Other Resources:
ncbi.nlm.nih.gov/pmc/oai/oai.cgi - OAI-PMH Service
How to use the OAI-PMH Service at ncbi.nlm.nih.gov/pmc/oai/oai.cgi?
✍: FYIcenter.com
The OAI-PMH Service at ncbi.nlm.nih.gov/pmc/oai/oai.cgi
allows to use OAI-PMH protocol to access
metadata of all items in the PubMed Central (PMC) archive,
as well as to the full text of a subset of these items.
Query parameters supported by ncbi.nlm.nih.gov/pmc/oai/oai.cgi are:
verb - Required. The verb of the query action: ListIdentifiers, ListSets, ... from - Optional. The start date of the DOI registration date range. until - Optional. The end date of the DOI registration date range. set - Optional. The container of DOI records. identifier - Optional. The identifier of a single record. metadataPrefix - Required for ListIdentifiers and ListRecords. The Metadata Format code. resumptionToken - Optional. The next page token returned from the last call.
PMC only 4 OAI verbs, Identify, ListMetadataFormats, ListSets, ListRecords, and ListIdentifiers.
1. Identify - Returns information about the OAI-PMH Service.
2. ListMetadataFormats - Returns a list for supported data formats, which are: oai_dc, pmc and pmc_fm.
3. ListSets - Returns a list of sets that act as containers of DOI records.
4. ListIdentifiers - Returns a list of DOIs.
5. ListRecords - Returns a list of DOI records.
Here is an example of downloading identifiers updated on 2022-10-01:
fyicenter$ curl 'https://ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=ListIdentifiers&from=2022-10-01&until=2022-10-01&metadataPrefix=oai_dc' <?xml version="1.0" encoding="UTF-8"?> <OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd"> <responseDate>2022-10-14T01:09:49Z</responseDate> <request verb="ListIdentifiers" from="2022-10-01" metadataPrefix="oai_dc" until="2022-10-01">https:/www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi</request> <ListIdentifiers> <header> <identifier>oai:pubmedcentral.nih.gov:6794671</identifier> <datestamp>2022-10-01</datestamp> <setSpec>jrsocmed</setSpec> </header> <header> <identifier>oai:pubmedcentral.nih.gov:6794673</identifier> <datestamp>2022-10-01</datestamp> <setSpec>jrsocmed</setSpec> </header> <header> <identifier>oai:pubmedcentral.nih.gov:6794674</identifier> <datestamp>2022-10-01</datestamp> <setSpec>jrsocmed</setSpec> </header> ... <header> <identifier>oai:pubmedcentral.nih.gov:7483116</identifier> <datestamp>2022-10-01</datestamp> <setSpec>amjph</setSpec> </header> <resumptionToken>oai%3Apubmedcentral.nih.gov%3A7483117!2022-10-01!2022-10-01!oai_dc!</resumptionToken> </ListIdentifiers> </OAI-PMH>
Here is an example of getting the record of a given identifier in PMC front matter format.
fyicenter$ curl 'https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:152494&metadataPrefix=pmc_fm' <?xml version="1.0" encoding="UTF-8"?> <OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd"> <responseDate>2022-10-14T01:36:35Z</responseDate> <request verb="GetRecord" identifier="oai:pubmedcentral.nih.gov:152494" metadataPrefix="pmc_fm">https:/www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi</request> <GetRecord> <record> <header> <identifier>oai:pubmedcentral.nih.gov:152494</identifier> <datestamp>2003-05-26</datestamp> <setSpec>aac</setSpec> </header> <metadata> <article xmlns="https://dtd.nlm.nih.gov/ns/archiving/2.3/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xsi:schemaLocation="https://dtd.nlm.nih.gov/ns/archiving/2.3/ https://dtd.nlm.nih.gov/archiving/2.3/xsd/archivearticle.xsd" article-type="research-article"> <front> <journal-meta> <journal-id journal-id-type="nlm-ta">Antimicrob Agents Chemother</journal-id> <journal-id journal-id-type="publisher-id">aac</journal-id> <journal-title>Antimicrobial Agents and Chemotherapy</journal-title> <issn pub-type="ppub">0066-4804</issn> <issn pub-type="epub">1098-6596</issn> <publisher> <publisher-name>American Society for Microbiology</publisher-name> </publisher> </journal-meta> <article-meta> <article-id pub-id-type="accession">PMC152494</article-id> <article-id pub-id-type="pmcid">PMC152494</article-id> <article-id pub-id-type="pmc-uid">152494</article-id> <article-id pub-id-type="pmid">12654674</article-id> <article-id pub-id-type="publisher-id">0514</article-id> <article-id pub-id-type="doi">10.1128/AAC.47.4.1382-1390.2003</article-id> <article-categories> <subj-group subj-group-type="heading"> <subject>Mechanisms of Resistance</subject> </subj-group> </article-categories> <title-group> <article-title>Epidemiology of Rifampin ADP-Ribosyltransferase (<italic>arr-2</italic>) and Metallo-β-Lactamase (<italic>bla</italic><sub>IMP-4</sub>) Gene Cassettes in Class 1 Integrons in <italic>Acinetobacter</italic> Strains Isolated from Blood Cultures in 1997 to 2000</article-title> </title-group> <contrib-group> <contrib contrib-type="author"> <name> <surname>Houang</surname> <given-names>Elizabeth T. S.</given-names> </name> <xref ref-type="aff" rid="aff1">1</xref> <xref ref-type="corresp" rid="cor1">*</xref> </contrib> <contrib contrib-type="author"> <name> <surname>Chu</surname> <given-names>Yiu-Wai</given-names> </name> <xref ref-type="aff" rid="aff1">2</xref> </contrib> ... </contrib-group> <pub-date pub-type="ppub"> <month>4</month> <year>2003</year> </pub-date> <volume>47</volume> <issue>4</issue> <fpage>1382</fpage> <lpage>1390</lpage> <history> <date date-type="accepted"> <day>23</day> <month>1</month> <year>2003</year> </date> </history> <copyright-statement>Copyright © 2003, American Society for Microbiology</copyright-statement> <copyright-year>2003</copyright-year> <abstract> <p>We characterized two new gene cassettes in an <italic>Acinetobacter</italic> isolate: ...</p> <p> </p> </abstract> </article-meta> </front> </article> </metadata> </record> </GetRecord> </OAI-PMH>
Here is an example of getting the record of a given identifier in PMC full-text XML format.
fyicenter$ curl 'https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:152494&metadataPrefix=pmc'
⇒ Other DOI Tools and Resources
⇐ PMC FTP Service - ID Map Download
2023-01-08, 166👍, 0💬
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