name."
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Form).Control, {
                         type: "text",
@@ -13719,53 +13746,45 @@ const $f511198465122338$var$ControlsBar = ({ ui: ui, onChange: onChange })=>/*#_
             })
         ]
     });
-const $f511198465122338$var$TermRow = ({ row: row, showType: showType, onAddFilter: onAddFilter })=>{
+const $597fe213417ee6ca$var$TermRow = ({ row: row, showType: showType, onAddFilter: onAddFilter })=>{
     const handleClick = ()=>onAddFilter && onAddFilter(row);
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
         onClick: handleClick,
         title: "Click to add as a filter",
         children: [
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                className: "gsea-term-id",
+                className: "oe-term-id",
                 children: row.term_display_id
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                className: "gsea-term-name",
+                className: "oe-term-name",
                 children: row.term_name || /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
                     children: "(loading\u2026)"
                 })
             }),
             showType && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                className: "gsea-term-type",
+                className: "oe-term-type",
                 children: row.term_namespace || ''
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
-                className: "gsea-num",
-                children: [
-                    row.k,
-                    " / ",
-                    row.n
-                ]
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "oe-num",
+                children: row.GeneRatio
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("td", {
-                className: "gsea-num",
-                children: [
-                    row.K,
-                    " / ",
-                    row.N
-                ]
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
+                className: "oe-num",
+                children: row.BgRatio
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                className: "gsea-num",
-                children: $f511198465122338$var$fmtFold(row.fold)
+                className: "oe-num",
+                children: $597fe213417ee6ca$var$fmtFold(row.FoldEnrichment)
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                className: "gsea-num",
-                children: $f511198465122338$var$fmtP(row.p)
+                className: "oe-num",
+                children: $597fe213417ee6ca$var$fmtP(row.pvalue)
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("td", {
-                className: "gsea-num",
-                children: $f511198465122338$var$fmtP(row.pAdj)
+                className: "oe-num",
+                children: $597fe213417ee6ca$var$fmtP(row.pAdjust)
             })
         ]
     });
@@ -13774,47 +13793,56 @@ const $f511198465122338$var$TermRow = ({ row: row, showType: showType, onAddFilt
 // (e.g. Domain vs Family vs Repeat for InterPro), and aren't reflected in
 // the section title the way GO namespaces are. Show a Type column for
 // those two ontologies only.
-const $f511198465122338$var$ONTS_WITH_TYPE_COLUMN = new Set([
+const $597fe213417ee6ca$var$ONTS_WITH_TYPE_COLUMN = new Set([
     'domains',
     'pathways'
 ]);
-const $f511198465122338$var$SORT_ACCESSORS = {
+const $597fe213417ee6ca$var$SORT_ACCESSORS = {
     term: (r)=>r.term_display_id || '',
     name: (r)=>(r.term_name || '').toLowerCase(),
     type: (r)=>(r.term_namespace || '').toLowerCase(),
-    k: (r)=>r.k,
-    K: (r)=>r.K,
-    fold: (r)=>r.fold,
-    p: (r)=>r.p,
-    pAdj: (r)=>r.pAdj
+    count: (r)=>r.Count,
+    setSize: (r)=>r.SetSize,
+    fold: (r)=>r.FoldEnrichment,
+    p: (r)=>r.pvalue,
+    pAdj: (r)=>r.pAdjust
 };
 // Defaults chosen so a single click does what the user usually wants:
-// numeric "more interesting" columns (k, K, fold) descend; p-values and
-// text columns ascend.
-const $f511198465122338$var$SORT_DEFAULT_DIR = {
+// numeric "more interesting" columns descend; p-values and text columns ascend.
+const $597fe213417ee6ca$var$SORT_DEFAULT_DIR = {
     term: 'asc',
     name: 'asc',
     type: 'asc',
-    k: 'desc',
-    K: 'desc',
+    count: 'desc',
+    setSize: 'desc',
     fold: 'desc',
     p: 'asc',
     pAdj: 'asc'
 };
-const $f511198465122338$var$SortableTh = ({ label: label, sortKey: sortKey, activeKey: activeKey, activeDir: activeDir, onSort: onSort, numeric: numeric })=>{
+const $597fe213417ee6ca$var$SortableTh = ({ label: label, sortKey: sortKey, activeKey: activeKey, activeDir: activeDir, onSort: onSort, numeric: numeric, help: help })=>{
     const active = activeKey === sortKey;
     const arrow = active ? activeDir === 'asc' ? " \u25B2" : " \u25BC" : '';
-    const cls = 'gsea-sort-th' + (active ? ' gsea-sort-th-active' : '') + (numeric ? ' gsea-num' : '');
-    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("th", {
-        className: cls,
-        onClick: ()=>onSort(sortKey),
+    const cls = 'oe-sort-th' + (active ? ' oe-sort-th-active' : '') + (numeric ? ' oe-num' : '');
+    const inner = /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+        className: "oe-th-inner",
         children: [
             label,
             arrow
         ]
     });
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("th", {
+        className: cls,
+        onClick: ()=>onSort(sortKey),
+        children: help ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.OverlayTrigger), {
+            placement: "top",
+            overlay: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Tooltip), {
+                children: help
+            }),
+            children: inner
+        }) : inner
+    });
 };
-const $f511198465122338$var$OntologySection = ({ block: block, search: search, onAddFilter: onAddFilter })=>{
+const $597fe213417ee6ca$var$OntologySection = ({ block: block, search: search, onAddFilter: onAddFilter })=>{
     const filtered = (0, $gXNCa$react.useMemo)(()=>{
         if (!search) return block.rows;
         const needle = search.toLowerCase();
@@ -13823,18 +13851,18 @@ const $f511198465122338$var$OntologySection = ({ block: block, search: search, o
         block.rows,
         search
     ]);
-    const showType = $f511198465122338$var$ONTS_WITH_TYPE_COLUMN.has(block.ontology);
+    const showType = $597fe213417ee6ca$var$ONTS_WITH_TYPE_COLUMN.has(block.ontology);
     const [sortKey, setSortKey] = (0, $gXNCa$react.useState)('pAdj');
     const [sortDir, setSortDir] = (0, $gXNCa$react.useState)('asc');
     const handleSort = (key)=>{
         if (key === sortKey) setSortDir((d)=>d === 'asc' ? 'desc' : 'asc');
         else {
             setSortKey(key);
-            setSortDir($f511198465122338$var$SORT_DEFAULT_DIR[key] || 'asc');
+            setSortDir($597fe213417ee6ca$var$SORT_DEFAULT_DIR[key] || 'asc');
         }
     };
     const sorted = (0, $gXNCa$react.useMemo)(()=>{
-        const accessor = $f511198465122338$var$SORT_ACCESSORS[sortKey];
+        const accessor = $597fe213417ee6ca$var$SORT_ACCESSORS[sortKey];
         if (!accessor) return filtered;
         const sign = sortDir === 'desc' ? -1 : 1;
         const arr = filtered.slice();
@@ -13859,18 +13887,29 @@ const $f511198465122338$var$OntologySection = ({ block: block, search: search, o
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Header, {
                 children: [
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
-                        className: "gsea-ont-title",
+                        className: "oe-ont-title",
                         children: block.label
                     }),
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Badge), {
                         bg: "secondary",
-                        className: "gsea-ont-badge",
+                        className: "oe-ont-badge",
                         children: [
                             block.passing,
                             " significant / ",
                             block.tested,
                             " tested"
                         ]
+                    }),
+                    block.universeSize > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Badge), {
+                        bg: "light",
+                        text: "dark",
+                        className: "oe-ont-badge",
+                        children: [
+                            "input ",
+                            block.deSize,
+                            " / universe ",
+                            block.universeSize.toLocaleString()
+                        ]
                     })
                 ]
             }),
@@ -13878,77 +13917,85 @@ const $f511198465122338$var$OntologySection = ({ block: block, search: search, o
                 children: sorted.length === 0 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
                     children: "No terms pass the current cutoffs."
                 }) : /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("table", {
-                    className: "gsea-table",
+                    className: "oe-table",
                     children: [
                         /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("thead", {
                             children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("tr", {
                                 children: [
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
                                         label: "Term",
                                         sortKey: "term",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
-                                        onSort: handleSort
+                                        onSort: handleSort,
+                                        help: "Ontology term identifier (e.g. GO:0008150). Click a row to add the term as a filter."
                                     }),
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
-                                        label: "Name",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
+                                        label: "Description",
                                         sortKey: "name",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
-                                        onSort: handleSort
+                                        onSort: handleSort,
+                                        help: "Human-readable name of the term."
                                     }),
-                                    showType && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
+                                    showType && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
                                         label: "Type",
                                         sortKey: "type",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
-                                        onSort: handleSort
+                                        onSort: handleSort,
+                                        help: "Sub-classification within the ontology (e.g. Domain / Family / Repeat for InterPro)."
                                     }),
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
-                                        label: "k / n",
-                                        sortKey: "k",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
+                                        label: "GeneRatio",
+                                        sortKey: "count",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
                                         onSort: handleSort,
-                                        numeric: true
+                                        numeric: true,
+                                        help: "Count / DESize: how many of the input genes are annotated to this term, over the total input genes that have any annotation in this ontology."
                                     }),
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
-                                        label: "K / N",
-                                        sortKey: "K",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
+                                        label: "BgRatio",
+                                        sortKey: "setSize",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
                                         onSort: handleSort,
-                                        numeric: true
+                                        numeric: true,
+                                        help: "SetSize / UniverseSize: how many genes in the species are annotated to this term, over the total genes annotated anywhere in this ontology (the universe)."
                                     }),
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
-                                        label: "Fold",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
+                                        label: "FoldEnrichment",
                                         sortKey: "fold",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
                                         onSort: handleSort,
-                                        numeric: true
+                                        numeric: true,
+                                        help: "(Count/DESize) / (SetSize/UniverseSize). Ratio of observed to expected overlap. Values > 1 mean the term is over-represented in the input."
                                     }),
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
-                                        label: "p",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
+                                        label: "pvalue",
                                         sortKey: "p",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
                                         onSort: handleSort,
-                                        numeric: true
+                                        numeric: true,
+                                        help: "Raw upper-tail hypergeometric p-value: P(overlap \u2265 observed) under the null that the input is a random sample from the universe."
                                     }),
-                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SortableTh, {
-                                        label: "p_adj",
+                                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SortableTh, {
+                                        label: "p.adjust",
                                         sortKey: "pAdj",
                                         activeKey: sortKey,
                                         activeDir: sortDir,
                                         onSort: handleSort,
-                                        numeric: true
+                                        numeric: true,
+                                        help: "Benjamini\u2013Hochberg adjusted p-value, computed across all terms tested in this ontology section. Use this (not the raw p-value) for significance."
                                     })
                                 ]
                             })
                         }),
                         /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("tbody", {
-                            children: sorted.map((r)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$TermRow, {
+                            children: sorted.map((r)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$TermRow, {
                                     row: r,
                                     showType: showType,
                                     onAddFilter: onAddFilter
@@ -13960,28 +14007,28 @@ const $f511198465122338$var$OntologySection = ({ block: block, search: search, o
         ]
     });
 };
-const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: results, ui: ui, onUiChange: onUiChange, onAddFilter: onAddFilter })=>{
+const $597fe213417ee6ca$var$TaxonPanel = ({ taxon: taxon, ontologyEnrichment: ontologyEnrichment, results: results, ui: ui, onUiChange: onUiChange, onAddFilter: onAddFilter })=>{
     if (!taxon) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-panel",
+        className: "oe-panel",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
             children: "Select a species on the left."
         })
     });
-    const t = gsea.byTaxon[taxon];
+    const t = ontologyEnrichment.byTaxon[taxon];
     if (!t) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-panel",
+        className: "oe-panel",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
             children: "Initializing\u2026"
         })
     });
     if (t.fg.status === 'loading' || t.bg.status === 'loading' || t.fg.status === 'idle' || t.bg.status === 'idle') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-panel gsea-loading",
+        className: "oe-panel oe-loading",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
             children: "Loading enrichment\u2026"
         })
     });
     if (t.fg.status === 'error') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-panel",
+        className: "oe-panel",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("em", {
             children: [
                 "Foreground error: ",
@@ -13990,7 +14037,7 @@ const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: r
         })
     });
     if (t.bg.status === 'error') return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-panel",
+        className: "oe-panel",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("em", {
             children: [
                 "Background error: ",
@@ -13999,7 +14046,7 @@ const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: r
         })
     });
     if (!results) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-panel",
+        className: "oe-panel",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
             children: "No data."
         })
@@ -14010,10 +14057,10 @@ const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: r
     // Hide ontologies that aren't used in this species at all.
     const blocks = allBlocks.filter((b)=>b.tested > 0);
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        className: "gsea-panel",
+        className: "oe-panel",
         children: [
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                className: "gsea-summary",
+                className: "oe-summary",
                 children: [
                     "Foreground: ",
                     /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
@@ -14026,14 +14073,14 @@ const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: r
                     " genes"
                 ]
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$ControlsBar, {
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$ControlsBar, {
                 ui: ui,
                 onChange: onUiChange
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion), {
                 alwaysOpen: true,
                 defaultActiveKey: blocks.length === 1 ? blocks[0].ontology : undefined,
-                children: blocks.map((b)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$OntologySection, {
+                children: blocks.map((b)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$OntologySection, {
                         block: b,
                         search: ui.search,
                         onAddFilter: onAddFilter
@@ -14042,8 +14089,8 @@ const $f511198465122338$var$TaxonPanel = ({ taxon: taxon, gsea: gsea, results: r
         ]
     });
 };
-const $f511198465122338$var$GseaViewCmp = (props)=>{
-    const { grameneSearch: grameneSearch, grameneMaps: grameneMaps, grameneTaxonomy: grameneTaxonomy, gsea: gsea, gseaUI: ui, gseaResults: results, doSetGseaActiveTaxon: doSetGseaActiveTaxon, doSetGseaUI: doSetGseaUI, doFetchGseaForeground: doFetchGseaForeground, doFetchGseaBackground: doFetchGseaBackground, doAcceptGrameneSuggestion: doAcceptGrameneSuggestion } = props;
+const $597fe213417ee6ca$var$OntologyEnrichmentViewCmp = (props)=>{
+    const { grameneSearch: grameneSearch, grameneMaps: grameneMaps, grameneTaxonomy: grameneTaxonomy, ontologyEnrichment: ontologyEnrichment, ontologyEnrichmentUI: ui, ontologyEnrichmentResults: results, doSetOntologyEnrichmentActiveTaxon: doSetOntologyEnrichmentActiveTaxon, doSetOntologyEnrichmentUI: doSetOntologyEnrichmentUI, doFetchOntologyEnrichmentForeground: doFetchOntologyEnrichmentForeground, doFetchOntologyEnrichmentBackground: doFetchOntologyEnrichmentBackground, doAcceptGrameneSuggestion: doAcceptGrameneSuggestion } = props;
     const taxa = (0, $gXNCa$react.useMemo)(()=>{
         if (!grameneSearch || !grameneSearch.facet_counts) return [];
         const arr = grameneSearch.facet_counts.facet_fields.taxon_id || [];
@@ -14054,8 +14101,8 @@ const $f511198465122338$var$GseaViewCmp = (props)=>{
             counts[arr[i]] = +arr[i + 1];
         }
         if (grameneMaps) ids.sort((a, b)=>{
-            const ma = grameneMaps[a] || grameneMaps[$f511198465122338$var$speciesTaxonId(a)];
-            const mb = grameneMaps[b] || grameneMaps[$f511198465122338$var$speciesTaxonId(b)];
+            const ma = grameneMaps[a] || grameneMaps[$597fe213417ee6ca$var$speciesTaxonId(a)];
+            const mb = grameneMaps[b] || grameneMaps[$597fe213417ee6ca$var$speciesTaxonId(b)];
             return (ma && ma.left_index || 0) - (mb && mb.left_index || 0);
         });
         return ids.map((tid)=>({
@@ -14066,7 +14113,7 @@ const $f511198465122338$var$GseaViewCmp = (props)=>{
         grameneSearch,
         grameneMaps
     ]);
-    const activeTaxon = gsea.activeTaxon;
+    const activeTaxon = ontologyEnrichment.activeTaxon;
     const [treeWidth, setTreeWidth] = (0, $gXNCa$react.useState)(280);
     const beginResize = (e)=>{
         e.preventDefault();
@@ -14089,32 +14136,32 @@ const $f511198465122338$var$GseaViewCmp = (props)=>{
     };
     (0, $gXNCa$react.useEffect)(()=>{
         if (taxa.length === 0) return;
-        if (!activeTaxon || !taxa.find((t)=>String(t.tid) === String(activeTaxon))) doSetGseaActiveTaxon(taxa[0].tid);
+        if (!activeTaxon || !taxa.find((t)=>String(t.tid) === String(activeTaxon))) doSetOntologyEnrichmentActiveTaxon(taxa[0].tid);
     }, [
         taxa,
         activeTaxon,
-        doSetGseaActiveTaxon
+        doSetOntologyEnrichmentActiveTaxon
     ]);
     (0, $gXNCa$react.useEffect)(()=>{
         if (!activeTaxon) return;
-        const t = gsea.byTaxon[activeTaxon];
+        const t = ontologyEnrichment.byTaxon[activeTaxon];
         if (!t) return;
-        if (t.fg.status === 'idle') doFetchGseaForeground(activeTaxon);
-        if (t.bg.status === 'idle') doFetchGseaBackground(activeTaxon);
+        if (t.fg.status === 'idle') doFetchOntologyEnrichmentForeground(activeTaxon);
+        if (t.bg.status === 'idle') doFetchOntologyEnrichmentBackground(activeTaxon);
     }, [
         activeTaxon,
-        gsea,
-        doFetchGseaForeground,
-        doFetchGseaBackground
+        ontologyEnrichment,
+        doFetchOntologyEnrichmentForeground,
+        doFetchOntologyEnrichmentBackground
     ]);
     if (taxa.length === 0) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-view",
+        className: "oe-view",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
             children: "No species in the current results."
         })
     });
     if (!grameneTaxonomy) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-        className: "gsea-view",
+        className: "oe-view",
         children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("em", {
             children: "Loading taxonomy\u2026"
         })
@@ -14130,41 +14177,41 @@ const $f511198465122338$var$GseaViewCmp = (props)=>{
         });
     };
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-        className: "gsea-view gsea-layout",
+        className: "oe-view oe-layout",
         children: [
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "gsea-layout-tree",
+                className: "oe-layout-tree",
                 style: {
                     flex: `0 0 ${treeWidth}px`
                 },
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$SpeciesTree, {
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$SpeciesTree, {
                     taxonomy: grameneTaxonomy,
                     grameneMaps: grameneMaps,
                     taxa: taxa,
                     activeTaxon: activeTaxon,
-                    onSelect: (tid)=>doSetGseaActiveTaxon(String(tid))
+                    onSelect: (tid)=>doSetOntologyEnrichmentActiveTaxon(String(tid))
                 })
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "gsea-splitter",
+                className: "oe-splitter",
                 onMouseDown: beginResize,
                 title: "Drag to resize"
             }),
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                className: "gsea-layout-panel",
-                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($f511198465122338$var$TaxonPanel, {
+                className: "oe-layout-panel",
+                children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($597fe213417ee6ca$var$TaxonPanel, {
                     taxon: activeTaxon ? String(activeTaxon) : null,
-                    gsea: gsea,
+                    ontologyEnrichment: ontologyEnrichment,
                     results: results,
                     ui: ui,
-                    onUiChange: doSetGseaUI,
+                    onUiChange: doSetOntologyEnrichmentUI,
                     onAddFilter: handleAddFilter
                 })
             })
         ]
     });
 };
-var $f511198465122338$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneSearch', 'selectGrameneMaps', 'selectGrameneTaxonomy', 'selectGsea', 'selectGseaUI', 'selectGseaResults', 'doSetGseaActiveTaxon', 'doSetGseaUI', 'doFetchGseaForeground', 'doFetchGseaBackground', 'doAcceptGrameneSuggestion', $f511198465122338$var$GseaViewCmp);
+var $597fe213417ee6ca$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)('selectGrameneSearch', 'selectGrameneMaps', 'selectGrameneTaxonomy', 'selectOntologyEnrichment', 'selectOntologyEnrichmentUI', 'selectOntologyEnrichmentResults', 'doSetOntologyEnrichmentActiveTaxon', 'doSetOntologyEnrichmentUI', 'doFetchOntologyEnrichmentForeground', 'doFetchOntologyEnrichmentBackground', 'doAcceptGrameneSuggestion', $597fe213417ee6ca$var$OntologyEnrichmentViewCmp);
 
 
 
@@ -14285,7 +14332,7 @@ const $693dd8c7a5607c3a$var$inventory = {
     attribs: (0, $67bf5a43401bffdc$export$2e2bcd8739ae039),
     expression: (0, $261baeb81c4d4d8a$export$2e2bcd8739ae039),
     exprViz: (0, $1fd2507769d5bd00$export$2e2bcd8739ae039),
-    gsea: (0, $f511198465122338$export$2e2bcd8739ae039),
+    ontologyEnrichment: (0, $597fe213417ee6ca$export$2e2bcd8739ae039),
     userLists: (0, $0f50f369018a42ef$export$2e2bcd8739ae039),
     export: (0, $37b3bb0145d266b0$export$2e2bcd8739ae039)
 };