For PMID there is one interactive function that inserts a bibtex entry: pubmed-insert-bibtex-from-pmid.
+This library is complementary to [[./doi-utils.org]].
* Header
#+BEGIN_SRC emacs-lisp :tangle pubmed.el
;;
;; Lisp code to interact with pubmed databases, links to pubmed
;; identifiers. See pubmed.org.
+;;;
+;; This library provides links that go to pubmed resources, e.g.
+;;
+;; pmcid:PMC3498956
+;;
+;; pmid:23162369
+;;
+;; and nihmsid:NIHMS395714
+;;
+;; See http://www.ncbi.nlm.nih.gov/pmc/about/public-access-info/#p3 for details of these identifiers.
+;;
+;; For PMID there is one interactive function that inserts a bibtex
+;; entry: `pubmed-insert-bibtex-from-pmid`.
#+END_SRC
* PMID (from PubMed) link and functions
A PMID is a number that identifies an entry in the Pubmed database. The PMID is a unique reference number for PubMed citations. The PMID is a distinctly different number from the PMCID and is used only for PubMed records.
-#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el :results silent
(org-add-link-type
"pmid"
;; clicking
;; formatting
(lambda (keyword desc format)
(cond
- ((eq format 'html) (format "")); no output for html
+ ((eq format 'html)
+ (format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s\">pmid:%s</a>" keyword keyword)); no output for html
((eq format 'latex)
;; write out the latex command
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}" keyword)))))
#+END_SRC
+
+
** Get MEDLINE metadata
We can get bibliographic metadata from a pmid. Here we get the MEDLINE text. The website wraps the data in <pre></pre> tags.
: pubmed-get-medline
Here is sample output:
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle no
(pubmed-get-medline "23162369")
#+END_SRC
VI - 24
IP - 4
DP - 2012 Dec
-TI - Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core
+TI - Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core
Methods.
PG - 569-608
AB - Approaches to classroom instruction have evolved considerably over the past 50
as complimentary components of a broader approach to classroom instruction called
transformational teaching. Transformational teaching involves creating dynamic
relationships between teachers, students, and a shared body of knowledge to
- promote student learning and personal growth. From this perspective, instructors
+ promote student learning and personal growth. From this perspective, instructors
are intellectual coaches who create teams of students who collaborate with each
other and with their teacher to master bodies of information. Teachers assume the
traditional role of facilitating students' acquisition of key course concepts,
#+RESULTS:
: pubmed-parse-medline
-#+BEGIN_SRC emacs-lisp :results code
+#+BEGIN_SRC emacs-lisp :tangle no
(pubmed-parse-medline "23162369")
#+END_SRC
-#+RESULTS:
-#+BEGIN_SRC emacs-lisp
-(("PMID" . "23162369")
- ("OWN" . "NLM")
- ("STAT" . "Publisher")
- ("DA" . "20121119")
- ("IS" . "1040-726X (Print)")
- ("IS" . "1040-726X (Linking)")
- ("VI" . "24")
- ("IP" . "4")
- ("DP" . "2012 Dec")
- ("TI" . "Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core \n Methods.")
- ("PG" . "569-608")
- ("AB" . "Approaches to classroom instruction have evolved considerably over the past 50\n years. This progress has been spurred by the development of several learning\n principles and methods of instruction, including active learning,\n student-centered learning, collaborative learning, experiential learning, and\n problem-based learning. In the present paper, we suggest that these seemingly\n different strategies share important underlying characteristics and can be viewed\n as complimentary components of a broader approach to classroom instruction called\n transformational teaching. Transformational teaching involves creating dynamic\n relationships between teachers, students, and a shared body of knowledge to\n promote student learning and personal growth. From this perspective, instructors \n are intellectual coaches who create teams of students who collaborate with each\n other and with their teacher to master bodies of information. Teachers assume the\n traditional role of facilitating students' acquisition of key course concepts,\n but do so while enhancing students' personal development and attitudes toward\n learning. They accomplish these goals by establishing a shared vision for a\n course, providing modeling and mastery experiences, challenging and encouraging\n students, personalizing attention and feedback, creating experiential lessons\n that transcend the boundaries of the classroom, and promoting ample opportunities\n for preflection and reflection. We propose that these methods are synergistically\n related and, when used together, maximize students' potential for intellectual\n and personal growth.")
- ("FAU" . "Slavich, George M")
- ("AU" . "Slavich GM")
- ("AD" . "Cousins Center for Psychoneuroimmunology and Department of Psychiatry and\n Biobehavioral Sciences, University of California, Los Angeles, UCLA Medical Plaza\n 300, Room 3156, Los Angeles, CA 90095-7076, USA.")
- ("FAU" . "Zimbardo, Philip G")
- ("AU" . "Zimbardo PG")
- ("LA" . "ENG")
- ("GR" . "R01 AG026364/AG/NIA NIH HHS/United States")
- ("GR" . "T32 MH019925/MH/NIMH NIH HHS/United States")
- ("PT" . "JOURNAL ARTICLE")
- ("DEP" . "20120724")
- ("TA" . "Educ Psychol Rev")
- ("JT" . "Educational psychology review")
- ("JID" . "9885342")
- ("PMC" . "PMC3498956")
- ("MID" . "NIHMS395714")
- ("EDAT" . "2012/11/20 06:00")
- ("MHDA" . "2012/11/20 06:00")
- ("CRDT" . "2012/11/20 06:00")
- ("PHST" . "2012/07/24 [epublish]")
- ("AID" . "10.1007/s10648-012-9199-6 [doi]")
- ("PST" . "ppublish")
- ("SO" . "\nSO - "))
-#+END_SRC
+
** PMID to bibtex entry
The point of parsing the MEDLINE text is so we can make bibtex entries. We only support Journal articles for now.
-Issues:
-1. The year is not quite right, it has the month in it.
-2. I do not use all the fields.
-
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el
(defun pubmed-pmid-to-bibtex (pmid)
"Convert a PMID to a bibtex entry."
(let* ((data (pubmed-parse-medline pmid))
#+begin_example
@article{,
author = {Slavich, George M and Zimbardo, Philip G},
- title = {Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core
+ title = {Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core
Methods.},
abstract = {Approaches to classroom instruction have evolved considerably over the past 50
years. This progress has been spurred by the development of several learning
as complimentary components of a broader approach to classroom instruction called
transformational teaching. Transformational teaching involves creating dynamic
relationships between teachers, students, and a shared body of knowledge to
- promote student learning and personal growth. From this perspective, instructors
+ promote student learning and personal growth. From this perspective, instructors
are intellectual coaches who create teams of students who collaborate with each
other and with their teacher to master bodies of information. Teachers assume the
traditional role of facilitating students' acquisition of key course concepts,
And we probably want to be able to insert a bibtex entry
-#+BEGIN_SRC emacs-lisp
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el
(defun pubmed-insert-bibtex-from-pmid (pmid)
"Insert a bibtex entry at point derived from PMID.
You must clean the entry after insertion."
(goto-char (point-min))
(while (search-forward ">" nil t)
(replace-match ">"))
- (goto-char (point-min))
-
+ (goto-char (point-min))
+
(let ((p1 (search-forward "<pre>"))
(p2 (search-forward "</pre>")))
(buffer-substring (+ 1 p1) (- p2 6)))))
Here we define a new link. Clicking on it simply opens a webpage to the article.
-#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el :results silent
(org-add-link-type
"pmcid"
;; clicking
(lambda (keyword desc format)
(cond
((eq format 'html)
- (format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/%s\">" keyword))
+ (format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/%s\">pmcid:%s</a>" keyword keyword))
((eq format 'latex)
(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/%s}" keyword)))))
#+END_SRC
-* NIHMSID
+* NIHMSID
The NIHMSID is a preliminary article identifier that applies only to manuscripts deposited through the NIHMS system. The NIHMSID is only valid for compliance reporting for 90 days after the publication date of an article. Once the Web version of the NIHMS submission is approved for inclusion in PMC and the corresponding citation is in PubMed, the article will also be assigned a PMCID.
-#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el :results silent
(org-add-link-type
"nihmsid"
;; clicking
;; formatting
(lambda (keyword desc format)
(cond
- ((eq format 'html) (format "")); no output for html
+ ((eq format 'html)
+ (format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid//%s\">nihmsid:%s</a>" keyword keyword))
((eq format 'latex)
;; write out the latex command
- (format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid//%s}" keyword)))))
+ (format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}" keyword)))))
#+END_SRC
-#+RESULTS:
-| lambda | (link-string) | (browse-url (format http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s link-string)) |
-| lambda | (keyword desc format) | (cond ((eq format (quote html)) (format )) ((eq format (quote latex)) (format \url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid//%s} keyword))) |
+
* End of code
This code will tangle the elisp code out to pubmed.el and load it.
[[elisp:(org-babel-load-file "pubmed.org")]]
-
-
-
projects / org-ref.git / blobdiff