29:null 2a:["$","title",null,{"children":"Find a publication using PMID or DOI | Liang-Bo Wang | Observable"}] 2f:[] 2d:{"id":"4285f4da63beaa7a","slug":"find-a-publication-using-pmid-or-doi","title":"Find a publication using PMID or DOI","thumbnail":"8f2bb21f58e8845b5cef8715bcaebc95f7de8585e513dd62f697b2a911d26aab","access_level":"public","create_time":"$D2019-11-04T20:17:48.148Z","update_time":"$D2019-11-04T21:23:03.568Z","view_time":null,"first_public_time":"$D2019-11-04T22:41:28.168Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"f990fc2122e0f4f0","login":"lbwang2","name":"Liang-Bo Wang","avatar_url":"https://avatars-next.observableusercontent.com/4e5363eb1e9955c37980f5ad8987936cdaa648c4771818b76d6786d2cf70a81b","tier":"starter_2024"},"version":200,"publish_version":200,"role":null,"authored":false,"authors":[{"type":"individual","id":"cb044e3888ac10f6","login":"lbwang2","name":"Liang-Bo Wang","avatar_url":"https://avatars-next.observableusercontent.com/4e5363eb1e9955c37980f5ad8987936cdaa648c4771818b76d6786d2cf70a81b","tier":null}],"members":[{"type":"individual","id":"cb044e3888ac10f6","login":"lbwang2","name":"Liang-Bo Wang","avatar_url":"https://avatars-next.observableusercontent.com/4e5363eb1e9955c37980f5ad8987936cdaa648c4771818b76d6786d2cf70a81b","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Find a publication using PMID or DOI","cells":[{"id":0,"value":"md`# Find a publication using PMID or DOI\n\nDOI input is preferred over PMID. The search will try to recover both PMID and DOI of the publication.\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":37,"value":"viewof doi = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2,"value":"viewof pmid = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":33,"value":"html`

PMID: ${paper['pmid']}
DOI: ${paper['doi']}
Source: ${paper['source']}

${bibliograph}

`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":177,"value":"md`The search is built on top of [Europe PMC] and [NCBI PMC/PubMed] APIs.\n\nNote: If the page shows many errors, disable the request blocking to www.ebi.ac.uk and www.ncbi.nlm.nih.gov by your browser's Add-Ons (e.g., EFF Privacy Badger).\n\n[Europe PMC]: https://europepmc.org/RestfulWebService\n[NCBI PMC/PubMed]: https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":160,"value":"md`## Usage of findPubliation()\n\nThe function will try to search on Europe PMC first, then fall back to NCBI if the record is missing.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":147,"value":"await findPublication({doi: '10.1126/science.1225829'})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":150,"value":"await findPublication({pmid: '22745249'})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":90,"value":"findPublication({})","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":168,"value":"md`## Definitions`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"findPublication = async function(option) {\n let paper = {pmid: 'NOT FOUND', doi: 'NOT FOUND', source: 'UNKNOWN', sourceObject: 'UNKNOWN'}\n let europePMCsearchResult = await searchEuropePMC(option)\n if (europePMCsearchResult['hitCount']) {\n let ePMCRecord = europePMCsearchResult['resultList']['result'][0]\n if (ePMCRecord['pmid']) {\n paper['pmid'] = ePMCRecord['pmid']\n paper['doi'] = ePMCRecord['doi']\n paper['source'] = 'Europe PMC'\n paper['sourceObject'] = ePMCRecord\n }\n }\n // only search NCBI PMC if Europe PMC failes\n if (paper['source'] == 'UNKNOWN'){\n let ncbiPMCSearchResult = await searchNCBIPMC(option)\n if (ncbiPMCSearchResult['status'] == 'ok') {\n let ncbiRecord = ncbiPMCSearchResult['records'][0]\n paper['pmid'] = ncbiRecord['pmid']\n paper['doi'] = ncbiRecord['doi']\n paper['source'] = 'NCBI PMC'\n paper['sourceObject'] = ncbiRecord\n }\n }\n return paper\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":83,"value":"searchEuropePMC = async function(option) {\n if (!(option.pmid || option.doi)) {\n throw \"Specify PMID or DOI\"\n }\n let query = option.doi ? `DOI:${option.doi}` :`ext_id:${option.pmid} src:med`\n let params = new URLSearchParams({\n \"query\": query,\n \"resultType\": \"lite\",\n \"cursorMark\": \"*\",\n \"pageSize\": 1,\n \"sort\": \"CITED desc\",\n \"synonym\": false,\n \"format\": \"json\"\n })\n let queryURL = new URL(\n `https://www.ebi.ac.uk/europepmc/webservices/rest/search?${params.toString()}`\n )\n let response = await fetch(queryURL)\n return await response.json()\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":115,"value":"searchNCBIPMC = async function(option) {\n if (!(option.pmid || option.doi)) {\n throw \"Specify PMID or DOI\"\n }\n let ncbiParams = new URLSearchParams({\n \"ids\": option.doi ? option.doi : option.pmid,\n \"tool\": \"observable@ccwang002\",\n \"email\": \"https://observablehq.com/@ccwang002\",\n \"format\": \"json\"\n })\n let ncbiResponse = await fetch(`https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?${ncbiParams.toString()}`)\n return await ncbiResponse.json()\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"paper = await findPublication({doi: doi, pmid: pmid})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":28,"value":"bibliograph = {\n let response = await fetch(`https://doi.org/${paper['doi']}`, {\n method: 'GET',\n headers: {\n \"Accept\": \"text/x-bibliography; style=cell-research; locale=en-US\"\n }\n })\n let refText = await response.text();\n if (refText.toLowerCase().includes('not found')) {\n return 'NOT FOUND'\n } else { \n return refText.slice(3)\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W2f","stdlib":"1","titling":"auto"}} 2e:"$2d:body"