Retrieves and creates publication citations from NCBI PubMed
Compatible with DokuWiki
Greebo, Frusterick Manners, Elenor Of Tsort, Detritus
Retrieves and creates publication citations from NCBI PubMed
This plugin retrieves the MedLine description of articles and books recorded in the NCBI PubMed and the PMC database and allow users to easily include article citation into their DokuWiki pages. The MedLine content is cached in the media directory of your wiki. This plugin is 100% compatible with the new citation interface of PubMed (as of 05/2020).
This plugin is perfectly adapted to dokuwiki farms and works with PHP 5.6+.
Install the plugin using the Plugin Manager and the download URL above, which points to latest version of the plugin. Refer to Plugins on how to install plugins manually. The local plugin directory must have the same name as the plugin is named, otherwise the plugin won't work properly.
{{pmid>___}} for the PubMed database{{pmcid>___}} for the PMC database (please note carrefully the c in pmcid)>, you can add{{pmid>long:012345678}} (see below){{pmcid>0123456}}{{pmid>01234567}} / {{pmcid>01234567}} {{pmid>command:01234567}} / {{pmcid>command:01234567}}{{pmid>24073682}} where 24073682 is the PMID of the article as notified by pubmed.{{pmcid>7241351}} where 7241351 is the PCMID of the article as notified by pubmed PMC.{{pmid>user:24073682}} where 24073682 is the PMID of the article as notified by pubmed and the default user parameter (see configuration) will be used to create the article citation.{{pmid>long:24073682}} where 24073682 is the PMID of the article as notified by pubmed and long is the selected article citation format.user command.{{pmid>vancouver:19171717,12142303,12028325,12084862,12166575,15857727}}{{pmid>vancouver:sort,19171717,12142303,12028325,12084862,12166575,15857727}}| char.// Basic search of terms
{{pmid>search:"Inappropriate Prescribing"[Mesh]}}
{{pmid>search:"Drug-Related Side Effects and Adverse Reactions"[Mesh] AND (Review[ptyp] AND "loattrfree full text"[sb])}}
// Search of terms with options
{{pmid>search:"Inappropriate Prescribing"[Mesh]|size=200|sort=pubdate}}
// Search passing a specific title for the link (just use a # for the first param)
{{pmid>search:#My Link Title|"Inappropriate Prescribing"[Mesh]|size=200|sort=pubdate}}
You can define in the configuration a simple string to define your own citation format. The following tokens are available.
| Token | Content |
|---|---|
| %pmid% | PMID with a link to pubmed citation |
| %pmcid% | PMCID with a link to pubmed PMC citation |
| %type% | Type of the citation (“article”, “book”) |
| %authors% | All authors (complete lastname) |
| %authorsVancouver% | All authors (initials lastname) |
| %first_author% | Only first author +/- “et al” |
| %corporate_author% | Author collective |
| %title% | Title of the article |
| %title_tt% | Translated title in the original language of the publication |
| %book_title% | Title of the Book |
| %collection_title% | Title of the collection |
| %copyright% | Copyright |
| %country% | Country |
| %lang% | Language of the article |
| %journal_iso% | ISO Journal title (abbrev) |
| %journal_title% | Full Journal title |
| %journal_id% | Journal ID |
| %iso% | Self computed ISO citation |
| %so% | Medline ISO citation |
| %vol% | Volume |
| %issue% | Issue |
| %year% | Year |
| %month% | Month |
| %pages% | Pages |
| %abstract% | Abstract (togglable) |
| %doi% | DOI of the publication |
| %pii% | PII of the publication |
| %journal_url% | Link to Journal web site using the DOI |
| %pmc_url% | If available, link to free PDF of the article. |
| %abstractFr% | Show french translated abstract (see specific doc) |
| %localpdf% | Add link to local PDF file (see specific doc) |
| Hard coded format | Content |
|---|---|
| short | %first_author%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% |
| long | %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% |
| long_pdf | %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %localpdf% %tweet% |
| long_abstract | %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr% %tweet% |
| long_abstract_pdf | %authors%. %title%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr% %localpdf% %tweet% |
| long_tt | %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %tweet% |
| long_tt_pdf | %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %localpdf% %tweet% |
| long_tt_abstract | %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr% %tweet% |
| long_tt_abstract_pdf | %authors%. %title_tt%. %iso%. %pmid%. %pmcid% %journal_url% %pmc_url% %abstract% %abstractFr% %localpdf% %tweet% |
{{pmid>doc_format:long_abstract_pdf}}style.css file for further information.media/pubmed/pmid_pdf or media/pubmed/doi_pdf. Just use the PMID or DOI as file name. It is recommanded to use the PMID mode.addtt add a translated to the raw medline data{{pmid>addtt:123456789|translated title to add is this current string}}addhash add a hashtags to the raw medline data (used for the Tweet URLs){{pmid>addhash:123456789|MyHash1,MyHash2,MyHash3}}test only for devsraw_medline show the retrieved MedLine code. summaryxml:24073682clear_raw_medline : clear all cached Medline filesremove_dir : remove the cache directory (by default /data/media/pubmed)recreate_cross_refs : recreate the crossref (DOI ↔ PMID)full_pdf_list : show all available PDF (see specific doc){{pmid>cmd:0123456789}}{{pmcid>cmd:01234567}}Please use the github repository to adress any comments, issues or wishes.