protvista-uniprot 2.9.5 → 2.10.0

package/dist/es/config.json

@@ -266,6 +266,19 @@
                     ],
                     "tooltip": "Modified residues such as phosphorylation, acetylation, acylation, methylation"
                 },
+                {
+                    "name": "mod_res_ls",
+                    "label": "Modified residue (large scale)",
+                    "filter": "MOD_RES_LS",
+                    "trackType": "protvista-track",
+                    "data": [
+                        {
+                            "adapter": "protvista-proteomics-ptm-adapter",
+                            "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
+                        }
+                    ],
+                    "tooltip": "Modified residues from Large scale studies"
+                },
                 {
                     "name": "carbohyd",
                     "label": "Glycosylation",

package/dist/es/protvista-ptm-exchange.d.ts

@@ -0,0 +1,53 @@
+declare type ProteomicsPtm = {
+    accession: string;
+    entryName: string;
+    sequence: string;
+    sequenceChecksum: string;
+    taxid: number;
+    features: ProteomicsPtmFeature[];
+};
+declare type ProteomicsPtmFeature = {
+    type: string;
+    begin: string;
+    end: string;
+    xrefs: Xref[];
+    evidences: Evidence[];
+    peptide: string;
+    unique: boolean;
+    ptms: PTM[];
+};
+declare type Evidence = {
+    code: string;
+    source: Source;
+};
+declare type Source = {
+    id: string;
+    url: string;
+};
+declare type Xref = {
+    name: string;
+    id: string;
+    url: string;
+};
+declare type PTM = {
+    name: string;
+    position: number;
+    sources: string[];
+    dbReferences: DBReference[];
+};
+declare type DBReference = {
+    id: string;
+    properties: {
+        [key: string]: string;
+    };
+};
+export declare const transformData: (data: ProteomicsPtm) => {
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    shape: string;
+    tooltipContent: string;
+    color: any;
+}[];
+export {};

package/dist/es/protvista-ptm-exchange.js

@@ -0,0 +1,84 @@
+var ConfidenceScoreColors;
+(function (ConfidenceScoreColors) {
+    ConfidenceScoreColors["Gold"] = "#c39b00";
+    ConfidenceScoreColors["Silver"] = "#8194a1";
+    ConfidenceScoreColors["Bronze"] = "#a65708";
+})(ConfidenceScoreColors || (ConfidenceScoreColors = {}));
+const aaToPhosphorylated = {
+    R: 'Phosphoarginine',
+    C: 'Phosphocysteine',
+    H: 'Phosphohistidine',
+    S: 'Phosphoserine',
+    T: 'Phosphothreonine',
+    Y: 'Phosphotyrosine',
+};
+const phosphorylate = (aa) => {
+    const AA = aa.toUpperCase();
+    if (AA in aaToPhosphorylated) {
+        return aaToPhosphorylated[AA];
+    }
+    console.error(`${AA} not a valid amino acid for phosphorylation`);
+    return '';
+};
+const convertPtmExchangePtms = (ptms, aa, absolutePosition) => {
+    const evidences = [
+        ...ptms.flatMap(({ dbReferences }) => dbReferences === null || dbReferences === void 0 ? void 0 : dbReferences.flatMap(({ id }) => [id])),
+    ];
+    const confidenceScores = new Set(ptms.flatMap(({ dbReferences }) => dbReferences.map(({ properties }) => properties['Confidence score'])));
+    let confidenceScore;
+    if (!confidenceScores.size) {
+        console.error('PTMeXchange PTM has no confidence score');
+    }
+    else if (confidenceScores.size > 1) {
+        console.error(`PTMeXchange PTM has a mixture of confidence scores: ${Array.from(confidenceScores)}`);
+    }
+    else {
+        [confidenceScore] = confidenceScores;
+    }
+    const tooltip = `
+  <h5>Description</h5><p>${phosphorylate(aa)}</p>
+  ${confidenceScore ? `<h5>Confidence Score</h5><p>${confidenceScore}</p>` : ''}
+  ${evidences
+        ? `<h5>Evidence</h5><ul>${evidences
+            .map((id) => `<li title='${id}' style="padding: .25rem 0">${id}&nbsp;(<a href="https://www.ebi.ac.uk/pride/archive/projects/${id}" style="color:#FFF" target="_blank">PRIDE</a>)</li>`)
+            .join('')}</ul>`
+        : ''}
+  `;
+    return {
+        source: 'PTMeXchange',
+        type: 'MOD_RES_LS',
+        start: absolutePosition,
+        end: absolutePosition,
+        shape: 'triangle',
+        tooltipContent: tooltip,
+        color: ConfidenceScoreColors[confidenceScore] || 'black',
+    };
+};
+export const transformData = (data) => {
+    const { features } = data;
+    const absolutePositionToPtms = {};
+    for (const feature of features) {
+        for (const ptm of feature.ptms) {
+            const absolutePosition = +feature.begin + ptm.position - 1;
+            if (!Number.isFinite(absolutePosition)) {
+                console.error(`Encountered infinite number: +feature.begin + ptm.position - 1 = ${+feature.begin} + ${ptm.position} - 1`);
+                // eslint-disable-next-line no-continue
+                continue;
+            }
+            const aa = feature.peptide[ptm.position - 1];
+            if (absolutePosition in absolutePositionToPtms) {
+                if (absolutePositionToPtms[absolutePosition].aa !== aa) {
+                    console.error(`One PTM has different amino acid values: [${absolutePositionToPtms[absolutePosition].aa}, ${aa}]`);
+                }
+                else {
+                    absolutePositionToPtms[absolutePosition].ptms.push(ptm);
+                }
+            }
+            else {
+                absolutePositionToPtms[absolutePosition] = { ptms: [ptm], aa };
+            }
+        }
+    }
+    return Object.entries(absolutePositionToPtms).map(([absolutePosition, { ptms, aa }]) => convertPtmExchangePtms(ptms, aa, +absolutePosition));
+};
+//# sourceMappingURL=protvista-ptm-exchange.js.map

package/dist/es/protvista-ptm-exchange.js.map

@@ -0,0 +1 @@
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package/dist/es/protvista-uniprot.d.ts

@@ -11,6 +11,51 @@ export declare const transformDataVariationAdapter: (data: import("protvista-var
     variants: any[];
 };
 export declare const transformDataInterproAdapter: any;
+export declare const transformDataProteomicsPTMApdapter: (data: {
+    accession: string;
+    entryName: string;
+    sequence: string;
+    sequenceChecksum: string;
+    taxid: number;
+    features: {
+        type: string;
+        begin: string;
+        end: string;
+        xrefs: {
+            name: string;
+            id: string;
+            url: string;
+        }[];
+        evidences: {
+            code: string;
+            source: {
+                id: string;
+                url: string;
+            };
+        }[];
+        peptide: string;
+        unique: boolean;
+        ptms: {
+            name: string;
+            position: number;
+            sources: string[];
+            dbReferences: {
+                id: string;
+                properties: {
+                    [key: string]: string;
+                };
+            }[];
+        }[];
+    }[];
+}) => {
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    shape: string;
+    tooltipContent: string;
+    color: any;
+}[];
 export declare const filterConfig: {
     name: string;
     type: {

package/dist/es/protvista-uniprot.js

@@ -18,6 +18,7 @@ import { transformData as _transformDataProteomicsAdapter } from 'protvista-prot
 import { transformData as _transformDataStructureAdapter } from 'protvista-structure-adapter';
 import { transformData as _transformDataVariationAdapter } from 'protvista-variation-adapter';
 import { transformData as _transformDataInterproAdapter } from 'protvista-interpro-adapter';
+import { transformData as _transformDataProteomicsPTMApdapter } from './protvista-ptm-exchange';
 import defaultConfig from './config.json';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
 import _DownloadPanel from './download-panel';
@@ -31,6 +32,7 @@ export const transformDataProteomicsAdapter = _transformDataProteomicsAdapter;
 export const transformDataStructureAdapter = _transformDataStructureAdapter;
 export const transformDataVariationAdapter = _transformDataVariationAdapter;
 export const transformDataInterproAdapter = _transformDataInterproAdapter;
+export const transformDataProteomicsPTMApdapter = _transformDataProteomicsPTMApdapter;
 export const filterConfig = _filterConfig;
 export const colorConfig = _colorConfig;
 export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure;
@@ -41,6 +43,7 @@ const adapters = {
     'protvista-proteomics-adapter': transformDataProteomicsAdapter,
     'protvista-structure-adapter': transformDataStructureAdapter,
     'protvista-variation-adapter': transformDataVariationAdapter,
+    'protvista-proteomics-ptm-adapter': transformDataProteomicsPTMApdapter
 };
 class ProtvistaUniprot extends LitElement {
     constructor() {

package/dist/es/protvista-uniprot.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "2.9.5",
+  "version": "2.10.0",
   "files": [
     "dist",
     "src"

package/src/config.json

@@ -267,6 +267,19 @@
           ],
           "tooltip": "Modified residues such as phosphorylation, acetylation, acylation, methylation"
         },
+        {
+          "name": "mod_res_ls",
+          "label": "Modified residue (large scale)",
+          "filter": "MOD_RES_LS",
+          "trackType": "protvista-track",
+          "data": [
+            {
+              "adapter": "protvista-proteomics-ptm-adapter",
+              "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
+            }
+          ],
+          "tooltip": "Modified residues from Large scale studies"
+        },
         {
           "name": "carbohyd",
           "label": "Glycosylation",

package/src/protvista-ptm-exchange.ts

@@ -0,0 +1,165 @@
+type ProteomicsPtm = {
+  accession: string;
+  entryName: string;
+  sequence: string;
+  sequenceChecksum: string;
+  taxid: number;
+  features: ProteomicsPtmFeature[];
+};
+
+type ProteomicsPtmFeature = {
+  type: string;
+  begin: string;
+  end: string;
+  xrefs: Xref[];
+  evidences: Evidence[];
+  peptide: string;
+  unique: boolean;
+  ptms: PTM[];
+};
+
+type Evidence = {
+  code: string;
+  source: Source;
+};
+
+type Source = {
+  id: string;
+  url: string;
+};
+
+type Xref = {
+  name: string;
+  id: string;
+  url: string;
+};
+
+type PTM = {
+  name: string;
+  position: number;
+  sources: string[];
+  dbReferences: DBReference[];
+};
+
+type DBReference = {
+  id: string;
+  properties: { [key: string]: string };
+};
+
+enum ConfidenceScoreColors {
+  Gold = '#c39b00',
+  Silver = '#8194a1',
+  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'])
+    )
+  );
+  let confidenceScore: string;
+
+  if (!confidenceScores.size) {
+    console.error('PTMeXchange PTM has no confidence score');
+  } else if (confidenceScores.size > 1) {
+    console.error(
+      `PTMeXchange PTM has a mixture of confidence scores: ${Array.from(
+        confidenceScores
+      )}`
+    );
+  } else {
+    [confidenceScore] = confidenceScores;
+  }
+
+  const tooltip = `
+  <h5>Description</h5><p>${phosphorylate(aa)}</p>
+  ${confidenceScore ? `<h5>Confidence Score</h5><p>${confidenceScore}</p>` : ''}
+  ${
+    evidences
+      ? `<h5>Evidence</h5><ul>${evidences
+          .map(
+            (id) =>
+              `<li title='${id}' style="padding: .25rem 0">${id}&nbsp;(<a href="https://www.ebi.ac.uk/pride/archive/projects/${id}" style="color:#FFF" target="_blank">PRIDE</a>)</li>`
+          )
+          .join('')}</ul>`
+      : ''
+  }
+  `;
+
+  return {
+    source: 'PTMeXchange',
+    type: 'MOD_RES_LS',
+    start: absolutePosition,
+    end: absolutePosition,
+    shape: 'triangle',
+    tooltipContent: tooltip,
+    color: ConfidenceScoreColors[confidenceScore] || 'black',
+  };
+};
+
+export const transformData = (data: ProteomicsPtm) => {
+  const { features } = data;
+
+  const absolutePositionToPtms: Record<number, { ptms: PTM[]; aa: string }> =
+    {};
+
+  for (const feature of features) {
+    for (const ptm of feature.ptms) {
+      const absolutePosition = +feature.begin + ptm.position - 1;
+      if (!Number.isFinite(absolutePosition)) {
+        console.error(
+          `Encountered infinite number: +feature.begin + ptm.position - 1 = ${+feature.begin} + ${
+            ptm.position
+          } - 1`
+        );
+        // eslint-disable-next-line no-continue
+        continue;
+      }
+      const aa = feature.peptide[ptm.position - 1];
+      if (absolutePosition in absolutePositionToPtms) {
+        if (absolutePositionToPtms[absolutePosition].aa !== aa) {
+          console.error(
+            `One PTM has different amino acid values: [${absolutePositionToPtms[absolutePosition].aa}, ${aa}]`
+          );
+        } else {
+          absolutePositionToPtms[absolutePosition].ptms.push(ptm);
+        }
+      } else {
+        absolutePositionToPtms[absolutePosition] = { ptms: [ptm], aa };
+      }
+    }
+  }
+
+  return Object.entries(absolutePositionToPtms).map(
+    ([absolutePosition, { ptms, aa }]) =>
+      convertPtmExchangePtms(ptms, aa, +absolutePosition)
+  );
+};

package/src/protvista-uniprot.ts

@@ -19,6 +19,7 @@ import { transformData as _transformDataProteomicsAdapter } from 'protvista-prot
 import { transformData as _transformDataStructureAdapter } from 'protvista-structure-adapter';
 import { transformData as _transformDataVariationAdapter } from 'protvista-variation-adapter';
 import { transformData as _transformDataInterproAdapter } from 'protvista-interpro-adapter';
+import { transformData as _transformDataProteomicsPTMApdapter } from './protvista-ptm-exchange';
 
 import defaultConfig from './config.json';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
@@ -36,6 +37,7 @@ export const transformDataProteomicsAdapter = _transformDataProteomicsAdapter;
 export const transformDataStructureAdapter = _transformDataStructureAdapter;
 export const transformDataVariationAdapter = _transformDataVariationAdapter;
 export const transformDataInterproAdapter = _transformDataInterproAdapter;
+export const transformDataProteomicsPTMApdapter = _transformDataProteomicsPTMApdapter;
 export const filterConfig = _filterConfig;
 export const colorConfig = _colorConfig;
 export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure;
@@ -47,6 +49,7 @@ const adapters = {
   'protvista-proteomics-adapter': transformDataProteomicsAdapter,
   'protvista-structure-adapter': transformDataStructureAdapter,
   'protvista-variation-adapter': transformDataVariationAdapter,
+  'protvista-proteomics-ptm-adapter': transformDataProteomicsPTMApdapter
 };
 
 type TrackType =