protvista-uniprot 4.0.0 → 4.2.0

package/src/tooltips/featureTooltip.ts

@@ -1,4 +1,5 @@
 import ecoMap from '../adapters/config/evidence';
+import { phosphorylate, sumoylate } from './ptmTooltip';
 
 const taxIdToPeptideAtlasBuildData = {
   '36329': { build: '542', organism: 'Plasmodium' },
@@ -98,27 +99,14 @@ const formatPTMPeptidoform = (peptide, ptms) => {
   return peptidoform;
 };
 
-// Amino acids for Phosphorylation modification
-const AAPhosphoSites = {
-  A: 'alanine',
-  S: 'serine',
-  T: 'threonine',
-  Y: 'tyrosine',
-};
-
-// Amino acids for SUMOylation modification
-const AASumoSites = {
-  K: 'lysine',
-};
-
 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 `${proteinLocation} phospho${AAPhosphoSites[modifiedResidue]}`;
+    return `${proteinLocation} ${phosphorylate(modifiedResidue)}`;
   } else if (ptm.name === 'SUMOylation') {
-    return `${proteinLocation} Sumoylated ${AASumoSites[modifiedResidue]}`;
+    return `${proteinLocation} ${sumoylate(modifiedResidue)}`;
   }
   return '';
 };
@@ -156,6 +144,11 @@ const formatTooltip = (feature, taxId?: string) => {
 
   try {
     return `
+        ${
+          feature.type && feature.begin && feature.end
+            ? `<h4>${feature.type} ${feature.begin}-${feature.end}</h4><hr />`
+            : ''
+        }
         ${description ? `<h5>Description</h5><p>${description}</p>` : ``}
         ${
           feature.matchScore
@@ -251,7 +244,7 @@ const formatTooltip = (feature, taxId?: string) => {
                 .join('')}</ul>`
             : ''
         }
-          `;
+      `;
   } catch (error) {
     console.error(error);
     return '';

package/src/tooltips/ptmTooltip.ts

@@ -0,0 +1,86 @@
+import { PTM } from "../adapters/ptm-exchange-adapter";
+
+type Modification = 'Phosphorylation' | 'SUMOylation';
+
+const aaToPhosphorylated = {
+  R: 'Phosphoarginine',
+  C: 'Phosphocysteine',
+  H: 'Phosphohistidine',
+  S: 'Phosphoserine',
+  T: 'Phosphothreonine',
+  Y: 'Phosphotyrosine',
+};
+
+const aaToSumoylated = {
+  K: 'Sumoylated lysine',
+};
+
+export const phosphorylate = (aa: string) => {
+  const AA = aa.toUpperCase();
+  if (AA in aaToPhosphorylated) {
+    return aaToPhosphorylated[AA as keyof typeof aaToPhosphorylated];
+  }
+  console.error(`${AA} not a valid amino acid for phosphorylation`);
+  return '';
+};
+
+export const sumoylate = (aa: string) => {
+  const AA = aa.toUpperCase();
+  if (AA in aaToSumoylated) {
+    return aaToSumoylated[AA as keyof typeof aaToSumoylated];
+  }
+  console.error(`${AA} not a valid amino acid for SUMOylation`);
+  return '';
+};
+
+const formatTooltip = (ptms: PTM[], aa: string, confidenceScore: string): string => {
+    const evidences = [
+        ...ptms.flatMap(({ dbReferences }) =>
+          dbReferences?.flatMap(({ id }) => [id])
+        ),
+      ];
+   
+      let modification: Modification | undefined;
+      const modifications = new Set(ptms.flatMap(({name}) => name as Modification));
+      if (modifications.size) {
+        if (modifications.size > 1) {
+          console.error(
+            `PTMeXchange PTM has a mixture of modifications: ${Array.from(
+              modifications
+            )}`
+          );
+        } else {
+          [modification] = modifications;
+        }
+      }
+      
+  return `
+  <h5>Description</h5><p>${
+    modification === 'Phosphorylation' ? phosphorylate(aa) : sumoylate(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>`
+      : ''
+  }`;
+};
+
+export default formatTooltip;

package/src/tooltips/rnaEditingTooltip.ts

@@ -0,0 +1,54 @@
+import { TransformedRnaEditing } from '../adapters/types/rna-editing';
+
+const getREDIportalId = (feature: TransformedRnaEditing) =>
+  feature.dbReferenceType.find((db) => db.type === 'rna_editing')?.id;
+
+const getREDIportalLink = (id: string) =>
+  `http://srv00.recas.ba.infn.it/cgi/atlas/getpage_dev.py?query9=hg&query10=hg38&acc=${id}`;
+
+const getEnsemblLink = (id: string) => `https://www.ensembl.org/id/${id}`;
+
+const getLinks = (feature: TransformedRnaEditing) => {
+  const links = [];
+  const rediPortalId = getREDIportalId(feature);
+  if (rediPortalId) {
+    links.push(
+      `REDIportal <a href="${getREDIportalLink(
+        rediPortalId
+      )}" target="_blank">${rediPortalId}</a>`
+    );
+  }
+  for (const variantLocation of feature.variantType.variantLocation) {
+    if (variantLocation.source === 'Ensembl') {
+      links.push(
+        `Ensembl <a href="${getEnsemblLink(variantLocation.seqId)}" target="_blank">${
+          variantLocation.seqId
+        }</a>`
+      );
+    }
+  }
+  return links.length === 0
+    ? ''
+    : `<br><ul class="no-bullet">${links
+        .map((link) => `<li>${link}</li>`)
+        .join('')}</ul>`;
+};
+
+const formatTooltip = (feature: TransformedRnaEditing): string => `
+  ${
+    feature.start && feature.end
+      ? `<h4>RNA Edit ${feature.start}-${feature.end}</h4><hr />`
+      : ''
+  }
+  <h5>Variant</h5>
+  <p>${feature.variantType.wildType} > ${feature.variantType.mutatedType}</p>
+  <h5>Consequence</h5>
+  <p>${feature.consequenceType}</p>
+  <h5>Location</h5>
+  <ul class="no-bullet">${feature.variantType.genomicLocation
+    .map((l) => `<li>${l}</li>`)
+    .join('')}
+  ${getLinks(feature)}
+  `;
+
+export default formatTooltip;

package/src/tooltips/structureTooltip.ts

@@ -14,7 +14,15 @@ const getStructuresHTML = (structureList) => {
 
 const formatTooltip = (feature) => {
   const structuresHTML = getStructuresHTML(feature.structures);
-  return `${structuresHTML ? `<h5>Structures</h5>${structuresHTML}` : ``}`;
+  return !structuresHTML
+    ? ''
+    : `
+    ${
+      feature.type && feature.start && feature.end
+        ? `<h4>${feature.type} ${feature.start}-${feature.end}</h4><hr />`
+        : ''
+    }
+    <h5>Structures</h5>${structuresHTML}`;
 };
 
 export default formatTooltip;

package/src/tooltips/variationTooltip.ts

@@ -87,53 +87,39 @@ const getPredictions = (predictions: Prediction[]): string => {
 
 const formatTooltip = (variant: Variant): string =>
   `
-                <h5>Variant</h5><p>${variant.wildType} > ${
+  ${
+    variant.type && variant.begin && variant.end
+      ? `<h4>${variant.type} ${variant.begin}-${variant.end}</h4><hr />`
+      : ''
+  }
+  <h5>Variant</h5><p>${variant.wildType} > ${
     variant.alternativeSequence || ''
   }</p>
-                ${
-                  variant.populationFrequencies
-                    ? getPopulationFrequencies(variant.populationFrequencies)
-                    : ''
-                }
-                ${
-                  variant.consequenceType
-                    ? `<h5>Consequence</h5><p>${variant.consequenceType}</p>`
-                    : ``
-                }
-                ${
-                  variant.somaticStatus
-                    ? `<h5>Somatic</h5><p>${
-                        variant.somaticStatus === 0 ? 'No' : 'Yes'
-                      }</p>`
-                    : ``
-                }
-                ${
-                  variant.genomicLocation?.length
-                    ? `<h5>Location</h5><p>${variant.genomicLocation.join(
-                        ', '
-                      )}</p>`
-                    : ``
-                }
-                ${
-                  variant.ftId
-                    ? `<h5>Feature ID</h5><p>${variant.ftId}</p>`
-                    : ``
-                }
-                ${
-                  variant.descriptions
-                    ? getDescriptions(variant.descriptions)
-                    : ''
-                }
-                ${
-                  variant.association
-                    ? getDiseaseAssociations(variant.association)
-                    : ''
-                }
-                ${
-                  variant.predictions ? getPredictions(variant.predictions) : ''
-                }
-                ${getEnsemblCovidLinks(variant)}
-                
-        `;
+  ${
+    variant.populationFrequencies
+      ? getPopulationFrequencies(variant.populationFrequencies)
+      : ''
+  }
+  ${
+    variant.consequenceType
+      ? `<h5>Consequence</h5><p>${variant.consequenceType}</p>`
+      : ``
+  }
+  ${
+    variant.somaticStatus
+      ? `<h5>Somatic</h5><p>${variant.somaticStatus === 0 ? 'No' : 'Yes'}</p>`
+      : ``
+  }
+  ${
+    variant.genomicLocation?.length
+      ? `<h5>Location</h5><p>${variant.genomicLocation.join(', ')}</p>`
+      : ``
+  }
+  ${variant.ftId ? `<h5>Feature ID</h5><p>${variant.ftId}</p>` : ``}
+  ${variant.descriptions ? getDescriptions(variant.descriptions) : ''}
+  ${variant.association ? getDiseaseAssociations(variant.association) : ''}
+  ${variant.predictions ? getPredictions(variant.predictions) : ''}
+  ${getEnsemblCovidLinks(variant)}
+`;
 
 export default formatTooltip;