Converting a DOI to other scientific identifiers in Pubmed

Posted June 09, 2015 at 07:29 AM | categories: orgmode, ref | tags:

Sometimes it is useful to convert a DOI to another type of identifier. For example, in this post we converted a DOI to a Scopus EID, and in this one we got the WOS accession number from a DOI. Today, we consider how to get Pubmed identifiers. Pubmed provides an API for this purpose:

http://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/

We will use the DOI tool. According to the documentation, we need to form a URL like this:

DOI: http://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?tool=my_tool&email=my_email@example.com&ids=10.1093/nar/gks1195

We will call our tool "org-ref" and use the value of user-mail-address. The URL above returns XML, so we can parse it, and then extract the identifiers. This is a simple http GET request, which we can construct using url-retrieve-synchronously. Here is what we get. 

(let* ((url-request-method "GET")
       (doi"10.1093/nar/gks1195")
       (my-tool "org-ref")
       (url (format "http://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?tool=%s&email=%s&ids=%s"
                    my-tool
                    user-mail-address
                    doi))
       (xml (with-current-buffer  (url-retrieve-synchronously url)
                (xml-parse-region url-http-end-of-headers (point-max)))))
xml)

((pmcids
  ((status . "ok"))
  "\n"
  (request
   ((idtype . "doi")
    (dois . "")
    (versions . "yes")
    (showaiid . "no"))
   "\n"
   (echo nil "tool=org-ref;email=jkitchin%40andrew.cmu.edu;ids=10.1093%2Fnar%2Fgks1195")
   "\n")
  "\n"
  (record
   ((requested-id . "10.1093/NAR/GKS1195")
    (pmcid . "PMC3531190")
    (pmid . "23193287")
    (doi . "10.1093/nar/gks1195"))
   (versions nil
             (version
              ((pmcid . "PMC3531190.1")
               (current . "true")))))
  "\n"))

The parsed xml is now just an emacs-lisp data structure. We need to get the record, and then get the attributes of it to extract the identifiers. Next, we create a plist of the identifiers. For fun, we add the Scopus EID and WOS accession number from the previous posts too. 

(let* ((url-request-method "GET")
       (doi"10.1093/nar/gks1195")
       (my-tool "org-ref")
       (url (format "http://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?tool=%s&email=%s&ids=%s"
                    my-tool
                    user-mail-address
                    doi))
       (xml (car (with-current-buffer  (url-retrieve-synchronously url)
                   (xml-parse-region url-http-end-of-headers (point-max)))))
       (record (first  (xml-get-children xml 'record)))
       (doi (xml-get-attribute record 'doi))
       (pmcid (xml-get-attribute record 'pmcid))
       (pmid (xml-get-attribute record 'pmid)))
  (list :doi doi :pmid pmid :pmcid pmcid :eid (scopus-doi-to-eid doi) :wos (wos-doi-to-accession-number doi)))

(:doi "10.1093/nar/gks1195" :pmid "23193287" :pmcid "PMC3531190" :eid "2-s2.0-80053651587" :wos "000312893300006")

Well, there you have it, four new scientific document ids from one DOI. Of course we have defined org-mode links for each one of these:

doi:10.1093/nar/gks1195

pmid:23193287

pmcid:PMC3531190

eid:2-s2.0-80053651587

wos:000312893300006

I have not tested this on too many DOIs yet. Not all of them are indexed by Pubmed.

Copyright (C) 2015 by John Kitchin. See the License for information about copying.

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Org-mode version = 8.2.10

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