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Merged
ctrlaltaf merged 9 commits into from
Jul 7, 2025
Merged

Escherichia coli #235

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cb4c031
Add data for Arabidopsis thaliana
oliverfanderson Jun 19, 2025
a0fb79e
Get Arabidopsis initially integrated
oliverfanderson Jun 20, 2025
544135a
Add BETA Arabidopsis Thaliana data
oliverfanderson Jun 23, 2025
0780be5
Add E. coli datasets
oliverfanderson Jun 25, 2025
133e7d8
Add E. coli data and import into Neo4j succesfully
oliverfanderson Jun 26, 2025
5b55e22
Wrap up E. coli import
oliverfanderson Jun 27, 2025
d0d1858
Update README.md
oliverfanderson Jul 1, 2025
8352b74
Update new-species.md
oliverfanderson Jul 1, 2025
69fd03c
fixed import bugs and added pickle files for graphs
ctrlaltaf Jul 7, 2025
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6 changes: 5 additions & 1 deletion client/src/components/EdgeTab.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,10 @@ export default function EdgeTab({
setInteractionSource("BioGRID");
} else if (source === "tf-link") {
setInteractionSource("TFLink");
} else if (source === "atrm") {
setInteractionSource("ATRM");
} else if (source === "regulonDB") {
setInteractionSource("RegulonDB");
} else {
setInteractionSource("");
}
Expand All @@ -67,7 +71,7 @@ export default function EdgeTab({
return evidence.split(";").map(i => `https://pubmed.ncbi.nlm.nih.gov/${i}`);
} else if (evidence.startsWith("WB")) {
return [`http://api.wormbase.org/species/all/interaction/${evidence}`];
} else {
} else {
return [];
}
};
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2 changes: 1 addition & 1 deletion client/src/components/Footer.jsx
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Expand Up @@ -14,7 +14,7 @@ export default function Footer() {
return (
<div className="footer-container">
<footer className="footer">
<p className="footer-title">ProteinWeaver © 2023</p>
<p className="footer-title">ProteinWeaver © 2025</p>
{/* Terms of Service */}
<Link to={"/tos"}>TOS</Link>
<p> | </p>
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4 changes: 2 additions & 2 deletions client/src/components/GraphSummary.jsx
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Expand Up @@ -50,7 +50,7 @@ export default function GraphSummary({
setSourceNodeLink(
`https://bsubcyc.org/gene?orgid=BSUB&id=${sourceNode.id.replace('_', '')}#tab=GO`
);
} else if (txid === "txid7955" || txid === "txid559292") {
} else if (txid === "txid7955" || txid === "txid559292" || txid === "txid3702" || txid === "txid511145") {
setSourceNodeLink(
`https://www.uniprot.org/uniprotkb/${sourceNode.id}/entry#function`
);
Expand All @@ -59,7 +59,7 @@ export default function GraphSummary({
`https://amigo.geneontology.org/amigo/gene_product/WB:${sourceNode.id}`
);
}
}, [txid]);
}, [searchExecuted]);

// Keep track of the proteins in the query
useEffect(() => {
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5 changes: 5 additions & 0 deletions client/src/components/MotifTab.jsx
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@@ -1,12 +1,17 @@
import React, { useState, useEffect } from "react";
import MotifTable from "./MotifTable";


// Constants for motif enrichment scores
// Format { "txidXXXX" : [(N.proteinClique/global.ppiDegree), (N.interactCoReg/global.mixedDegree), (N.feedFwdLoop/global.grnDegree), (N.coRegInteract/global.mixedDegree), (N.mixedFeedback/global.mixedDegree)] }
const txidMapping = {
"txid7227": [(1267922 / 466108), (5049 / 501168), (3706 / 35060), (3236 / 501168), (1439 / 501168)],
"txid224308": [(43088 / 12882), (164 / 24150), (972 / 11268), (1359 / 24150), (65 / 24150)],
"txid7955": [(319540 / 90006), (960 / 141926), (2257 / 51920), (523 / 141926), (14 / 141926)],
"txid559292": [(1816919 / 328864), (171664 / 803494), (1036451 / 474630), (522163 / 803494), (76231 / 803494)],
"txid6239": [(16880 / 27830), (28856 / 184276), (457362 / 156446), (82309 / 184276), (18579 / 184276)],
"txid3702": [(318826 / 102768), (215 / 105518), (158 / 2750), (78 / 105518), (47 / 105518)],
"txid511145": [(1238392 / 58764), (18 / 64754), (53 / 5990), (480 / 64754), (2 / 64754)],
};

export default function MotifTab({ nodeList, query, searchExecuted }) {
Expand Down
14 changes: 13 additions & 1 deletion client/src/components/NodeTab.jsx
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Expand Up @@ -18,6 +18,8 @@ export default function NodeTab({ currentNode, query, goTerm, predictionValue, s
"txid7955": `https://www.uniprot.org/uniprotkb/${currentNode.id}/entry`,
"txid559292": `https://www.uniprot.org/uniprotkb/${currentNode.id}/entry`,
"txid6239": `https://www.wormbase.org/species/c_elegans/gene/${currentNode.id}`,
"txid3702": `https://www.uniprot.org/uniprotkb/${currentNode.id}/entry`,
"txid511145": `https://www.uniprot.org/uniprotkb/${currentNode.id}/entry`,
};
setSelectedDbLink(speciesLinkMap[txid] || "");
}
Expand Down Expand Up @@ -53,6 +55,16 @@ export default function NodeTab({ currentNode, query, goTerm, predictionValue, s
Alternate Name(s): {currentNode.alt_name}
</h5>
)}
{currentNode.alt_id && currentNode.alt_id !== currentNode.label && (
<h5 className="node-tab-text">
Alternate ID(s): {currentNode.alt_id}
</h5>
)}
{currentNode.alt_gene_id && currentNode.alt_gene_id !== currentNode.label && (
<h5 className="node-tab-text">
Alternate Gene ID(s): {currentNode.alt_gene_id}
</h5>
)}
<Degree id={currentNode.id} />
<h5 className="node-tab-text">
Prediction Rank: {predictionValue.rank}
Expand All @@ -76,7 +88,7 @@ export default function NodeTab({ currentNode, query, goTerm, predictionValue, s
</p>
) : (
<p className="go-annotation-info">
*{currentNode.label} is <b>{currentNode.go_protein.replaceAll("_", " ")}</b> {goTerm.name}.
*{currentNode.label} is <b>{currentNode.go_protein?.replaceAll("_", " ") || "unavailable"}</b> {goTerm.name}.
</p>
)}
</div>
Expand Down
88 changes: 87 additions & 1 deletion client/src/components/Query.jsx
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Expand Up @@ -172,10 +172,12 @@ export default function Query() {
const proteinNames = data.map((item) => item.name);
const proteinIds = data.map((item) => item.id);
const proteinAltNames = data.map((item) => item.alt_name);
const proteinAltIds = data.map((item) => item.alt_id);
const geneAltIds = data.map((item) => item.gene_alt_id);
const geneNames = data.map((item) => item.gene_name);
const proteinMerged = [
...new Set(
proteinNames.concat(proteinIds).concat(proteinAltNames).concat(geneNames)
proteinNames.concat(proteinIds).concat(proteinAltNames).concat(geneNames).concat(proteinAltIds).concat(geneAltIds)
),
].filter((item) => item !== undefined);
setProteinOptions(proteinMerged);
Expand Down Expand Up @@ -848,6 +850,90 @@ export default function Query() {
setExState(String(i));
break;
}
} else if (query.species == "txid3702") {
switch (i) {
case 1:
setQuery({
mode: "path",
species: "txid3702",
protein: "NPR1",
goTerm: "immune response",
k: "7",
ppi: true,
regulatory: true,
});
setActiveModeButton("path");
setExState(String(i));
break;
case 2:
setQuery({
mode: "node",
species: "txid3702",
protein: "TGA3",
goTerm: "response to stimulus",
k: "10",
ppi: true,
regulatory: true,
});
setActiveModeButton("node");
setExState(String(i));
break;
case 3:
setQuery({
mode: "node",
species: "txid3702",
protein: "RAD51",
goTerm: "homologous recombination",
k: "6",
ppi: true,
regulatory: true,
});
setActiveModeButton("node");
setExState(String(i));
break;
}
} else if (query.species == "txid511145") {
switch (i) {
case 1:
setQuery({
mode: "path",
species: "txid511145",
protein: "OxyR",
goTerm: "regulation of RNA metabolic process",
k: "7",
ppi: true,
regulatory: true,
});
setActiveModeButton("path");
setExState(String(i));
break;
case 2:
setQuery({
mode: "node",
species: "txid511145",
protein: "ZntR",
goTerm: "zinc ion transmembrane transporter activity",
k: "10",
ppi: true,
regulatory: true,
});
setActiveModeButton("node");
setExState(String(i));
break;
case 3:
setQuery({
mode: "node",
species: "txid511145",
protein: "Crp",
goTerm: "regulation of growth",
k: "6",
ppi: true,
regulatory: true,
});
setActiveModeButton("node");
setExState(String(i));
break;
}
}
};

Expand Down
10 changes: 10 additions & 0 deletions client/src/components/SearchBar.jsx
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Expand Up @@ -28,6 +28,10 @@ export default function SearchBar({
spName = "S. cerevisiae";
} else if (query.species == "txid6239") {
spName = "C. elegans";
} else if (query.species == "txid3702") {
spName = "A. thaliana";
} else if (query.species == "txid511145") {
spName = "E. coli K-12";
}

return (
Expand Down Expand Up @@ -100,6 +104,12 @@ export default function SearchBar({
<option value="txid6239">
C. elegans (6239)
</option>
<option value="txid3702">
A. thaliana (3702)
</option>
<option value="txid511145">
E. coli K-12 (511145)
</option>
</select>
</div>
<button
Expand Down
85 changes: 49 additions & 36 deletions client/src/tools/Parser.jsx
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Expand Up @@ -2,19 +2,24 @@ export function NetworkParserPath(data) {
const parsedData = { nodes: [], edges: [], nodeList: [], edgeList: [] };

const getNodeLabel = (node) => {
const { name, id, alt_name, gene_name } = node.properties;
const { name, id, alt_name, gene_name, alt_id, alt_gene_id } = node.properties;
if (name && name !== "-") return name;
if (gene_name && gene_name !== "-") return gene_name;
return alt_name || id;
if (alt_name && alt_name !== "-") return alt_name;
if (id && id !== "-") return id;
if (alt_id && alt_id !== "-") return alt_id;
return alt_id || alt_gene_id;
};

const createNodeEntry = (node, nodeType, degree) => ({
data: {
id: node.properties.id,
label: getNodeLabel(node),
degree: degree.low,
alt_name: node.properties.alt_name,
gene_name: node.properties.gene_name,
alt_name: node.properties.alt_name,
alt_id: node.properties.alt_id,
alt_gene_id: node.properties.alt_gene_id,
type: nodeType,
},
});
Expand Down Expand Up @@ -140,34 +145,33 @@ export function EdgeDataParser(networkData, edgeData, ppi, regulatory) {
const sharedEdgeExists = networkData.edgeList.includes(endNode + startNode);

// Handle edge existence
if (edgeExists) {
// Handle ProPro edges
if (relType === "ProPro" && ppi && edgeExists) {
processProProEdge(startNode, endNode, relType, evidence, dataSource);
}
// Handle Reg edges
else if (relType === "Reg" && regulatory && edgeExists) {
processRegEdge(startNode, endNode, relType, evidence, dataSource, regType);
}
// Handle ProGo edges
else if (relType === "ProGo") {
processProGoEdge(startNode, properties.relationship);
if (relType === "ProGo") {
processProGoEdge(startNode, properties.relationship);
} else
if (edgeExists) {
// Handle ProPro edges
if (relType === "ProPro" && ppi && edgeExists) {
processProProEdge(startNode, endNode, relType, evidence, dataSource);
}
// Handle Reg edges
else if (relType === "Reg" && regulatory && edgeExists) {
processRegEdge(startNode, endNode, relType, evidence, dataSource, regType);
}
} else if (sharedEdgeExists) {
// Edge exists but in reversed order, label it as "shared"
if (relType === "ProPro" && ppi && sharedEdgeExists) {
processProProEdge(startNode, endNode, relType, evidence, dataSource);
} else if (relType === "Reg" && sharedEdgeExists) {
processRegEdge(startNode, endNode, relType, evidence, dataSource, regType, "shared");
}
} else if (!edgeExists) {
// Edge exists but in reversed order, label it as "shared"
if (relType === "ProPro") {
processProProEdge(startNode, endNode, relType, evidence, dataSource, "shared");
} else if (relType === "Reg") {
processRegEdge(startNode, endNode, relType, evidence, dataSource, regType, "shared");
}
}
} else if (sharedEdgeExists) {
// Edge exists but in reversed order, label it as "shared"
if (relType === "ProPro" && ppi && sharedEdgeExists) {
processProProEdge(startNode, endNode, relType, evidence, dataSource);
} else if (relType === "Reg" && sharedEdgeExists) {
processRegEdge(startNode, endNode, relType, evidence, dataSource, regType, "shared");
}
} else if (!edgeExists) {
// Edge exists but in reversed order, label it as "shared"
if (relType === "ProPro") {
processProProEdge(startNode, endNode, relType, evidence, dataSource, "shared");
} else if (relType === "Reg") {
processRegEdge(startNode, endNode, relType, evidence, dataSource, regType, "shared");
}
}
}

networkData.edgeList = tempEdgeList;
Expand All @@ -179,19 +183,24 @@ export function NetworkParserNode(data, k) {
const parsedData = { nodes: [], edges: [], nodeList: [], edgeList: [] };

const getNodeLabel = (node) => {
const { name, id, alt_name, gene_name } = node.properties;
const { name, id, alt_name, gene_name, alt_id, alt_gene_id } = node.properties;
if (name && name !== "-") return name;
if (gene_name && gene_name !== "-") return gene_name;
return alt_name || id;
if (alt_name && alt_name !== "-") return alt_name;
if (id && id !== "-") return id;
if (alt_id && alt_id !== "-") return alt_id;
return alt_id || alt_gene_id;
};

const createNodeEntry = (node, nodeType, degree) => ({
data: {
id: node.properties.id,
label: getNodeLabel(node),
degree: degree.low,
alt_name: node.properties.alt_name,
gene_name: node.properties.gene_name,
alt_name: node.properties.alt_name,
alt_id: node.properties.alt_id,
alt_gene_id: node.properties.alt_gene_id,
type: nodeType,
},
});
Expand Down Expand Up @@ -231,10 +240,14 @@ export function NetworkParserNode(data, k) {

currentPath.forEach((node, index) => {
const nodeType = determineNodeType(node, sourceId, index, currentPath.length);
const nodeEntry = createNodeEntry(node, nodeType, node.properties.degree);
addNodeIfNotExists(nodeEntry, parsedData);
if (nodeType === "go_protein" || nodeType === "go_source") {
const nodeEntry = createNodeEntry(node, nodeType, node.properties.degree, node.properties.relationship);
addNodeIfNotExists(nodeEntry, parsedData);
} else {
const nodeEntry = createNodeEntry(node, nodeType, node.properties.degree);
addNodeIfNotExists(nodeEntry, parsedData);
}
});

addEdges(currentPath, parsedData);
});

Expand Down
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