protvista-uniprot 4.0.0 → 4.2.0

package/dist/types/adapters/ptm-exchange-adapter.d.ts

@@ -29,7 +29,7 @@ type Xref = {
     id: string;
     url: string;
 };
-type PTM = {
+export type PTM = {
     name: string;
     position: number;
     sources: string[];

package/dist/types/adapters/rna-editing-adapter.d.ts

@@ -0,0 +1,6 @@
+import { RnaEditing, TransformedRnaEditing } from './types/rna-editing';
+declare const transformData: ({ sequence, features, }: RnaEditing) => {
+    sequence: string;
+    variants: TransformedRnaEditing[];
+};
+export default transformData;

package/dist/types/adapters/rna-editing-graph-adapter.d.ts

@@ -0,0 +1,11 @@
+import { RnaEditing } from './types/rna-editing';
+declare const transformData: (data: RnaEditing) => {
+    name: string;
+    range: number[];
+    color: string;
+    values: {
+        position: number;
+        value: number;
+    }[];
+}[];
+export default transformData;

package/dist/types/adapters/types/rna-editing.d.ts

@@ -0,0 +1,69 @@
+export type RnaEditing = {
+    accession: string;
+    entryName: string;
+    sequence: string;
+    sequenceChecksum: string;
+    taxid: number;
+    features: RnaEditingFeature[];
+};
+export type RnaEditingFeature = {
+    type: Type;
+    xrefs: Xref[];
+    dbReferenceType: DBReferenceType[];
+    variantType: VariantType;
+    rnaEditingInfo: RnaEditingInfo;
+    locationType: LocationType;
+    variantlocation: string[];
+};
+export type TransformedRnaEditing = RnaEditingFeature & {
+    accession: string;
+    variant: string;
+    start: number;
+    end: number;
+    tooltipContent: string;
+    consequenceType: string;
+};
+type DBReferenceType = {
+    id: string;
+    type: Type;
+};
+type Type = 'rna_editing';
+type LocationType = {
+    position: Position;
+};
+type Position = {
+    position: number;
+    status: Status;
+};
+type Status = 'certain';
+type RnaEditingInfo = {
+    nedBS: number;
+    nsamples: number;
+    nbodySites: number;
+    ntissues: number;
+    nedInd: number;
+};
+type VariantType = {
+    genomicLocation: string[];
+    variantLocation: VariantLocation[];
+    codon: Codon;
+    consequenceType: ConsequenceType;
+    wildType: DType;
+    mutatedType: DType;
+    somaticStatus: boolean;
+    sourceType: SourceType;
+};
+type Codon = 'aCa' | 'aCg' | 'aCc' | 'aCu' | 'aGa' | 'aGc' | 'aGg' | 'aGu' | 'auG' | 'cCa' | 'cCg' | 'cCc' | 'cCu' | 'Cga' | 'cGa' | 'cGc' | 'cGg' | 'cGu' | 'Cac' | 'Cag' | 'Cau' | 'Cca' | 'Ccc' | 'Ccg' | 'Ccu' | 'Cgc' | 'Cgg' | 'Cgu' | 'Cuc' | 'Cuu' | 'gCa' | 'Gcc' | 'gCg' | 'gCc' | 'gCu' | 'gGa' | 'gGc' | 'gGg' | 'gGu' | 'Gaa' | 'Gac' | 'Gag' | 'Gau' | 'Gca' | 'Gcg' | 'Gcu' | 'Gga' | 'Ggc' | 'Ggg' | 'Ggu' | 'Gua' | 'Guc' | 'Gug' | 'Guu' | 'uCa' | 'uCg' | 'uCc' | 'uCu' | 'uGc' | 'uGu' | 'ugG';
+type ConsequenceType = 'missense';
+type DType = 'A' | 'C' | 'D' | 'E' | 'F' | 'G' | 'H' | 'I' | 'K' | 'L' | 'M' | 'N' | 'P' | 'Q' | 'R' | 'S' | 'T' | 'U' | 'V' | 'W' | 'Y';
+type SourceType = 'Rna Editing';
+type VariantLocation = {
+    loc: string;
+    seqId: string;
+    source: Source;
+};
+type Source = 'Ensembl';
+type Xref = {
+    id: string;
+};
+export {};

package/dist/types/config.d.ts

@@ -7,7 +7,7 @@ export type ProtvistaTrackConfig = {
     trackType: TrackType;
     data: {
         url: string | string[];
-        adapter?: 'feature-adapter' | 'structure-adapter' | 'proteomics-adapter' | 'variation-adapter' | 'variation-graph-adapter' | 'interpro-adapter' | 'alphafold-confidence-adapter' | 'alphamissense-pathogenicity-adapter' | 'alphamissense-heatmap-adapter' | 'proteomics-ptm-adapter';
+        adapter?: 'feature-adapter' | 'structure-adapter' | 'proteomics-adapter' | 'variation-adapter' | 'variation-graph-adapter' | 'interpro-adapter' | 'alphafold-confidence-adapter' | 'alphamissense-pathogenicity-adapter' | 'alphamissense-heatmap-adapter' | 'proteomics-ptm-adapter' | 'rna-editing-adapter' | 'rna-editing-graph-adapter';
     }[];
     tooltip: string;
     color?: string;

package/dist/types/tooltips/ptmTooltip.d.ts

@@ -0,0 +1,5 @@
+import { PTM } from '../adapters/ptm-exchange-adapter';
+export declare const phosphorylate: (aa: string) => string;
+export declare const sumoylate: (aa: string) => string;
+declare const formatTooltip: (ptms: PTM[], aa: string, confidenceScore: string) => string;
+export default formatTooltip;

package/dist/types/tooltips/rnaEditingTooltip.d.ts

@@ -0,0 +1,3 @@
+import { TransformedRnaEditing } from '../adapters/types/rna-editing';
+declare const formatTooltip: (feature: TransformedRnaEditing) => string;
+export default formatTooltip;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "4.0.0",
+  "version": "4.2.0",
   "files": [
     "dist",
     "src"
@@ -29,17 +29,17 @@
   "author": "Xavier Watkins <xwatkins@ebi.ac.uk>",
   "license": "MIT",
   "dependencies": {
-    "@nightingale-elements/nightingale-colored-sequence": "5.3.0",
-    "@nightingale-elements/nightingale-filter": "5.3.0",
-    "@nightingale-elements/nightingale-interpro-track": "5.3.0",
-    "@nightingale-elements/nightingale-linegraph-track": "5.3.0",
-    "@nightingale-elements/nightingale-manager": "5.3.0",
-    "@nightingale-elements/nightingale-navigation": "5.3.0",
-    "@nightingale-elements/nightingale-sequence": "5.3.0",
+    "@nightingale-elements/nightingale-colored-sequence": "5.4.0",
+    "@nightingale-elements/nightingale-filter": "5.4.0",
+    "@nightingale-elements/nightingale-interpro-track": "5.4.0",
+    "@nightingale-elements/nightingale-linegraph-track": "5.4.0",
+    "@nightingale-elements/nightingale-manager": "5.4.0",
+    "@nightingale-elements/nightingale-navigation": "5.4.0",
+    "@nightingale-elements/nightingale-sequence": "5.4.0",
     "@nightingale-elements/nightingale-sequence-heatmap": "5.4.0",
-    "@nightingale-elements/nightingale-structure": "5.3.1",
-    "@nightingale-elements/nightingale-track": "5.3.0",
-    "@nightingale-elements/nightingale-variation": "5.3.0",
+    "@nightingale-elements/nightingale-structure": "5.4.0",
+    "@nightingale-elements/nightingale-track": "5.4.0",
+    "@nightingale-elements/nightingale-variation": "5.4.0",
     "color-hash": "2.0.2",
     "core-js": "3.13.0",
     "lit": "3.1.3",

package/src/.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+  "window.title": "${rootPath}${separator}[new-ptm-builds]"
+}

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

@@ -1,3 +1,5 @@
+import formatTooltip from "../tooltips/ptmTooltip";
+
 type ProteomicsPtm = {
   accession: string;
   entryName: string;
@@ -34,7 +36,7 @@ type Xref = {
   url: string;
 };
 
-type PTM = {
+export type PTM = {
   name: string;
   position: number;
   sources: string[];
@@ -52,34 +54,11 @@ enum ConfidenceScoreColors {
   Bronze = '#a65708',
 }
 
-const aaToPhosphorylated = {
-  R: 'Phosphoarginine',
-  C: 'Phosphocysteine',
-  H: 'Phosphohistidine',
-  S: 'Phosphoserine',
-  T: 'Phosphothreonine',
-  Y: 'Phosphotyrosine',
-};
-
-const phosphorylate = (aa: string) => {
-  const AA = aa.toUpperCase();
-  if (AA in aaToPhosphorylated) {
-    return aaToPhosphorylated[AA as keyof typeof aaToPhosphorylated];
-  }
-  console.error(`${AA} not a valid amino acid for phosphorylation`);
-  return '';
-};
-
 const convertPtmExchangePtms = (
   ptms: PTM[],
   aa: string,
   absolutePosition: number
 ) => {
-  const evidences = [
-    ...ptms.flatMap(({ dbReferences }) =>
-      dbReferences?.flatMap(({ id }) => [id])
-    ),
-  ];
   const confidenceScores = new Set(
     ptms.flatMap(({ dbReferences }) =>
       dbReferences?.map(({ properties }) => properties['Confidence score'])
@@ -97,40 +76,13 @@ const convertPtmExchangePtms = (
     [confidenceScore] = confidenceScores;
   }
 
-  const tooltip = `
-  <h5>Description</h5><p>${phosphorylate(aa)}</p>
-  ${
-    confidenceScore
-      ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>`
-      : ''
-  }
-  ${
-    evidences
-      ? `<h5>Evidence</h5><ul class="no-bullet">${evidences
-          .map((id) => {
-            const datasetID = id === 'Glue project' ? 'PXD012174' : id;
-            return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;
-              (<a href="https://proteomecentral.proteomexchange.org/dataset/${datasetID}" style="color:#FFF" target="_blank">ProteomeXchange</a>)
-              </li>
-              ${
-                id === 'Glue project'
-                  ? `<li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
-                  : ''
-              }
-              `;
-          })
-          .join('')}</ul>`
-      : ''
-  }
-  `;
-
   return {
     source: 'PTMeXchange',
     type: 'MOD_RES_LS',
     start: absolutePosition,
     end: absolutePosition,
     shape: 'triangle',
-    tooltipContent: tooltip,
+    tooltipContent: formatTooltip(ptms, aa, confidenceScore),
     color:
       (confidenceScore && ConfidenceScoreColors[confidenceScore]) || 'black',
   };

package/src/adapters/rna-editing-adapter.ts

@@ -0,0 +1,29 @@
+import { AminoAcid } from '@nightingale-elements/nightingale-variation';
+
+import { RnaEditing, TransformedRnaEditing } from './types/rna-editing';
+import formatTooltip from '../tooltips/rnaEditingTooltip';
+
+const transformData = ({
+  sequence,
+  features = [],
+}: RnaEditing): {
+  sequence: string;
+  variants: TransformedRnaEditing[];
+} => ({
+  sequence,
+  variants: features.map((feature) => {
+    const transformed: TransformedRnaEditing = {
+      ...feature,
+      accession: feature.variantType.genomicLocation?.join(', '),
+      variant: feature.variantType.mutatedType || AminoAcid.Empty,
+      start: +feature.locationType.position.position,
+      end: +feature.locationType.position.position,
+      consequenceType: feature.variantType.consequenceType,
+      tooltipContent: '', // Set with transformed feature below,
+    };
+    transformed.tooltipContent = formatTooltip(transformed);
+    return transformed;
+  }),
+});
+
+export default transformData;

package/src/adapters/rna-editing-graph-adapter.ts

@@ -0,0 +1,48 @@
+import { RnaEditing } from './types/rna-editing';
+
+const transformData = (data: RnaEditing) => {
+  if (data.sequence && data.features.length) {
+    const total = new Uint8ClampedArray(data.sequence.length);
+    const missense = new Uint8ClampedArray(data.sequence.length);
+    const synonymous = new Uint8ClampedArray(data.sequence.length);
+    for (const feature of data.features) {
+      const index = +feature.locationType.position.position;
+      const consequence = feature.variantType.consequenceType;
+      if (index >= 0 && index <= data.sequence.length) {
+        total[index] += 1;
+        if (consequence === 'missense') {
+          missense[index] += 1;
+        } else if (consequence === 'synonymous') {
+          // TODO: at present the data contains only missense
+          synonymous[index] += 1;
+        }
+      }
+    }
+
+    const range = [0, Math.max(...total)];
+    const graphData = [
+      {
+        name: 'missense',
+        range,
+        color: 'darkgrey',
+        values: [...missense].map((value, index) => ({
+          position: index,
+          value: value,
+        })),
+      },
+      // TODO: at present the data contains only missense
+      // {
+      //   name: 'synonymous',
+      //   range,
+      //   color: 'red',
+      //   values: [...synonymous].map((value, index) => ({
+      //     position: index,
+      //     value: value,
+      //   })),
+      // },
+    ];
+    return graphData;
+  }
+};
+
+export default transformData;

package/src/adapters/types/rna-editing.ts

@@ -0,0 +1,175 @@
+// Yvonne Lussi: This first dataset is for human proteins, and we decided to only show
+// the RNA editing events that have missense consequence. It may be possible to import
+// the synonymous events at a later timepoint.
+// Fetch all of the available human rna-editing entries
+// Source: https://www.ebi.ac.uk/proteins/api/rna-editing?offset=0&size=-1&taxid=9606
+// Save above request to rna-editing.json then using quicktype tool (https://github.com/glideapps/quicktype):
+// quicktype rna-editing.json -o rna-editing.ts --just-types
+// Changed interfaces for types and replaced enums string literal types
+
+export type RnaEditing = {
+  accession: string;
+  entryName: string;
+  sequence: string;
+  sequenceChecksum: string;
+  taxid: number;
+  features: RnaEditingFeature[];
+};
+
+export type RnaEditingFeature = {
+  type: Type;
+  xrefs: Xref[];
+  dbReferenceType: DBReferenceType[];
+  variantType: VariantType;
+  rnaEditingInfo: RnaEditingInfo;
+  locationType: LocationType;
+  variantlocation: string[];
+};
+
+export type TransformedRnaEditing = RnaEditingFeature & {
+  accession: string;
+  variant: string;
+  start: number;
+  end: number;
+  tooltipContent: string;
+  consequenceType: string;
+};
+
+type DBReferenceType = {
+  id: string;
+  type: Type;
+};
+
+type Type = 'rna_editing';
+
+type LocationType = {
+  position: Position;
+};
+
+type Position = {
+  position: number;
+  status: Status;
+};
+
+type Status = 'certain';
+
+type RnaEditingInfo = {
+  nedBS: number;
+  nsamples: number;
+  nbodySites: number;
+  ntissues: number;
+  nedInd: number;
+};
+
+type VariantType = {
+  genomicLocation: string[];
+  variantLocation: VariantLocation[];
+  codon: Codon;
+  consequenceType: ConsequenceType;
+  wildType: DType;
+  mutatedType: DType;
+  somaticStatus: boolean;
+  sourceType: SourceType;
+};
+
+type Codon =
+  | 'aCa'
+  | 'aCg'
+  | 'aCc'
+  | 'aCu'
+  | 'aGa'
+  | 'aGc'
+  | 'aGg'
+  | 'aGu'
+  | 'auG'
+  | 'cCa'
+  | 'cCg'
+  | 'cCc'
+  | 'cCu'
+  | 'Cga'
+  | 'cGa'
+  | 'cGc'
+  | 'cGg'
+  | 'cGu'
+  | 'Cac'
+  | 'Cag'
+  | 'Cau'
+  | 'Cca'
+  | 'Ccc'
+  | 'Ccg'
+  | 'Ccu'
+  | 'Cgc'
+  | 'Cgg'
+  | 'Cgu'
+  | 'Cuc'
+  | 'Cuu'
+  | 'gCa'
+  | 'Gcc'
+  | 'gCg'
+  | 'gCc'
+  | 'gCu'
+  | 'gGa'
+  | 'gGc'
+  | 'gGg'
+  | 'gGu'
+  | 'Gaa'
+  | 'Gac'
+  | 'Gag'
+  | 'Gau'
+  | 'Gca'
+  | 'Gcg'
+  | 'Gcu'
+  | 'Gga'
+  | 'Ggc'
+  | 'Ggg'
+  | 'Ggu'
+  | 'Gua'
+  | 'Guc'
+  | 'Gug'
+  | 'Guu'
+  | 'uCa'
+  | 'uCg'
+  | 'uCc'
+  | 'uCu'
+  | 'uGc'
+  | 'uGu'
+  | 'ugG';
+
+type ConsequenceType = 'missense';
+
+type DType =
+  | 'A'
+  | 'C'
+  | 'D'
+  | 'E'
+  | 'F'
+  | 'G'
+  | 'H'
+  | 'I'
+  | 'K'
+  | 'L'
+  | 'M'
+  | 'N'
+  | 'P'
+  | 'Q'
+  | 'R'
+  | 'S'
+  | 'T'
+  | 'U'
+  | 'V'
+  | 'W'
+  | 'Y';
+
+type SourceType = 'Rna Editing';
+
+type VariantLocation = {
+  loc: string;
+  seqId: string;
+  source: Source;
+};
+
+type Source = 'Ensembl';
+
+type Xref = {
+  id: string;
+};

package/src/adapters/variation-adapter.ts

@@ -29,9 +29,7 @@ const transformData = (
   const variants = features.map((variant) => ({
     ...variant,
     accession: variant.genomicLocation?.join(', '),
-    variant: variant.alternativeSequence
-      ? variant.alternativeSequence
-      : AminoAcid.Empty,
+    variant: variant.alternativeSequence || AminoAcid.Empty,
     start: +variant.begin,
     xrefNames: getSourceType(variant.xrefs, variant.sourceType),
     hasPredictions: variant.predictions && variant.predictions.length > 0,

package/src/adapters/variation-graph-adapter.ts

@@ -15,22 +15,21 @@ const transformData = (data) => {
       // eslint-disable-next-line no-continue
       if (index < 1 || index > data.sequence.length) continue;
 
-      // eslint-disable-next-line no-plusplus
-      total[index]++;
+      total[index] += 1;
 
       // eslint-disable-next-line no-continue
       if (!association) continue;
       const hasDisease = association.find(
         (association) => association.disease === true
       );
-      // eslint-disable-next-line no-plusplus
-      if (hasDisease) diseaseTotal[index]++;
+      if (hasDisease) diseaseTotal[index] += 1;
     }
 
+    const range = [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))];
     const graphData = [
       {
         name: 'variant',
-        range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))],
+        range,
         color: 'darkgrey',
         values: [...total].map((value, index) => ({
           position: index,
@@ -39,7 +38,7 @@ const transformData = (data) => {
       },
       {
         name: 'disease causing variant',
-        range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))],
+        range,
         color: 'red',
         values: [...diseaseTotal].map((value, index) => ({
           position: index,

package/src/config.ts

@@ -41,7 +41,9 @@ export type ProtvistaTrackConfig = {
       | 'alphafold-confidence-adapter'
       | 'alphamissense-pathogenicity-adapter'
       | 'alphamissense-heatmap-adapter'
-      | 'proteomics-ptm-adapter';
+      | 'proteomics-ptm-adapter'
+      | 'rna-editing-adapter'
+      | 'rna-editing-graph-adapter';
   }[];
   tooltip: string;
   color?: string;
@@ -676,6 +678,38 @@ const config: ProtvistaConfig = {
         },
       ],
     },
+    {
+      name: 'RNA_EDITING',
+      label: 'RNA Editing',
+      trackType: 'nightingale-linegraph-track',
+      tracks: [
+        {
+          name: 'rna_editing_graph',
+          label: 'Counts',
+          trackType: 'nightingale-linegraph-track',
+          data: [
+            {
+              adapter: 'rna-editing-graph-adapter',
+              url: `${proteinsApi}rna-editing/{accession}`,
+            },
+          ],
+          tooltip:
+            'RNA editing events leading to one or more amino acid changes compared to the translation of the non-edited RNA version.',
+        },
+        {
+          name: 'RNA Editing',
+          trackType: 'nightingale-variation',
+          data: [
+            {
+              adapter: 'rna-editing-adapter',
+              url: `${proteinsApi}rna-editing/{accession}`,
+            },
+          ],
+          tooltip:
+            'RNA editing events leading to one or more amino acid changes compared to the translation of the non-edited RNA version.',
+        },
+      ],
+    },
     {
       name: 'PROTEOMICS',
       label: 'Proteomics',

package/src/protvista-uniprot.ts

@@ -27,6 +27,8 @@ import variationAdapter, {
 } from './adapters/variation-adapter';
 import interproAdapter from './adapters/interpro-adapter';
 import variationGraphAdapter from './adapters/variation-graph-adapter';
+import rnaEditingGraphAdapter from './adapters/rna-editing-graph-adapter';
+import rnaEditingAdapter from './adapters/rna-editing-adapter';
 import proteomicsPTMApdapter from './adapters/ptm-exchange-adapter';
 import alphaFoldConfidenceAdapter from './adapters/alphafold-confidence-adapter';
 import alphaMissensePathogenicityAdapter from './adapters/alphamissense-pathogenicity-adapter';
@@ -56,6 +58,8 @@ const adapters = {
   'structure-adapter': structureAdapter,
   'variation-adapter': variationAdapter,
   'variation-graph-adapter': variationGraphAdapter,
+  'rna-editing-adapter': rnaEditingAdapter,
+  'rna-editing-graph-adapter': rnaEditingGraphAdapter,
   'proteomics-ptm-adapter': proteomicsPTMApdapter,
   'alphafold-confidence-adapter': alphaFoldConfidenceAdapter,
   'alphamissense-pathogenicity-adapter': alphaMissensePathogenicityAdapter,
@@ -99,8 +103,8 @@ class ProtvistaUniprot extends LitElement {
     this.data = {};
     this.rawData = {};
     this.displayCoordinates = {};
-    (this.transformedVariants = { sequence: '', variants: [] }),
-      this.addStyles();
+    this.transformedVariants = { sequence: '', variants: [] };
+    this.addStyles();
   }
 
   static get properties() {
@@ -117,9 +121,7 @@ class ProtvistaUniprot extends LitElement {
   }
 
   addStyles() {
-    // We are not using static get styles()
-    // as we are not using the shadowDOM
-    // because of Mol*
+    // We are not using static get styles() as we are not using the shadowDOM because of Mol*
     const styleTag = document.createElement('style');
     styleTag.innerHTML = `${protvistaStyles.toString()} ${loaderStyles.toString()}`;
     document.querySelector('head')?.append(styleTag);