protvista-uniprot 4.3.2 → 4.3.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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@@ -241,7 +241,9 @@ const Tm = {
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)
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];
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let a;
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const o = new Set(
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const o = new Set(
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t.flatMap(({ name: s }) => s)
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);
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return o.size && (o.size > 1 ? console.error(
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`PTMeXchange PTM has a mixture of modifications: ${Array.from(
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o
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@@ -252,10 +254,10 @@ const Tm = {
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${n ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${n}</p>` : ""}
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${i ? `<h5>Evidence</h5><ul class="no-bullet">${i.map((s) => {
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const u = s === "Glue project" ? "PXD012174" : s;
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return `<li title='${u}'
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(<a href="https://proteomecentral.proteomexchange.org/dataset/${u}"
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return `<li title='${u}'>${u}
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(<a href="https://proteomecentral.proteomexchange.org/dataset/${u}" target="_blank">ProteomeXchange</a>)
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</li>
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${s === "Glue project" ? '<li title="publication"
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${s === "Glue project" ? '<li title="publication">Publication: 31819260 (<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" target="_blank">PubMed</a>)</li>' : ""}
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`;
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}).join("")}</ul>` : ""}`;
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}, EBe = {
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@@ -268,16 +270,16 @@ const Tm = {
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185431: { build: "590", organism: "T Brucei" }
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}, MBe = (e) => {
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if (e.name?.toLowerCase() === "PubMed".toLowerCase())
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return `${e.id} (<a href='${e.url}'
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const t = ` <a href='${e.url}'
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return `${e.id} (<a href='${e.url}' target='_blank'>${e.name}</a> <a href='${e.alternativeUrl}' target='_blank'>EuropePMC</a>)`;
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const t = ` <a href='${e.url}' target='_blank'>${e.id}</a>`;
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return e.name ? e.name.startsWith("Hpp") ? `${t} (${e.name.slice(3)})` : `${t} (${e.name})` : t;
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}, vAe = (e) => e ? `
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<ul class="no-bullet">${e.map((t) => {
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const r = TBe.find((n) => n.name === t.code);
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return r ? `<li title='${r.description}'
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return r ? `<li title='${r.description}'>${r.shortDescription}: ${t.source ? MBe(t.source) : ""}</li>` : "";
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}).join("")}</ul>
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` : "", gAe = (e) => `<ul class="no-bullet">${e.map(
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(t) => `<li
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(t) => `<li>${t.name} ${t.url ? `<a href="${t.url}" target="_blank">${t.id}</a>` : `${t.name} ${t.id}`}</li>`
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).join("")}</ul>`, $Be = (e, t) => {
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if (!e) return "";
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const r = e.flatMap(
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@@ -286,7 +288,7 @@ const Tm = {
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return `
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<ul class="no-bullet">${n.map((a) => {
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const o = a === "Glue project" ? "PXD012174" : a;
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return `<li title='${o}'
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return `<li title='${o}'>${o} (<a href="${i}${o}" target="_blank">ProteomeXchange</a>${a === "Glue project" ? ')</li><li title="publication">Publication: 31819260 (<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" target="_blank">PubMed</a>)</li>' : ` <a href="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=${EBe[t].build}" target="_blank">PeptideAtlas</a>)</li>`}`;
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}).join("")}</ul>
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`;
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}, kBe = (e, t) => {
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@@ -306,7 +308,9 @@ const Tm = {
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const { peptide: r, begin: n } = e, i = Number(n) + t.position - 1, a = r.charAt(t.position - 1);
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return t.name === "Phosphorylation" ? `${i} ${pAe(a)}` : t.name === "SUMOylation" ? `${i} ${mAe(a)}` : "";
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}, yAe = (e, t) => {
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const r = e.type === "PROTEOMICS_PTM" ? $Be(e.residuesToHighlight, t) : vAe(e.evidences), n = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.map(
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const r = e.type === "PROTEOMICS_PTM" ? $Be(e.residuesToHighlight, t) : vAe(e.evidences), n = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.map(
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(o) => Ene(e, o)
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), i = e.type === "PROTEOMICS_PTM" && e.residuesToHighlight.flatMap(
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({ dbReferences: o }) => o.map((s) => s.id)
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);
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let { description: a } = e;
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@@ -330,20 +334,20 @@ const Tm = {
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${e.unique ? `<h5>Unique</h5><p>${e.unique ? "Yes" : "No"}</p>` : ""}
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${e.xrefs ? `<h5>Cross-references</h5>${gAe(e.xrefs)}` : ""}
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${r ? `<h5>Evidence</h5>${r}` : ""}
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${e.residuesToHighlight && i && !i.includes("Glue project") ? `<hr /><h5 data-article-id="mod_res_large_scale#what-is-the-goldsilverbronze-criterion">PTM statistical attributes</h5><ul class="no-bullet">${e.residuesToHighlight.map(
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${e.residuesToHighlight && i && !i.includes("Glue project") ? `<hr /><h5 class="margin-bottom" data-article-id="mod_res_large_scale#what-is-the-goldsilverbronze-criterion">PTM statistical attributes</h5><ul class="no-bullet">${e.residuesToHighlight.map(
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(o) => o.dbReferences.map(
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(s) => `<li><b>${s.id}</b></li>
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<li
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<li class="text-indent-1"><b>${Ene(
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e,
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o
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)}</b></li>
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${s.properties["Pubmed ID"] ? `<li
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${s.properties["Confidence score"] ? `<li
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${s.properties["Sumo isoforms"] ? `<li
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${s.properties["Organism part"] ? `<li
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${s.properties["PSM Count (0.05 gFLR)"] ? `<li
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${s.properties["Final site probability"] ? `<li
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${s.properties["Universal Spectrum Id"] ? `<li
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${s.properties["Pubmed ID"] ? `<li class="text-indent-2">PubMed ID: <a href="https://europepmc.org/article/MED/${s.properties["Pubmed ID"]}" target="_blank">${s.properties["Pubmed ID"]}</a></li>` : ""}
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${s.properties["Confidence score"] ? `<li class="text-indent-2"><span data-article-id="mod_res_large_scale#confidence-score">Confidence score</span>: ${s.properties["Confidence score"]}</li>` : ""}
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${s.properties["Sumo isoforms"] ? `<li class="text-indent-2">SUMO family member: ${s.properties["Sumo isoforms"]}</li>` : ""}
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${s.properties["Organism part"] ? `<li class="text-indent-2">Organism part: ${s.properties["Organism part"]}</li>` : ""}
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${s.properties["PSM Count (0.05 gFLR)"] ? `<li class="text-indent-2">PSM Count (0.05 gFLR): ${s.properties["PSM Count (0.05 gFLR)"]}</li>` : ""}
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${s.properties["Final site probability"] ? `<li class="text-indent-2">Final site probability: ${s.properties["Final site probability"]}</li>` : ""}
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${s.properties["Universal Spectrum Id"] ? `<li class="text-indent-2 nowrap">Universal Spectrum Id:
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<a href="http://proteomecentral.proteomexchange.org/usi/?usi=${s.properties["Universal Spectrum Id"]}" target="_blank">View on ProteomeXchange</a>
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</li>` : ""}
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`
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@@ -355,7 +359,7 @@ const Tm = {
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}
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}, IBe = (e) => `<ul>
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${e.map(
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(t) => `<li
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(t) => `<li><a href='${t.source.url}' target='_blank'>
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${t.source.id}
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</a> (${t.start}-${t.end})</li>`
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).join("")}
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