2e:["$","title",null,{"children":"COVID-19 serologic data | Jonas Almeida | Observable"}] 33:T71e,md` # COVID-19 serologic data Poking around serotracker.com and covid19serohub.nih.gov for COVID-19 serological data in the Summer of 2021 ... ## Abstract During the Summer months of 2021, when these two aggregators of serological data matured as software constructs, it became apparent that they illustrate two very different approaches to the dissemination and computational of epidemiological data. Serohub exposes data for client-side computing, while Serotracker primarily relies on server-side rendering of data that is not itself served. The realization that the landing interface of the latter does not expose the data is straightforward to the programmer, who typically checks the browser network traffic for that data stream. In fairness, Serotracker offers a mechanism to request access to the REST data API, and the argument here is that it is not FAIR enough when such barriers are raised to programmatic access. This is not to say that seroHub is flawlessly FAIR, as it omits the Cross-Origin Resource Sharing (CORS) header that inhibits web computing at domains distinct from its own. However, consumer-facing cloud environments such as Google Workspaces, now offer *serverless computing solutions* where CORS can by sidestepped by proxying, such as script.google.com. `34:T412,{ let div = DOM.element('div'); let pops = Object.keys(byPopulationGroup).sort( (a, b) => byPopulationGroup[a].seroprevalence_percent - byPopulationGroup[b].seroprevalence_percent ); let trace = { x: pops.map(ag => `${ag}`), y: pops.map(ag => byPopulationGroup[ag].seroprevalence_percent), text: pops.map( ag => `${ag}
${byPopulationGroup[ag].n_studies} studies, n=${byPopulationGroup[ag].total_N}` ), error_y: { type: 'data', symmetric: false, array: pops.map(ag => byPopulationGroup[ag].error_percent[1]), arrayminus: pops.map(ag => byPopulationGroup[ag].error_percent[0]), visible: true }, type: 'bar' }; let layout = { title: `by population group
(${Date().slice( 0, 15 )})`, yaxis: { title: '% sero prevalance', type: 'log' } }; Plotly.newPlot(div, [trace], layout); return div; }35:[] 31:{"id":"c2e8e66a61dc5405","slug":"sero","title":"COVID-19 serologic data","thumbnail":"b06287cfce77d1af8697bbf515d5542439910ecc877073bec666e5289fe3e193","access_level":"public","create_time":"$D2021-02-02T21:07:01.720Z","update_time":"$D2021-09-04T15:43:48.726Z","view_time":null,"first_public_time":"$D2021-02-02T21:07:05.982Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"0f2e596d5bd6ef6e","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":"starter_2024"},"version":354,"publish_version":354,"role":null,"authored":false,"authors":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null}],"members":[{"type":"individual","id":"4355fe13cb71b11d","login":"episphere","name":"Jonas Almeida","avatar_url":"https://avatars-next.observableusercontent.com/3a0ff5abff6da0cdbd100da305ba323e12d43c8fcb7604275e6c72591db9dc69","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"COVID-19 serologic data","cells":[{"id":0,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"md`## Data\n### Serotracker\nSerotracker data covers locations accross the world with estimates at country, state, and city level. It presently includes ${\n records.length\n} reccords from ${Object.keys(byCountry).length} countries.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":11,"value":"records = {\n let xx = await sero.tracker.records();\n xx = xx.map(x => {\n x.sampling_start_date = new Date(x.sampling_start_date);\n x.sampling_end_date = new Date(x.sampling_end_date);\n\n if (Array.isArray(x.population_group)) {\n x.population_group = x.population_group.sort().join(', ');\n }\n if (!x.population_group) {\n x.population_group = \"NA\";\n }\n if (x.population_group.length == 0) {\n x.population_group = \"NA\";\n }\n return x;\n });\n return xx;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"byCountry = sero.tracker.queryBy('country')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":152,"value":"countries = Object.keys(byCountry).sort()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":54,"value":"serotrackerWorld = {\n let div = DOM.element('div');\n let countries = Object.keys(byCountry);\n let seroprevalence = countries.map(c => byCountry[c].seroprevalence_percent);\n let prevalence = {\n type: 'choropleth',\n locationmode: 'country names',\n locations: countries,\n z: seroprevalence,\n text: countries,\n autocolorscale: true\n };\n let layout = {\n title:\n 'Sero prevalence
% of population (serotracker)'\n };\n Plotly.newPlot(div, [prevalence], layout);\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":241,"value":"byAge = sero.tracker.queryBy('age')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":166,"value":"{\n let div = DOM.element('div');\n let ages = [\n \"Children and Youth (0-17 years)\",\n \"Adults (18-64 years)\",\n \"Seniors (65+ years)\",\n \"Multiple groups\"\n ];\n let trace = {\n x: ages.map(\n ag =>\n `${ag}
${byAge[ag].n_studies} studies, n=${byAge[ag].total_N}`\n ),\n y: ages.map(ag => byAge[ag].seroprevalence_percent),\n error_y: {\n type: 'data',\n symmetric: false,\n array: ages.map(ag => byAge[ag].error_percent[1]),\n arrayminus: ages.map(ag => byAge[ag].error_percent[0]),\n visible: true\n },\n type: 'bar'\n };\n let layout = {\n title: `by age group
(${Date().slice(\n 0,\n 15\n )})`,\n yaxis: { title: '% sero prevalance', type: 'log' }\n };\n Plotly.newPlot(div, [trace], layout);\n\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":285,"value":"byPopulationGroup = sero.tracker.queryBy('population_group')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":288,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":88,"value":"md`\n### Serohub\nFound ${studies.studies.length} studies using ${sampleTypes.length} types of tissues.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":92,"value":"studies = (await fetch(\"https://covid19serohub.nih.gov/api/v1/studies\")).json()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":100,"value":"sampleTypes = [\n ...new Set(\n studies.studies.map(s => s.study_sample_types).reduce((a, b) => a.concat(b))\n )\n].sort()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":49,"value":"md`## Methods\nSero library with open source in the public domain at github.com/episphere/sero.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":52,"value":"Plotly = require('https://cdn.plot.ly/plotly-latest.min.js')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":221,"value":"//sero = require('http://localhost:8000/sero/sero.js')\nsero = require('https://episphere.github.io/sero/sero.js')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":337,"value":"localforage = require('https://cdnjs.cloudflare.com/ajax/libs/localforage/1.9.0/localforage.min.js')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W35","stdlib":"1","titling":"auto"}} 32:"$31:body" 2d:E{"digest":"NEXT_REDIRECT;replace;/@episphere/sero;307;"}