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add micro RNA interactor type
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@colin-combe
colin-combe committed Mar 20, 2021
1 parent ac6bcba commit 45c9044
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194 changes: 194 additions & 0 deletions data/EBI-25437853.json
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{
"data": [
{
"object": "interactor",
"id": "ensembl_ENST00000627532",
"sequence": "AGTTCTAACCTGCTCTGCAGGAATAACGGTCCTGCCTCCCGACACTCTTGGCGAGGTTTTTGTACAGTTTGCTCCGGGAGCTGTTTCTTCGCTTCCACCTTTTTCTCCCCCACACTTCGCGGCTTCTTCATGCTTTTTCTTCTCACCATTTCTGGCCAAAACTACAAACAAGACTTCGCAGATCGAGCCTGCGTGCTGCCGAAGCAGGGCGCCGAGTCCATGCGAACTGCCATCTGATCCGCTCTTATCAATGAAGCAGCCGATCATGGCGGATGGCCCCCGGTGCAAGAGGCGCAAACAAGCCAATCCCAGGAGGAAAAACGTGGTGAACTATGACAATGTAGTGGACACAGGTTCTGAAACAGATGAGGAAGACAAGCTTCATATTGCTGAGGATGACGGTATTGCCAACCCTCTGGACCAGGAGACGAGTCCAGCTAGTGTGCCCAACCATGAGTCCTCCCCACACGTGAGCCAAGCTCTGTTGCCAAGAGAGGAAGAGGAAGATGAAATAAGGGAGGGTGGAGTGGAACACCCCTGGCACAACAACGAGATTCTACAAGCCTCTGTAGATGGTCCAGAAGAAATGAAGGAAGACTATGACACTATGGGGCCAGAAGCCACGATCCAGACCGCAATTAACAATGGTACAGTGAAGAATGCAAATTGCACATCAGATTTTGAGGAATACTTTGCCAAAAGAAAACTGGAGGAACGCGATGGTCATGCAGTCAGCATCGAGGAGTACCTTCAGCGCAGTGACACAGCCATTATTTACCCAGAAGCCCCTGAGGAGCTGTCTCGCCTTGGCACGCCAGAGGCCAATGGGCAAGAAGAAAATGACCTGCCACCTGGAACTCCAGATGCTTTTGCCCAACTGCTGACCTGCCCCTACTGCGACCGGGGCTACAAGCGCTTGACATCACTGAAGGAGCACATCAAGTACCGCCACGAGAAGAATGAAGAGAACTTTTCCTGCCCTCTCTGTAGCTACACGTTTGCCTACCGCACCCAGCTCGAGCGGCATATGGTGACACACAAGCCAGGGACAGATCAGCACCAAATGCTAACCCAAGGAGCAGGTAATCGCAAGTTCAAATGCACAGAGTGTGGCAAGGCCTTCAAATATAAACACCATCTGAAAGAACACCTGCGAATTCACAGTGGTGAAAAACCTTACGAGTGCCCAAACTGCAAGAAACGTTTCTCCCATTCTGGTTCCTACAGTTCGCACATCAGCAGCAAGAAATGTATTGGTTTAATCTCTGTAAATGGCCGAATGAGAAACAATATCAAGACGGGTTCTTCCCCTAATTCTGTTTCTTCTTCTCCTACTAATTCAGCCATTACCCAGTTAAGAAACAAGTTGGAGAATGGAAAACCACTTAGTATGTCTGAACAGACAGGCTTACTTAAAATTAAAACAGAACCACTAGACTTCAATGACTATAAAGTTCTTATGGCTACACACGGGTTTAGTGGCACTAGTCCCTTTATGAATGGTGGGCTTGGAGCCACCAGCCCTTTAGGAGTTCATCCATCTGCTCAGAGTCCAATGCAGCACTTAGGTGTAGGGATGGAAGCCCCTTTACTTGGGTTTCCCACCATGAATAGTAATTTAAGTGAGGTACAAAAGGTTCTACAGATTGTGGACAATACTGTTTCCAGGCAAAAAATGGACTGCAAGGCTGAAGAAATTTCAAAGTTGAAAGGTTATCACATGAAGGATCCATGCTCTCAACCTGAGGAACAAGGAGTTACTTCTCCTAATATTCCGCCTGTCGGTCTTCCGGTAGTGAGTCATAATGGTGCCACTAAAAGTATTATTGACTATACGTTGGAAAAAGTCAATGAAGCCAAAGCTTGCCTCCAGAGCTTGACTACTGACTCAAGGAGACAGATCAGTAATATAAAGAAAGAGAAGCTACGTACTTTAATAGATTTGGTCACTGATGACAAAATGATTGAGAACCACAACATATCCACTCCATTTTCATGCCAGTTCTGTAAAGAAAGTTTTCCTGGCCCCATCCCTTTGCATCAGCATGAACGTTACCTTTGTAAGATGAATGAAGAGATCAAGGCGGTCCTGCAGCCTCATGAAAACATAGTCCCCAACAAAGCCGGAGTTTTTGTTGATAATAAAGCCCTCCTCTTGTCATCTGTACTTTCTGAGAAAGGAATGACAAGCCCCATCAACCCATACAAGGACCACATGTCTGTACTCAAAGCATACTATGCTATGAACATGGAGCCCAACTCCGATGAACTGCTGAAAATTTCCATTGCTGTGGGCCTTCCTCAGGAATTTGTGAAGGAATGGTTTGAACAACGAAAAGTCTACCAGTACTCAAATTCCAGGTCCCCATCCCTGGAAAGAAGCTCCAAGCCGTTAGCTCCCAACAGTAACCCTCCCACAAAAGACTCTTTATTACCCAGGTCTCCTGTAAAACCTATGGACTCCATAACATCACCATCTATAGCAGAACTCCACAACAGTGTTACGAATTGTGATCCTCCTCTCAGGCTAACAAAACCTTCCCATTTTACCAATATTAAACCAGTTGAAAAATTGGACCACTCCAGGAGTAATACTCCTTCTCCCTTAAATCTTTCCTCCACATCTTCTAAAAACTCCCACAGTAGTTCATACACTCCAAACAGCTTCTCTTCTGAGGAGCTCCAGGCTGAGCCTTTAGACTTGTCATTACCAAAACAAATGAAAGAACCCAAAAGTATTATAGCCACAAAGAACAAAACAAAAGCTAGTAGCATCAGTTTAGATCATAACAGTGTTTCTTCCTCATCTGAAAACTCAGATGAGCCTCTGAACTTGACTTTTATCAAGAAGGAATTTTCAAATTCAAATAATCTGGACAACAAAAGCACTAACCCAGTGTTCAGCATGAACCCATTTAGTGCCAAACCTTTATACACAGCTCTTCCACCTCAAAGCGCATTTCCCCCTGCTACTTTCATGCCACCAGTCCAGACCAGTATTCCTGGGCTACGACCATACCCAGGACTGGATCAGATGAGCTTCCTACCACATATGGCCTACACCTACCCAACTGGAGCAGCTACTTTTGCTGATATGCAGCAAAGGAGAAAGTACCAGCGGAAACAAGGATTTCAGGGAGAATTGCTTGATGGAGCACAAGACTACATGTCAGGCCTAGATGATATGACAGACTCCGACTCCTGTCTGTCTCGCAAAAAGATCAAGAAGACAGAGAGTGGCATGTATGCATGTGACTTATGTGACAAGACATTCCAGAAAAGCAGTTCCCTTCTGCGACATAAATACGAACACACAGGAAAAAGACCACATCAGTGTCAGATTTGTAAGAAAGCGTTTAAACACAAGCACCACCTTATCGAGCACTCAAGGCTTCACTCGGGCGAGAAGCCCTATCAGTGTGATAAATGTGGCAAGCGCTTCTCACACTCGGGCTCGTACTCGCAGCACATGAATCACAGGTATTCCTACTGCAAGCGGGAGGCGGAGGAGCGGGAAGCGGCGGAGCGCGAGGCGCGCGAGAAAGGGCACTTGGAACCCACCGAGCTGCTGATGAACCGGGCTTACTTGCAGAGCATTACCCCTCAGGGGTACTCTGACTCGGAGGAGAGGGAGAGTATGCCGAGGGATGGCGAGAGCGAGAAGGAGCACGAGAAAGAAGGCGAGGATGGCTACGGGAAGCTGGGCAGACAGGATGGCGACGAGGAGTTCGAGGAGGAAGAGGAAGAAAGTGAAAATAAAAGTATGGATACGGATCCCGAAACGATACGAGATGAAGAAGAGACTGGAGATCACTCCATGGACGATAGTTCGGAGGATGGGAAAATGGAAACCAAATCAGACCACGAGGAAGACAATATGGAAGATGGCATGTAATAAACTACTGCATTTTAAGCTTCCTATTTTTTTTTCCAGTAGTATTGTTACCTGCTTGAAAACACTGCTGTGTTAAGCTGTTCATGCACGTGCCTGACGCTTCCAGGAAGCTGTAGAGAGGGACAGAAGGGGCGGTTCAGCCAAGACAGATGTAGACGGAGTTGGAGCTGGGTATTGTTAAAAACTGCATTATGCAAAAATTTTGTACAGTGTTAAGGCCTAAAAACTGTGTGGTTCAGAGACTAATTCCTGTGTTTAATAGCATTTATACTTTAAGCACAACTAGAAAATTGTAAGAATTGCACTCTACTTATGTATCACTACAAACTTTAAAAAACTATGTCTAATTTATATTAATACATTTTAAAAAGGTGCCCGCACTACCATACATCAGTATTTTTATTATTATTATTGTTATTCCTTTTTAATTTAATGTGCTCGCACTACAATGCATCAGTATTATGATTCCTCTGTACTTTCCTTTCGCTATTCATCAATTTCCCATTTTTTTTTTCAGCTTAAGTAACCACACAATTTTAGGCCTCAATTTTTTTTTTTTTCTGTGAAGGAACTTGAAGTGATGCATGTGTGAATTTAAGATACCGAAGTCTTAAAGTGACCTGGACGTGAAGGAAAAAGTAAGATGAGAAATAAAGAAAGCCTTTGTAAGGTGGTTTTAAAAGCCTTATATGCAAACCTTTTAATCTGTGTTTCTGCAAGTGCCATCCTTGTACAGTGTTAAGAGGGTAACATGGGTTACCTTTGCACCAGCTTCAGTGTTAAGCTCACCCTGTTCTTTGAAGCACCCATGTCAGTATTAGAAGAATAGGCAGCAGTTCCTTAGTTTACATATGTTTGTGCAATTATTTTCTGTACTTTTTTGTTCATTAATTTTGTCAGTATTACACCAAACTGTTTTTGCAACAAAAAAATTTTTTTTGCATTCATTTAATTTTAGGTCAAATAACATTTTATTTATGTGGCTCATTTTATATTTCCTAATTTTATTTATTTCATACTGTAGTGTACAGTATTATAGTTCTTCAATATATAGATATATTTTAGTAAAAAAGGAACATGACGTTGATCATTTGGGCAAATTTTACGTAAAGAGAAGAGCATTTATTGTGTTTTGGAACATTAATTGTGAGATGGGATTTTTCAATTTTATTATTTTATTTTTGTTTTTTTCCAATTACTGGAAATTCCAAATTTGGGAACTTTTGATACGATCTTGTGAAAACACTGTATTTTCGACTGAAAATTCCACTTTCTTCATCTTGTTTTTTAGCTAAAAAGAGGGACTGTTAAATACAATGTATGATACCATGACAAAAATCTTTCCTGAATTGTCTTTGTAAAAGTATTATTGAATTTTCAATTTGTAATTTCTTTTGAAAATGACCATGCTCGAATAAAAATGTAGCCAAACTAAGAATGTAGTTAATGAGTTCTGTACTTTTAGAGAGTTTTCCTTCAATGACCATTAACATGTAACATGCTTTATGCTTATAATAATGCTAATTATGTTTTTTTCATATAATTTTAGTTTAGCAATAATTTTGACTGGTACCAATAACTGTTTTTTAAAATTCCATACCTATGTACAGCAATTTTACAGCTTTTCTCAACTGATCCTGATTCCAGATTGTGTATTTTTATGTGAGGTTATATTATTCAAATTTAGTCTATTTACTTTACAGACATTTCTACTTTTGCATTACGAGTATTTAGAGATTATGTGTTAAAAATTCACTTCTCTGTCCAAGGGGTCTTTGTGATTTATTCAAAAAAAAGTCTAATTTCAAAAAGACAGCTATTATTCAGTGTTATTTATAATATGTAACCTTTTTTAAAGGATTGGGATAGTTTATCTCACTTTTTGAAATGCAGACAGTAGTTTACCGTTTATCTGAAACTAGAAGGCGTGGGTGGGAGAGGAAAAGCTAAAAGCAAATGCTAACAAAAATAACCGTGATTTTCTAAGACAGTTTTTCAGTTTTTACAAGATGACCCTAATATTCAGAATATGAATGTATTCGTAGGTTTTACATAATGACTTTTATCAAGAAACTAGATTCTGCTTCTTAAATCTAATTGCCAAGTGAAGAATAACAGAAAAAACAGATTACCTTATCAAATTTACAGCTCTTGAATATACAGAACTATAATATAGTAGCTGTCCATGTATTTTTTCTACTTTAGAATCAAAGAAGAAAAGCATCATTTTGCTATTAAATTTGCTAAAATTTTGAGTATGATATTTCCAGTTGGCAAGAACAACATATTTATATTTATTCCTTAGCCATAATACCACTTTCCTAAATTTCACAAAAGTCATTCTTTGCAACTTGAAACTCAATAGAAAGTGTGTATGTGTGTGTGTGTATATATATATATATATACACACACACACATACACAGAAAGGATGTAATGAAGATACAGTAATAGTTGAGCAGACCTTTTTAGAAAAACATGTTTTTAGCTCTATCTTCAAACTTTCTGGCAGAGGGGGTGGGGGGGGCAGGGGGAGGAGTGGCATCAAAATGCTATGCCTCCTGTTATCCACAGCCTAGAGTTTTTATATTTGGAAAGTTTAGAAAATTCTATCCTCGTTTCTCCTTCTTTGAATGGCACAAATAAATACACTACATAAATTTTTCTGGTTTGAAAGGCTCTAGGCGATAACTTTATTAATTCAACCTGAAAATATCAAGCCATTAAATTTTGTCCGGGTAGAATAAATCCCTGTGGCCTCTTTTAAAGCAATGTAGGTCTCTGTTGCCCATGGGGCATATCTGTGTCCCAATCCACAAGAGATAGGACCAACAAACAATGAATGTGCAACCTAACTCTTTCTCCTTGGAAAGAAGAAAGTGTGCACGAAGTAGAGGAGGGTGGGCAGACCCTGCCTTGCCCCTCCTGTTACCCCCTTCTCTGTCATTTGTTCCTAACTCCATTTCATAGGCAGGCTCAGAATACCTGAGTCTGAAAATATCAGGATAACACTTGTGAATTGTGACAATCACTACAATGTCCCATATCTGAGGAGTTTTTTTTAATGCTATTTATCCGCTGGACACGATTGCACATTAGGGCTGCATAATCCTCTAACTCTAGGGAAAAATAAAAACTTTTGATTTGTCTTAAGATTCTTCTCCAAGGTCGCAAACAAGAAATTCCCCTCCACAACCAAGAGATGTGCATTTTAGTAACATCAGATGTGTTCTTCTGTTTTATCAACTACTTACTCTTCCCACACGCTTAGTTCTAAATCTAACCTTTCCCCCCTCGAATAGGGGGCAGGGGAGGATGAGGAAACACTGGAACAACTGAACACCCCTGCCCATTTTCTCCAAGAGCCTTTTGTATTCTAGCATATCTGTGCAATCTTTTCTTTTTTCTTCACATGACACTGTAAGCTTAGGCCTGAAATAACTGGGAAGAGAGATGCGTATCAGAATTTCTCCGCAAGAGCTAAACAAAACATACATCTTCCTTAGCATGAATTGGACTGGGGGCGGAGTGGGAGGGCTTGGAGGAAAGGGGAAAGAAGGGACTATATTTGAATAAATATGAATAAATGTATTAGATACTTTTCACAATCAGATAACTTTTAAAAAGGTCATTTTTTATCTTTCTAATAATGTAAGCCTTAATAAAAGCAAATCTTAGTCACAAATTTGAGGAGACTGCCCAATAATAAGTTTACATGTATTTGAACTGAAAAATTGTTAACCATGCTTTTGCTCCAAGATGTGTGAGGCCATTCAGGGGCTGTAGGGCCCTGGATATACACACAAACAAGTGTGTGTATATCTGGAGCCCCACACATTGTAATAAACACAGCTGCATTTATTTGACTATGTGATCCCATGTACATGTAAAAACATTCAAACAAACACACTCAGCGGATTTATTTATTGTGCAATGGGGCAATTATTCAAATAAACATGCTCAATGCAATTATTTGAATCTCACATTGCATGTTCATCAATCATAGCACTAAAAAAAGAGGGGGAAAAAACACCAAAGAATTCACATGGGGAAAAAATATATATATGAAAACCACCTTATTATAGATTTTATAGGGCAGCTGAGGTTATGGCTCCCTTCTTAACTGTAACTCAACTATTCTGTATTCAATGACATTTGTTTCTAATGATTAATTGGTTCACTCACTTGATCATATAATAGCAAACTTTATAAACCTGTATTGTGTAGAGATGTGAAATCTCTATATTTCAAGAGCAGAAGAGTTCTTTCTAGACACCTTACATCAAGGGACACTGGTCCAATTATTATCGCTTATATAAGCACTCCTATAAATTCTGAAAAATTTTATACATGCAACAAAACATTCCTACATTTGAAGACATTAAGAAAAATCACAGGTGACTCATCTGATCATTCTATATATTAATAAATATTATGACATATATGTGAACACATCACAAATCATATTGGTGTACCAAGAGGCAATTTATGCCTCTCTTAAGTATGTACTGACATAACCTAATATACTAAAATGGGAAGGGGCTTTTAGTCACTGAAATATGCATCGTGTAACAAAGATGAAGAAAATACATGGCTTGTGCCCATCATAAAAAAAGATTCAGACTGAAGGCTTAGCTTTGGTTTTTTCAATTAAATTGTTAAACTGTGCACAGTGATTTTTTTTTAGAACTTGAGACATTTGTGATGTTGGCTGTTTAAATCTTTGTTACCTTCGCTGTGAATTGAAATTGTACATATTTAGTAAATCATGCAGACAAAACAAACTTTTTAGACAATATTTTTATTGGAGAGTTTTCTTTTCCTGTATCCATGTTAAAAAAAAAAAAGACCTCCTTTCCCAAAATAAAAATGTCAATACTAAATTTAAAGAAGTATAAAGGAATGATTGCTTCCTTTAGAGCAAAATATTTAAATAAACATGGAGATAATTGGCAACATGTTCTTTTTGGGCTAGTAGGCTGTGTCCAATTTTTTGGGTCTGATGTTTCAGAGGGCCTCTGTTTCAGGGTTGAAGATGATATATTAATCTCGGAATTAAACAAATGCTATTAAATAACAGAAATAAATCCTTCAGTCTTCATTTGTATCTGAAATGTGGAATTAGTCAGAGAAATGGCACCGAGATAATATGATGCTGAATATGCCACAAGCTAAAACTTTCTCTATTAAACGAGTCGCCTACTACCTATAATCTAGCATGACATGTTAAAATGCTCCAAAATACTGAAAATAGAAAATGAACACTACTGTTCCGATTTGGTCTTGAGATTAATATGACAAAGATTCTAATAATTTTAGTCAAAGAAAATGATGAGTAAAAAATACATGAAGATTAAAGTGATGACAAATGA",
"type": {
"id": "MI:0324",
"name": "messenger rna"
},
"organism": {
"taxid": "9606",
"common": "human",
"scientific": "Homo sapiens"
},
"identifier": {
"db": "ensembl",
"id": "ENST00000627532"
},
"label": "mrna_zeb2"
},
{
"object": "interactor",
"id": "rnacentral_URS000043D1A9_9606",
"sequence": "UGUAAACAUCCUCGACUGGAAG",
"type": {
"id": "MI:2204",
"name": "micro rna"
},
"organism": {
"taxid": "9606",
"common": "human",
"scientific": "Homo sapiens"
},
"identifier": {
"db": "rnacentral",
"id": "URS000043D1A9_9606"
},
"label": "hsa-mir-30a-5p"
},
{
"object": "interaction",
"id": "intact_EBI-25437853",
"interactionType": {
"id": "MI:0915",
"name": "physical association"
},
"experiment": {
"detmethod": {
"id": "MI:2285",
"name": "miRNA interference luciferase reporter assay"
},
"host": {
"taxid": "9606",
"common": "human-769p",
"cellType": {
"id": "IA:3374",
"name": "769-P human"
}
},
"pubid": [
{
"db": "intact",
"id": "EBI-25436167"
},
{
"db": "pubmed",
"id": "28569782"
},
{
"db": "imex",
"id": "IM-27965"
}
],
"sourceDatabase": {
"id": "MI:0469",
"name": "European Bioinformatics Institute"
},
"figures": [
"Fig 2 A, B"
]
},
"identifiers": [
{
"db": "intact",
"id": "EBI-25437853"
},
{
"db": "imex",
"id": "IM-27965-1"
}
],
"participants": [
{
"id": "1",
"interactorRef": "ensembl_ENST00000627532",
"bioRole": {
"id": "MI:2275",
"name": "regulator target"
},
"expRole": {
"id": "MI:0497",
"name": "neutral component"
},
"identificationMethods": [
{
"id": "MI:1220",
"name": "tag visualisation by luciferase assay"
}
],
"features": [
{
"id": "2",
"name": "tag",
"category": "experimentalFeatures",
"type": {
"id": "MI:1205",
"name": "luciferase tag"
},
"sequenceData": [
{
"pos": "0-0",
"interactorRef": "ensembl_ENST00000627532",
"participantRef": "1"
}
]
},
{
"id": "3",
"name": "r.4739_4744delinsggttcc",
"category": "pointMutations",
"type": {
"id": "MI:0119",
"name": "mutation decreasing interaction"
},
"sequenceData": [
{
"pos": "4739-4744",
"resultingSequence": "GGTTCC",
"interactorRef": "ensembl_ENST00000627532",
"participantRef": "1"
}
]
},
{
"id": "4",
"name": "region",
"category": "bindingSites",
"type": {
"id": "MI:0117",
"name": "binding-associated region"
},
"detmethods": [
{
"id": "MI:0033",
"name": "deletion analysis"
}
],
"sequenceData": [
{
"pos": "3896-4745",
"interactorRef": "ensembl_ENST00000627532",
"participantRef": "1"
}
]
}
]
},
{
"id": "5",
"interactorRef": "rnacentral_URS000043D1A9_9606",
"bioRole": {
"id": "MI:2274",
"name": "regulator"
},
"expRole": {
"id": "MI:0497",
"name": "neutral component"
},
"identificationMethods": [
{
"id": "MI:1220",
"name": "tag visualisation by luciferase assay"
},
{
"id": "MI:0396",
"name": "predetermined participant"
}
]
}
]
}
]
}
5 changes: 5 additions & 0 deletions data/index.js
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@@ -1,5 +1,10 @@
// eslint-disable-next-line no-unused-vars
const exampleIndex = [
{
"ac": "EBI-25437853",
"name": "EBI-25437853",
"url": "https://wwwdev.ebi.ac.uk/intact/beta/details/interaction/EBI-25437853",
},
{
"ac": "EBI-25776165",
"name": "EBI-25776165",
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2 changes: 1 addition & 1 deletion dist/complexviewer.js
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5 changes: 3 additions & 2 deletions src/js/read-mijson.js
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Expand Up @@ -226,8 +226,7 @@ export function readMijson (/*miJson*/miJson, /*App*/ app, expand = true) {
break;
}
}



if (interactionExists) {
participant = new Complex(participantId, app, interactorRef);
complexes.set(participantId, participant);
Expand Down Expand Up @@ -283,6 +282,8 @@ export function readMijson (/*miJson*/miJson, /*App*/ app, expand = true) {
interactor.type.id === "IA:2966" // RNA - double stranded ribonucleic acid
||
interactor.type.id === "MI:0318" // nucleic acid
||
interactor.type.id === "MI:2204" // micro RNA
) {
participant = new RNA(participantId, app, interactor, interactor.label);
} else if (interactor.type.id === "MI:0319" // DNA
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