protvista-uniprot 4.4.0 → 4.4.1

package/dist/types/tooltips/ptm-tooltip.d.ts

@@ -1,5 +1,7 @@
 import { PTM } from '../adapters/ptm-exchange-adapter';
 export declare const phosphorylate: (aa: string) => string;
 export declare const sumoylate: (aa: string) => string;
+export declare const ubiquitinate: (aa: string) => string;
+export declare const acetylate: (aa: string) => string;
 declare const formatTooltip: (title: string, ptms: PTM[], aa: string, confidenceScore: string) => string;
 export default formatTooltip;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "4.4.0",
+  "version": "4.4.1",
   "files": [
     "dist",
     "src"
@@ -36,7 +36,7 @@
     "@nightingale-elements/nightingale-manager": "5.6.0",
     "@nightingale-elements/nightingale-navigation": "5.6.0",
     "@nightingale-elements/nightingale-sequence": "5.6.0",
-    "@nightingale-elements/nightingale-sequence-heatmap": "5.6.0",
+    "@nightingale-elements/nightingale-sequence-heatmap": "5.6.2",
     "@nightingale-elements/nightingale-structure": "5.7.0",
     "@nightingale-elements/nightingale-track-canvas": "5.6.0",
     "@nightingale-elements/nightingale-variation": "5.6.0",

package/src/adapters/alphamissense-pathogenicity-adapter.ts

@@ -1,15 +1,38 @@
 import { AlphafoldPayload } from './types/alphafold';
 
-// from example data
-// benign: [0.0448,0.3397]: x < 0.34
-// ambiguous: [0.34,0.564]: 0.34 <= x <= 0.564
-// pathogenic: [0.5646,0.9999]: 0.564 < x
-const benign = 0.34;
-const pathogenic = 0.564;
+// from color scale B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1
+const certainlyBenign = 0;
+const benign = 0.1132;
+const veryLikelyBenign = 0.2264;
+const likelyBenign = 0.3395;
+const ambiguous = 0.4527;
+const likelyAmbiguous = 0.5895;
+const likelyPathogenic = 0.7264;
+const pathogenic = 0.8632;
+const certainlyPathogenic = 1;
 
 export const rowSplitter = /\s*\n\s*/;
 export const cellSplitter = /^(.)(\d+)(.),(.+),(\w+)$/;
 
+const pathogenicityCategories = [
+  { min: certainlyBenign, max: benign, code: 'H' },
+  { min: benign, max: veryLikelyBenign, code: 'V' },
+  { min: veryLikelyBenign, max: likelyBenign, code: 'L' },
+  { min: likelyBenign, max: ambiguous, code: 'A' },
+  { min: ambiguous, max: likelyAmbiguous, code: 'l' },
+  { min: likelyAmbiguous, max: likelyPathogenic, code: 'h' },
+  { min: likelyPathogenic, max: pathogenic, code: 'p' },
+  { min: pathogenic, max: certainlyPathogenic, code: 'P' },
+];
+
+const getPathogenicityCode = (score) => {
+  for (const { min, max, code } of pathogenicityCategories) {
+    if (score >= min && score < max) {
+      return code;
+    }
+  }
+};
+
 type Row = {
   wildType: string;
   position: number;
@@ -48,7 +71,6 @@ const parseCSV = (rawText: string): string => {
 
   const out = [];
   for (const position of positions) {
-    let letter = 'A';
     // maximum
     // const value = Math.max(
     //   ...position.map((variation) => variation.pathogenicityScore)
@@ -59,11 +81,7 @@ const parseCSV = (rawText: string): string => {
         (acc, variation) => acc + +variation.pathogenicityScore,
         0
       ) / position.length;
-    if (value > pathogenic) {
-      letter = 'P';
-    } else if (value < benign) {
-      letter = 'B';
-    }
+    const letter = getPathogenicityCode(value);
     out.push(letter);
   }
 

package/src/adapters/proteomics-adapter.ts

@@ -13,64 +13,19 @@ const transformData = (data) => {
   let adaptedData = [];
 
   if (data && data.length !== 0) {
-    /* Important: The PTM map is a temporary patch until multiple modifications are shown in the peptide. At this point, only 'phospho' sites are of interest. 
-      Once they are available in the data, there is no need for the below merging */
-
-    // To merge PTM data present in same residue in a same length peptide, have a map [key: start-end-phospho site 1-... phosphosite n, value: corresponding feature elements]
-    const ptmMap: Record<string, any> = {};
-    data.features.forEach((feature) => {
-      let ft = `${feature.begin}-${feature.end}`;
-      if (feature.ptms) {
-        feature.ptms.forEach((ptm) => {
-          ft += `-${ptm.position}`;
-        });
-        ptmMap[ft] = ft in ptmMap ? [...ptmMap[ft], feature] : [feature];
-      }
+    adaptedData = data.features.map((feature) => {
+      feature.residuesToHighlight = feature.ptms?.map((ptm) => ({
+        name: ptm.name,
+        position: ptm.position,
+        sources: ptm.sources,
+        dbReferences: ptm.dbReferences,
+      }));
+      return Object.assign(
+        feature,
+        proteomicsTrackProperties(feature, data.taxid)
+      );
     });
 
-    // The else part alone is enough if the PTM information need not be merged.
-    if (Object.keys(ptmMap).length) {
-      adaptedData = Object.values(ptmMap).map((features) => {
-        // Only the dbReferences have to be merged as the rest is all the same
-        const mergedDbReferences = [];
-        features.forEach((feature) => {
-          feature.ptms.forEach((ptm) => {
-            ptm.dbReferences.forEach((dbReference) => {
-              mergedDbReferences.push(dbReference);
-            });
-          });
-        });
-
-        const mergedFeatures = {
-          type: features[0].type,
-          begin: features[0].begin,
-          end: features[0].end,
-          xrefs: features[0].xrefs,
-          evidences: features[0].evidences,
-          peptide: features[0].peptide,
-          unique: features[0].unique,
-          residuesToHighlight: features[0].ptms.map((ptm) => ({
-            name: ptm.name,
-            position: ptm.position,
-            sources: ptm.sources,
-            dbReferences: mergedDbReferences,
-          })),
-        };
-
-        return Object.assign(
-          mergedFeatures,
-          proteomicsTrackProperties(mergedFeatures, data.taxid)
-        );
-      }, []);
-    } else {
-      adaptedData = data.features.map((feature) => {
-        return Object.assign(
-          feature,
-          proteomicsTrackProperties(feature, data.taxid)
-        );
-      });
-    }
-
     adaptedData = renameProperties(adaptedData);
   }
   return adaptedData;

package/src/adapters/ptm-exchange-adapter.ts

@@ -59,38 +59,50 @@ const convertPtmExchangePtms = (
   aa: string,
   absolutePosition: number
 ) => {
-  const confidenceScores = new Set(
-    ptms.flatMap(({ dbReferences }) =>
-      dbReferences?.map(({ properties }) => properties['Confidence score'])
-    )
-  );
-  let confidenceScore: string | null = null;
-
-  if (!confidenceScores.size) {
-    console.log('PTM has no confidence score');
-  } else if (confidenceScores.size > 1) {
-    console.error(
-      `PTM has a mixture of confidence scores: ${Array.from(confidenceScores)}`
-    );
-  } else {
-    [confidenceScore] = confidenceScores;
+  const groupPtmsByModification: Record<string, PTM[]> = {};
+  for (const ptm of ptms) {
+    if (groupPtmsByModification[ptm.name]) {
+      groupPtmsByModification[ptm.name].push(ptm);
+    } else {
+      groupPtmsByModification[ptm.name] = [ptm];
+    }
   }
 
-  return {
-    source: 'PTMeXchange',
-    type: 'MOD_RES_LS',
-    start: absolutePosition,
-    end: absolutePosition,
-    shape: 'triangle',
-    tooltipContent: formatTooltip(
-      `MOD_RES_LS ${absolutePosition}-${absolutePosition}`,
-      ptms,
-      aa,
-      confidenceScore
-    ),
-    color:
-      (confidenceScore && ConfidenceScoreColors[confidenceScore]) || 'black',
-  };
+  return Object.values(groupPtmsByModification).map((groupedPtms) => {
+    const confidenceScores = new Set(
+      groupedPtms.flatMap(({ dbReferences }) =>
+        dbReferences?.map(({ properties }) => properties['Confidence score'])
+      )
+    );
+    let confidenceScore: string | null = null;
+    if (confidenceScores.size) {
+      if (confidenceScores.size > 1) {
+        console.error(
+          `PTMeXchange PTM has a mixture of confidence scores: ${Array.from(
+            confidenceScores
+          )}`
+        );
+      } else {
+        [confidenceScore] = confidenceScores;
+      }
+    }
+
+    return {
+      source: 'PTMeXchange',
+      type: 'MOD_RES_LS',
+      start: absolutePosition,
+      end: absolutePosition,
+      shape: 'triangle',
+      tooltipContent: formatTooltip(
+        `MOD_RES_LS ${absolutePosition}-${absolutePosition}`,
+        groupedPtms,
+        aa,
+        confidenceScore
+      ),
+      color:
+        (confidenceScore && ConfidenceScoreColors[confidenceScore]) || 'black',
+    };
+  });
 };
 
 const transformData = (data: ProteomicsPtm) => {
@@ -130,7 +142,7 @@ const transformData = (data: ProteomicsPtm) => {
       return Object.entries(absolutePositionToPtms).map(
         ([absolutePosition, { ptms, aa }]) =>
           convertPtmExchangePtms(ptms, aa, +absolutePosition)
-      );
+      ).flat();
     }
   }
   return [];

package/src/config.ts

@@ -815,8 +815,8 @@ const config: ProtvistaConfig = {
       name: 'ALPHAMISSENSE_PATHOGENICITY',
       label: 'AlphaMissense',
       trackType: 'nightingale-colored-sequence',
-      scale: 'P:100,A:50,B:0',
-      'color-range': '#9a131a:100,#a8a9ad:50,#3d5493:0',
+      scale: 'B:0,H:0.1132,V:0.2264,L:0.3395,A:0.4527,l:0.5895,h:0.7264,p:0.8632,P:1',
+      'color-range': '#2166ac:0,#4290bf:0.1132,#8cbcd4:0.2264,#c3d6e0:0.3395,#e2e2e2:0.4527,#edcdba:0.5895,#e99e7c:0.7264,#d15e4b:0.8632,#b2182b:1',
       tracks: [
         {
           name: 'alphamissense_pathogenicity',

package/src/protvista-uniprot.ts

@@ -16,6 +16,7 @@ import NightingaleSequenceHeatmap from '@nightingale-elements/nightingale-sequen
 import NightingaleFilter, {
   Filter,
 } from '@nightingale-elements/nightingale-filter';
+import { amColorScale } from '@nightingale-elements/nightingale-structure';
 
 // adapters
 import featureAdapter from './adapters/feature-adapter';
@@ -294,6 +295,11 @@ class ProtvistaUniprot extends LitElement {
                 ...new Set(heatmapData.map((hotMapItem) => hotMapItem.yValue)),
               ] as string[];
               heatmapComponent.setHeatmapData(xDomain, yDomain, heatmapData);
+              heatmapComponent.updateComplete.then(() => {
+                heatmapComponent.heatmapInstance.setColor((d) =>
+                  amColorScale(d.score)
+                );
+              });
             }
           }
         }

package/src/tooltips/feature-tooltip.ts

@@ -1,5 +1,10 @@
 import ecoMap from '../adapters/config/evidence';
-import { phosphorylate, sumoylate } from './ptm-tooltip';
+import {
+  acetylate,
+  phosphorylate,
+  sumoylate,
+  ubiquitinate,
+} from './ptm-tooltip';
 
 const taxIdToPeptideAtlasBuildData = {
   '36329': { build: '542', organism: 'Plasmodium' },
@@ -101,12 +106,18 @@ const findModifiedResidueName = (feature, ptm) => {
   const { peptide, begin: peptideStart } = feature;
   const proteinLocation = Number(peptideStart) + ptm.position - 1;
   const modifiedResidue = peptide.charAt(ptm.position - 1); // CharAt index starts from 0
-  if (ptm.name === 'Phosphorylation') {
-    return `${proteinLocation} ${phosphorylate(modifiedResidue)}`;
-  } else if (ptm.name === 'SUMOylation') {
-    return `${proteinLocation} ${sumoylate(modifiedResidue)}`;
+  switch (ptm.name) {
+    case 'Phosphorylation':
+      return `${proteinLocation} ${phosphorylate(modifiedResidue)}`;
+    case 'SUMOylation':
+      return `${proteinLocation} ${sumoylate(modifiedResidue)}`;
+    case 'Ubiquitinylation':
+      return `${proteinLocation} ${ubiquitinate(modifiedResidue)}`;
+    case 'Acetylation':
+      return `${proteinLocation} ${acetylate(modifiedResidue)}`;
+    default:
+      return '';
   }
-  return '';
 };
 
 const formatTooltip = (feature, taxId?: string) => {
@@ -234,8 +245,10 @@ const formatTooltip = (feature, taxId?: string) => {
                         }
                         ${
                           ref.properties['Universal Spectrum Id']
-                            ? `<li class="text-indent-2 nowrap">Universal Spectrum Id: 
-                        <a href="http://proteomecentral.proteomexchange.org/usi/?usi=${ref.properties['Universal Spectrum Id']}" target="_blank">View on ProteomeXchange</a>
+                            ? `<li class="text-indent-2 nowrap margin-bottom">Universal Spectrum Id: 
+                        <a href="http://proteomecentral.proteomexchange.org/usi/?usi=${encodeURIComponent(
+                          ref.properties['Universal Spectrum Id']
+                        )}" target="_blank">View on ProteomeXchange</a>
                         </li>`
                             : ``
                         }                        

package/src/tooltips/ptm-tooltip.ts

@@ -1,6 +1,10 @@
 import { PTM } from '../adapters/ptm-exchange-adapter';
 
-type Modification = 'Phosphorylation' | 'SUMOylation';
+type Modification =
+  | 'Phosphorylation'
+  | 'SUMOylation'
+  | 'Ubiquitinylation'
+  | 'Acetylation';
 
 const aaToPhosphorylated = {
   R: 'Phosphoarginine',
@@ -15,6 +19,31 @@ const aaToSumoylated = {
   K: 'Sumoylated lysine',
 };
 
+const aaToUbiquitinated = {
+  K: 'Ubiquitinated lysine',
+  S: 'Ubiquitinated serine',
+  T: 'Ubiquitinated threonine',
+  C: 'Ubiquitinated cysteine',
+};
+
+const aaToAcetylated = {
+  S: 'Acetylserine',
+  A: 'Acetylalanine',
+  G: 'Acetylglycine',
+  T: 'Acetylthreonine',
+  V: 'Acetylvaline',
+  C: 'Acetylcysteine',
+  E: 'Acetylglutamin acid',
+  D: 'Acetylaspartic acid',
+  N: 'Acetylasparagine',
+  Q: 'Acetylglutamine',
+  L: 'Acetyllucine',
+  I: 'Acetlyisolucine',
+  W: 'Acetyltryptophan',
+  F: 'Acetylphenylalanine',
+  K: 'Acetyllysine',
+};
+
 export const phosphorylate = (aa: string) => {
   const AA = aa.toUpperCase();
   if (AA in aaToPhosphorylated) {
@@ -33,6 +62,39 @@ export const sumoylate = (aa: string) => {
   return '';
 };
 
+export const ubiquitinate = (aa: string) => {
+  const AA = aa.toUpperCase();
+  if (AA in aaToUbiquitinated) {
+    return aaToUbiquitinated[AA as keyof typeof aaToUbiquitinated];
+  }
+  console.error(`${AA} not a valid amino acid for Ubiquitinylation`);
+  return '';
+};
+
+export const acetylate = (aa: string) => {
+  const AA = aa.toUpperCase();
+  if (AA in aaToAcetylated) {
+    return aaToAcetylated[AA as keyof typeof aaToAcetylated];
+  }
+  console.error(`${AA} not a valid amino acid for Acetylation`);
+  return '';
+};
+
+const getDescription = (modification: Modification, aa: string) => {
+  switch (modification) {
+    case 'Phosphorylation':
+      return phosphorylate(aa);
+    case 'SUMOylation':
+      return sumoylate(aa);
+    case 'Ubiquitinylation':
+      return ubiquitinate(aa);
+    case 'Acetylation':
+      return acetylate(aa);
+    default:
+      return '';
+  }
+};
+
 const formatTooltip = (
   title: string,
   ptms: PTM[],
@@ -52,7 +114,7 @@ const formatTooltip = (
   if (modifications.size) {
     if (modifications.size > 1) {
       console.error(
-        `PTMeXchange PTM has a mixture of modifications: ${Array.from(
+        `The ptms are grouped by modification, but more than one type detected: ${Array.from(
           modifications
         )}`
       );
@@ -63,9 +125,7 @@ const formatTooltip = (
 
   return `
   ${title ? `<h4>${title}</h4><hr />` : ''}
-  <h5>Description</h5><p>${
-    modification === 'Phosphorylation' ? phosphorylate(aa) : sumoylate(aa)
-  }</p>
+  <h5>Description</h5><p>${getDescription(modification, aa)}</p>
   ${
     confidenceScore
       ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>`