From 2a289f8b9588c92f0fc0d2f1d1f1b029766f9107 Mon Sep 17 00:00:00 2001 From: "Bruce W. Herr II" Date: Tue, 5 Sep 2023 16:20:41 -0400 Subject: [PATCH] Some refactoring, implemented base cell summary similarities and rui location distances. WIP. --- data-processor/package-lock.json | 96 + data-processor/package.json | 1 + data-processor/src/ctpop-db.js | 43 - .../src/gen-cell-summary-similarities.js | 21 + data-processor/src/gen-registrations.js | 2 +- data-processor/src/gen-reports.js | 2 +- .../src/gen-rui-location-distances.js | 25 + .../src/utils/cell-summary-similarity.js | 61 + .../src/{ => utils}/hubmap-uuid-lookup.js | 0 data-processor/src/{ => utils}/sparql.js | 0 .../src/utils/spatial-entity-distance.js | 70 + data/cell-summary-similarities.jsonld | 678570 +++++++++++++++ data/rui-location-distances.jsonld | 106770 +++ 13 files changed, 785616 insertions(+), 45 deletions(-) delete mode 100644 data-processor/src/ctpop-db.js create mode 100644 data-processor/src/gen-cell-summary-similarities.js create mode 100644 data-processor/src/gen-rui-location-distances.js create mode 100644 data-processor/src/utils/cell-summary-similarity.js rename data-processor/src/{ => utils}/hubmap-uuid-lookup.js (100%) rename data-processor/src/{ => utils}/sparql.js (100%) create mode 100644 data-processor/src/utils/spatial-entity-distance.js create mode 100644 data/cell-summary-similarities.jsonld create mode 100644 data/rui-location-distances.jsonld diff --git a/data-processor/package-lock.json b/data-processor/package-lock.json index 45f53aa..851d42c 100644 --- a/data-processor/package-lock.json +++ b/data-processor/package-lock.json @@ -12,10 +12,22 @@ "fetch-sparql-endpoint": "^3.3.3", "glob": "^10.3.0", "jsonld": "^8.2.0", + "mathjs": "^11.10.1", "papaparse": "^5.4.1", "shelljs": "^0.8.5" } }, + "node_modules/@babel/runtime": { + "version": "7.22.11", + "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.22.11.tgz", + "integrity": "sha512-ee7jVNlWN09+KftVOu9n7S8gQzD/Z6hN/I8VBRXW4P1+Xe7kJGXMwu8vds4aGIMHZnNbdpSWCfZZtinytpcAvA==", + "dependencies": { + "regenerator-runtime": "^0.14.0" + }, + "engines": { + "node": ">=6.9.0" + } + }, "node_modules/@bergos/jsonparse": { "version": "1.4.1", "resolved": "https://registry.npmjs.org/@bergos/jsonparse/-/jsonparse-1.4.1.tgz", @@ -226,6 +238,18 @@ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz", "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==" }, + "node_modules/complex.js": { + "version": "2.1.1", + "resolved": "https://registry.npmjs.org/complex.js/-/complex.js-2.1.1.tgz", + "integrity": "sha512-8njCHOTtFFLtegk6zQo0kkVX1rngygb/KQI6z1qZxlFI3scluC+LVTCFbrkWjBv4vvLlbQ9t88IPMC6k95VTTg==", + "engines": { + "node": "*" + }, + "funding": { + "type": "patreon", + "url": "https://www.patreon.com/infusion" + } + }, "node_modules/concat-map": { "version": "0.0.1", "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz", @@ -279,6 +303,11 @@ "node": ">= 12" } }, + "node_modules/decimal.js": { + "version": "10.4.3", + "resolved": "https://registry.npmjs.org/decimal.js/-/decimal.js-10.4.3.tgz", + "integrity": "sha512-VBBaLc1MgL5XpzgIP7ny5Z6Nx3UrRkIViUkPUdtl9aya5amy3De1gsUUSB1g3+3sExYNjCAsAznmukyxCb1GRA==" + }, "node_modules/eastasianwidth": { "version": "0.2.0", "resolved": "https://registry.npmjs.org/eastasianwidth/-/eastasianwidth-0.2.0.tgz", @@ -289,6 +318,11 @@ "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-9.2.2.tgz", "integrity": "sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==" }, + "node_modules/escape-latex": { + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/escape-latex/-/escape-latex-1.2.0.tgz", + "integrity": "sha512-nV5aVWW1K0wEiUIEdZ4erkGGH8mDxGyxSeqPzRNtWP7ataw+/olFObw7hujFWlVjNsaDFw5VZ5NzVSIqRgfTiw==" + }, "node_modules/event-target-shim": { "version": "5.0.1", "resolved": "https://registry.npmjs.org/event-target-shim/-/event-target-shim-5.0.1.tgz", @@ -377,6 +411,18 @@ "node": ">=12.20.0" } }, + "node_modules/fraction.js": { + "version": "4.3.6", + "resolved": "https://registry.npmjs.org/fraction.js/-/fraction.js-4.3.6.tgz", + "integrity": "sha512-n2aZ9tNfYDwaHhvFTkhFErqOMIb8uyzSQ+vGJBjZyanAKZVbGUQ1sngfk9FdkBw7G26O7AgNjLcecLffD1c7eg==", + "engines": { + "node": "*" + }, + "funding": { + "type": "patreon", + "url": "https://github.com/sponsors/rawify" + } + }, "node_modules/fs.realpath": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz", @@ -512,6 +558,11 @@ "@pkgjs/parseargs": "^0.11.0" } }, + "node_modules/javascript-natural-sort": { + "version": "0.7.1", + "resolved": "https://registry.npmjs.org/javascript-natural-sort/-/javascript-natural-sort-0.7.1.tgz", + "integrity": "sha512-nO6jcEfZWQXDhOiBtG2KvKyEptz7RVbpGP4vTD2hLBdmNQSsCiicO2Ioinv6UI4y9ukqnBpy+XZ9H6uLNgJTlw==" + }, "node_modules/jsonld": { "version": "8.2.0", "resolved": "https://registry.npmjs.org/jsonld/-/jsonld-8.2.0.tgz", @@ -580,6 +631,28 @@ "node": "14 || >=16.14" } }, + "node_modules/mathjs": { + "version": "11.10.1", + "resolved": "https://registry.npmjs.org/mathjs/-/mathjs-11.10.1.tgz", + "integrity": "sha512-XcYBJFM7hsIXcE9443RxxMmK3sI41RJo0GltX4vZ8NlVg+puGAwyhTUBUoa4orLkBbbnetGCdqEPrOQvhToi2A==", + "dependencies": { + "@babel/runtime": "^7.22.6", + "complex.js": "^2.1.1", + "decimal.js": "^10.4.3", + "escape-latex": "^1.2.0", + "fraction.js": "^4.3.4", + "javascript-natural-sort": "^0.7.1", + "seedrandom": "^3.0.5", + "tiny-emitter": "^2.1.0", + "typed-function": "^4.1.0" + }, + "bin": { + "mathjs": "bin/cli.js" + }, + "engines": { + "node": ">= 14" + } + }, "node_modules/minimatch": { "version": "9.0.1", "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.1.tgz", @@ -827,6 +900,11 @@ "node": ">= 0.10" } }, + "node_modules/regenerator-runtime": { + "version": "0.14.0", + "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.14.0.tgz", + "integrity": "sha512-srw17NI0TUWHuGa5CFGGmhfNIeja30WMBfbslPNhf6JrqQlLN5gcrvig1oqPxiVaXb0oW0XRKtH6Nngs5lKCIA==" + }, "node_modules/resolve": { "version": "1.22.2", "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.2.tgz", @@ -848,6 +926,11 @@ "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz", "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g==" }, + "node_modules/seedrandom": { + "version": "3.0.5", + "resolved": "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz", + "integrity": "sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==" + }, "node_modules/setimmediate": { "version": "1.0.5", "resolved": "https://registry.npmjs.org/setimmediate/-/setimmediate-1.0.5.tgz", @@ -1119,11 +1202,24 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/tiny-emitter": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/tiny-emitter/-/tiny-emitter-2.1.0.tgz", + "integrity": "sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q==" + }, "node_modules/tr46": { "version": "0.0.3", "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz", "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw==" }, + "node_modules/typed-function": { + "version": "4.1.0", + "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.1.0.tgz", + "integrity": "sha512-DGwUl6cioBW5gw2L+6SMupGwH/kZOqivy17E4nsh1JI9fKF87orMmlQx3KISQPmg3sfnOUGlwVkroosvgddrlg==", + "engines": { + "node": ">= 14" + } + }, "node_modules/undici": { "version": "5.22.1", "resolved": "https://registry.npmjs.org/undici/-/undici-5.22.1.tgz", diff --git a/data-processor/package.json b/data-processor/package.json index f5ee49a..c6026cf 100644 --- a/data-processor/package.json +++ b/data-processor/package.json @@ -22,6 +22,7 @@ "fetch-sparql-endpoint": "^3.3.3", "glob": "^10.3.0", "jsonld": "^8.2.0", + "mathjs": "^11.10.1", "papaparse": "^5.4.1", "shelljs": "^0.8.5" } diff --git a/data-processor/src/ctpop-db.js b/data-processor/src/ctpop-db.js deleted file mode 100644 index 5c7ea85..0000000 --- a/data-processor/src/ctpop-db.js +++ /dev/null @@ -1,43 +0,0 @@ -import { existsSync, readFileSync, writeFileSync } from 'fs'; -import jsonld from 'jsonld'; -import { namedNode } from 'oxigraph'; -import { SparqlRunner } from './sparql.js'; - -const HRA_URL = 'https://purl.org/ccf/2.2.1/ccf.owl'; -const HRA_PATH = '../data/ccf.owl'; -const CTPOP_IRI = - 'https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#graph'; -const CTPOP_PATH = '../data/enriched_rui_locations.jsonld'; - -function fetchText(url) { - return fetch(url, { - redirect: 'follow', - }).then((r) => r.text()); -} - -export async function getCtPopDb() { - const engine = new SparqlRunner(); - const oxigraph = engine.engine; - - const ctpopData = JSON.parse(readFileSync(CTPOP_PATH)); - const ctpopQuads = await jsonld.toRDF(ctpopData, { - format: 'application/n-quads', - }); - oxigraph.load( - ctpopQuads.toString(), - 'text/turtle', - undefined, - namedNode(CTPOP_IRI) - ); - - let hraOwl; - if (!existsSync(HRA_PATH)) { - hraOwl = await fetchText(HRA_URL); - writeFileSync(HRA_PATH, hraOwl); - } else { - hraOwl = readFileSync(HRA_PATH).toString(); - } - oxigraph.load(hraOwl, 'application/rdf+xml', undefined, namedNode(HRA_URL)); - - return engine; -} diff --git a/data-processor/src/gen-cell-summary-similarities.js b/data-processor/src/gen-cell-summary-similarities.js new file mode 100644 index 0000000..9b0d78a --- /dev/null +++ b/data-processor/src/gen-cell-summary-similarities.js @@ -0,0 +1,21 @@ +import { readFileSync, writeFileSync } from 'fs'; +import { getAllCellSummarySimilarities } from './utils/cell-summary-similarity.js'; + +const OUTPUT = '../data/cell-summary-similarities.jsonld'; + +const allSummaries = [ + '../data/dataset-cell-summaries.jsonld', + '../data/as-cell-summaries.jsonld', + '../data/rui-location-cell-summaries.jsonld', +] + .map((path) => JSON.parse(readFileSync(path))['@graph']) + .reduce((acc, arr) => acc.concat(arr), []); + +const results = [...getAllCellSummarySimilarities(allSummaries)]; + +// Write out the new enriched_rui_locations.jsonld file +const jsonld = { + ...JSON.parse(readFileSync('ccf-context.jsonld')), + '@graph': results, +}; +writeFileSync(OUTPUT, JSON.stringify(jsonld, null, 2)); diff --git a/data-processor/src/gen-registrations.js b/data-processor/src/gen-registrations.js index 8baa9b5..1074eed 100644 --- a/data-processor/src/gen-registrations.js +++ b/data-processor/src/gen-registrations.js @@ -1,7 +1,7 @@ // Requires Node v18+ (for fetch support) import { readFileSync, writeFileSync } from 'fs'; import Papa from 'papaparse'; -import { getHbmToUuidLookup } from './hubmap-uuid-lookup.js'; +import { getHbmToUuidLookup } from './utils/hubmap-uuid-lookup.js'; const CSV_URL = 'https://docs.google.com/spreadsheets/d/1cwxztPg9sLq0ASjJ5bntivUk6dSKHsVyR1bE6bXvMkY/export?format=csv&gid=1529271254'; diff --git a/data-processor/src/gen-reports.js b/data-processor/src/gen-reports.js index a34ced7..d48e4c5 100644 --- a/data-processor/src/gen-reports.js +++ b/data-processor/src/gen-reports.js @@ -2,7 +2,7 @@ import { readFileSync, writeFileSync } from 'fs'; import { globSync } from 'glob'; import { basename } from 'path'; import sh from 'shelljs'; -import { selectCsvRemote } from './sparql.js'; +import { selectCsvRemote } from './utils/sparql.js'; // SPARQL endpoint with ctpop data loaded //const SPARQL_ENDPOINT = 'https://api.triplydb.com/datasets/bherr/ctpop/services/ctpop/sparql'; diff --git a/data-processor/src/gen-rui-location-distances.js b/data-processor/src/gen-rui-location-distances.js new file mode 100644 index 0000000..9ac6c76 --- /dev/null +++ b/data-processor/src/gen-rui-location-distances.js @@ -0,0 +1,25 @@ +import { readFileSync, writeFileSync } from 'fs'; +import { getAllSpatialEntityDistances } from './utils/spatial-entity-distance.js'; + +const OUTPUT = '../data/rui-location-distances.jsonld'; +const donors = JSON.parse(readFileSync('../data/rui_locations.jsonld'))['@graph']; + +const ruiLocations = []; +for (const donor of donors) { + for (const block of donor['samples']) { + const ruiLocation = block.rui_location; + ruiLocations.push(ruiLocation); + } +} + +const results = []; +for await (const distance of getAllSpatialEntityDistances(ruiLocations)) { + results.push(distance); +}; + +// Write out the new enriched_rui_locations.jsonld file +const jsonld = { + ...JSON.parse(readFileSync('ccf-context.jsonld')), + '@graph': results, +}; +writeFileSync(OUTPUT, JSON.stringify(jsonld, null, 2)); diff --git a/data-processor/src/utils/cell-summary-similarity.js b/data-processor/src/utils/cell-summary-similarity.js new file mode 100644 index 0000000..6c634c8 --- /dev/null +++ b/data-processor/src/utils/cell-summary-similarity.js @@ -0,0 +1,61 @@ +import { dot, norm } from 'mathjs'; + +/** + * A function to return a cosine sim for two vectors + * + * @param {number[]} a + * @param {number[]} b + * @returns cosine similarity between a and b + */ +function cosineSim(a, b) { + return dot(a, b) / (norm(a) * norm(b)); +} + +function getCellCountsSimilarity(cellsA, cellsB) { + const keySet = new Set(Object.keys(cellsA)); + let sharedKey = false; + for (const key of Object.keys(cellsB)) { + if (keySet.has(key)) { + sharedKey = true; + } + keySet.add(key); + } + + // Only compute cosine sim if there is at least one shared key + if (sharedKey) { + const keys = [...keySet]; + const valuesA = keys.map((key) => cellsA[key] ?? 0); + const valuesB = keys.map((key) => cellsB[key] ?? 0); + return cosineSim(valuesA, valuesB); + } else { + return 0; + } +} + +function getCellDistribution(summary) { + return summary['summary'].reduce((acc, row) => ((acc[row['cell_id']] = row['percentage']), acc), {}); +} + +export function getCellSummarySimilarity(summaryA, summaryB) { + const cellsA = getCellDistribution(summaryA); + const cellsB = getCellDistribution(summaryB); + return getCellCountsSimilarity(cellsA, cellsB); +} + +export function* getAllCellSummarySimilarities(summaries, minSimilarity = 0) { + for (let i = 0; i < summaries.length; i++) { + for (let j = i + 1; j < summaries.length; j++) { + const summaryA = summaries[i]; + const summaryB = summaries[j]; + const similarity = getCellSummarySimilarity(summaryA, summaryB); + if (similarity > minSimilarity) { + yield { + '@type': 'CellSummarySimilarity', + cell_source_a: summaryA['cell_source'], + cell_source_b: summaryB['cell_source'], + similarity, + }; + } + } + } +} diff --git a/data-processor/src/hubmap-uuid-lookup.js b/data-processor/src/utils/hubmap-uuid-lookup.js similarity index 100% rename from data-processor/src/hubmap-uuid-lookup.js rename to data-processor/src/utils/hubmap-uuid-lookup.js diff --git a/data-processor/src/sparql.js b/data-processor/src/utils/sparql.js similarity index 100% rename from data-processor/src/sparql.js rename to data-processor/src/utils/sparql.js diff --git a/data-processor/src/utils/spatial-entity-distance.js b/data-processor/src/utils/spatial-entity-distance.js new file mode 100644 index 0000000..316de2b --- /dev/null +++ b/data-processor/src/utils/spatial-entity-distance.js @@ -0,0 +1,70 @@ +import { distance } from 'mathjs'; + +const SPATIAL_PLACEMENT_LOOKUP = 'https://ccf-api.hubmapconsortium.org/v1/get-spatial-placement'; +const GLOBAL_ENTITY_ID = 'http://purl.org/ccf/latest/ccf.owl#VHBothSexes'; +const GLOBAL_POINT_CACHE = {}; + +async function getGlobalPoint(entity) { + let point = GLOBAL_POINT_CACHE[entity['@id']]; + if (!point) { + point = await fetch(SPATIAL_PLACEMENT_LOOKUP, { + method: 'POST', + headers: { + 'Content-Type': 'application/json', + }, + body: JSON.stringify({ + target_iri: GLOBAL_ENTITY_ID, + rui_location: entity, + }), + }) + .catch((e) => console.log(e)) + .then((r) => r.json()) + .then((p) => [p.x_translation, p.y_translation, p.z_translation]); + GLOBAL_POINT_CACHE[entity['@id']] = point; + } + return point; +} + +function getPlacement(entity) { + return Array.isArray(entity.placement) ? entity.placement[0] : entity.placement; +} + +function getLocalPoint(entity) { + const p = getPlacement(entity); + return [p.x_translation, p.y_translation, p.z_translation]; +} + +export async function getSpatialEntityDistance(entityA, entityB) { + const targetA = getPlacement(entityA).target; + const targetB = getPlacement(entityB).target; + + let pointA; + let pointB; + if (targetA === targetB) { + pointA = getLocalPoint(entityA); + pointB = getLocalPoint(entityB); + } else { + pointA = await getGlobalPoint(entityA); + pointB = await getGlobalPoint(entityB); + } + + return distance(pointA, pointB); +} + +export async function* getAllSpatialEntityDistances(entities, maxDistance = 10000) { + for (let i = 0; i < entities.length; i++) { + for (let j = i + 1; j < entities.length; j++) { + const entityA = entities[i]; + const entityB = entities[j]; + const distance = await getSpatialEntityDistance(entityA, entityB); + if (distance !== undefined && distance < maxDistance) { + yield { + '@type': 'SpatialEntityDistance', + entity_a: entityA['@id'], + entity_b: entityB['@id'], + distance, + }; + } + } + } +} diff --git a/data/cell-summary-similarities.jsonld b/data/cell-summary-similarities.jsonld new file mode 100644 index 0000000..d003295 --- /dev/null +++ b/data/cell-summary-similarities.jsonld @@ -0,0 +1,678570 @@ +{ + "@context": { + "CL": { + "@id": "http://purl.obolibrary.org/obo/CL_", + "@prefix": true + }, + "ASCTB-TEMP": { + "@id": "https://purl.org/ccf/ASCTB-TEMP_", + "@prefix": true + }, + "ctpop": { + "@id": "https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#", + "@prefix": true + }, + "as_3d_id": { + "@type": "@id" + }, + "as_id": { + "@type": "@id" + }, + "all_collisions": { + "@id": "ccf:has_collision_summary" + }, + "collision_source": { + "@reverse": "ccf:has_collision_summary", + "@type": "@id" + }, + "collisions": { + "@id": "ccf:has_collision_item" + }, + "corridor_source": { + "@reverse": "ccf:has_corridor", + "@type": "@id" + }, + "corridor": { + "@id": "ccf:has_corridor" + }, + "summaries": { + "@id": "ccf:has_cell_summary" + }, + "cell_source": { + "@reverse": "ccf:has_cell_summary", + "@type": "@id" + }, + "annotation_method": { + "@id": "ccf:cell_annotation_method" + }, + "summary": { + "@id": "ccf:has_cell_summary_row" + }, + "cell_id": { + "@type": "@id" + }, + "count": { + "@id": "ccf:cell_count" + }, + "percentage": { + "@id": "ccf:percentage_of_total" + }, + "@base": "http://purl.org/ccf/", + "@vocab": "http://purl.org/ccf/", + "ccf": "http://purl.org/ccf/", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "dcterms": "http://purl.org/dc/terms/", + "label": "rdfs:label", + 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