From 2f31ee6bfd946f7f7cfa22d72cec8b94560cd789 Mon Sep 17 00:00:00 2001 From: John Kitchin Date: Mon, 5 Jan 2015 14:35:02 -0500 Subject: [PATCH 1/1] initial commit --- pubmed.org | 578 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 578 insertions(+) create mode 100644 pubmed.org diff --git a/pubmed.org b/pubmed.org new file mode 100644 index 0000000..e7905b7 --- /dev/null +++ b/pubmed.org @@ -0,0 +1,578 @@ +#+TITLE: Links and functions for Pubmed and NIH databases + +* Introduction + +This document is an experiment at creating a literate program to provide functions for interacting with pubmed databases. + +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. + + + +* Header +#+BEGIN_SRC emacs-lisp :tangle org-ref.el +;;; pubmed.el --- Links and functions to interact with pubmed databases. + +;; Copyright(C) 2015 John Kitchin + +;; Author: John Kitchin +;; This file is not currently part of GNU Emacs. + +;; This program is free software; you can redistribute it and/or +;; modify it under the terms of the GNU General Public License as +;; published by the Free Software Foundation; either version 2, or (at +;; your option) any later version. + +;; This program is distributed in the hope that it will be useful, but +;; WITHOUT ANY WARRANTY; without even the implied warranty of +;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +;; General Public License for more details. + +;; You should have received a copy of the GNU General Public License +;; along with this program ; see the file COPYING. If not, write to +;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330, +;; Boston, MA 02111-1307, USA. + +;;; Commentary: +;; +;; Lisp code to setup bibliography cite, ref and label org-mode links. +;; also sets up reftex for org-mode. The links are clickable and do +;; things that are useful. You should really read org-ref.org for details. +;; +;; Package-Requires: ((dash)) +#+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 +(org-add-link-type + "pmid" + ;; clicking + (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pubmed/%s" link-string))) + ;; formatting +(lambda (keyword desc format) + (cond + ((eq format 'html) (format "")); 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 
 tags.
+
+
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+(defun pubmed-get-medline (pmid)
+  "Get MEDLINE text for PMID as a string."
+  (with-current-buffer
+    (url-retrieve-synchronously
+     (format "http://www.ncbi.nlm.nih.gov/pubmed/%s/?report=medline&format=text" pmid))
+    (goto-char (point-min))
+    (let ((p1 (search-forward "
"))
+	  (p2 (search-forward "
")))
+      (buffer-substring (+ 1 p1) (- p2 6)))))
+#+END_SRC
+
+#+RESULTS:
+: pubmed-get-medline
+
+Here is sample output:
+#+BEGIN_SRC emacs-lisp
+(pubmed-get-medline "23162369")
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+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 
+      Methods.
+PG  - 569-608
+AB  - Approaches to classroom instruction have evolved considerably over the past 50
+      years. This progress has been spurred by the development of several learning
+      principles and methods of instruction, including active learning,
+      student-centered learning, collaborative learning, experiential learning, and
+      problem-based learning. In the present paper, we suggest that these seemingly
+      different strategies share important underlying characteristics and can be viewed
+      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 
+      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,
+      but do so while enhancing students' personal development and attitudes toward
+      learning. They accomplish these goals by establishing a shared vision for a
+      course, providing modeling and mastery experiences, challenging and encouraging
+      students, personalizing attention and feedback, creating experiential lessons
+      that transcend the boundaries of the classroom, and promoting ample opportunities
+      for preflection and reflection. We propose that these methods are synergistically
+      related and, when used together, maximize students' potential for intellectual
+      and personal growth.
+FAU - Slavich, George M
+AU  - Slavich GM
+AD  - Cousins Center for Psychoneuroimmunology and Department of Psychiatry and
+      Biobehavioral Sciences, University of California, Los Angeles, UCLA Medical Plaza
+      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  - Educ Psychol Rev. 2012 Dec;24(4):569-608. Epub 2012 Jul 24.
+#+end_example
+
+** Parse the PMID MEDLINE data
+We can parse this into a data structure
+
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+(defun pubmed-parse-medline (pmid)
+  "Parse the medline text for PMID and return a list of cons cells."
+  (let ((data '())
+	(p1)
+	(p2)
+	(tag)
+	(value))
+    (with-temp-buffer (insert (pubmed-get-medline pmid))
+		      (goto-char (point-min))
+		      (while (re-search-forward "\\(^[A-Z]\\{2,4\\}\\)\\s-*- " nil t)
+			(setq tag (match-string 1))
+			;; point is at end of the search
+			(setq p1 (point))
+			;; now go to next tag
+			(re-search-forward "\\(^[A-Z]\\{2,4\\}\\)\\s-*- " nil t)
+			(setq p2 (- (match-beginning 1) 1))
+			(setq value (buffer-substring p1 p2))
+			(setq data (append data (list (cons tag value))))
+			;; now go back to last tag to get the next one
+			(goto-char p1)))
+    data))
+#+END_SRC
+
+#+RESULTS:
+: pubmed-parse-medline
+
+#+BEGIN_SRC emacs-lisp :results code
+(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
+(defun pubmed-pmid-to-bibtex (pmid)
+  "Convert a PMID to a bibtex entry."
+  (let* ((data (org-ref-parse-medline pmid))
+	 (type (cdr (assoc "PT" data)))
+	 (title (cdr (assoc "TI" data)))
+	 (authors (mapconcat 'cdr
+			     (-filter (lambda (x)
+					(string= (car x) "FAU"))
+				      data)
+			     " and "))
+	 (abstract (cdr (assoc "AB" data)))
+	 (volume (cdr (assoc "VI" data)))
+	 (issue (cdr (assoc "IP" data)))
+	 (journal (cdr (assoc "JT" data)))
+	 (year (cdr (assoc "DP" data)))
+	 (pages (cdr (assoc "PG" data)))
+	 (aid (cdr (assoc "AID" data))))
+
+    (cond
+     ((string= type "JOURNAL ARTICLE")
+      (concat "@article{,
+ author = {" authors "},
+ title = {" title "},
+ abstract = {" abstract "},
+ journal = {" journal "},
+ volume = {" volume "},
+ number = {" issue "},
+ year = {" (car (split-string year)) "},
+ pages = {" pages "},
+ doi = {" (replace-regexp-in-string " \\[doi\\]" "" aid) "},
+}"))
+    (t
+     (message "No conversion for type: %s" type)))))
+#+END_SRC
+
+#+RESULTS:
+: pubmed-pmid-to-bibtex
+
+#+BEGIN_SRC emacs-lisp :tangle no
+(pubmed-pmid-to-bibtex "23162369")
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+@article{,
+ author = {Slavich, George M and Zimbardo, Philip G},
+ 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
+      principles and methods of instruction, including active learning,
+      student-centered learning, collaborative learning, experiential learning, and
+      problem-based learning. In the present paper, we suggest that these seemingly
+      different strategies share important underlying characteristics and can be viewed
+      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 
+      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,
+      but do so while enhancing students' personal development and attitudes toward
+      learning. They accomplish these goals by establishing a shared vision for a
+      course, providing modeling and mastery experiences, challenging and encouraging
+      students, personalizing attention and feedback, creating experiential lessons
+      that transcend the boundaries of the classroom, and promoting ample opportunities
+      for preflection and reflection. We propose that these methods are synergistically
+      related and, when used together, maximize students' potential for intellectual
+      and personal growth.},
+ journal = {Educational psychology review},
+ volume = {24},
+ number = {4},
+ year = {2012},
+ pages = {569-608},
+ doi = {10.1007/s10648-012-9199-6},
+}
+#+end_example
+
+And we probably want to be able to insert a bibtex entry
+
+#+BEGIN_SRC emacs-lisp
+(defun pubmed-insert-bibtex-from-pmid (pmid)
+ "Insert a bibtex entry at point derived from PMID.
+You must clean the entry after insertion."
+ (interactive "sPMID: ")
+ (insert (pubmed-pmid-to-bibtex pmid)))
+#+END_SRC
+
+#+RESULTS:
+: pubmed-insert-bibtex-from-pmid
+
+Here is an example of a cleaned entry:
+#+BEGIN_SRC bibtex :tangle no
+@article{slavich-2012-trans-teach,
+  author =	 {Slavich, George M and Zimbardo, Philip G},
+  title =	 {Transformational Teaching: Theoretical
+                  Underpinnings, Basic Principles, and Core Methods.},
+  journal =	 {Educational psychology review},
+  volume =	 24,
+  number =	 4,
+  pages =	 {569-608},
+  year =	 2012,
+  doi =		 {10.1007/s10648-012-9199-6},
+  abstract =	 {Approaches to classroom instruction have evolved
+                  considerably over the past 50 years. This progress
+                  has been spurred by the development of several
+                  learning principles and methods of instruction,
+                  including active learning, student-centered
+                  learning, collaborative learning, experiential
+                  learning, and problem-based learning. In the present
+                  paper, we suggest that these seemingly different
+                  strategies share important underlying
+                  characteristics and can be viewed 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 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, but do so while enhancing students'
+                  personal development and attitudes toward
+                  learning. They accomplish these goals by
+                  establishing a shared vision for a course, providing
+                  modeling and mastery experiences, challenging and
+                  encouraging students, personalizing attention and
+                  feedback, creating experiential lessons that
+                  transcend the boundaries of the classroom, and
+                  promoting ample opportunities for preflection and
+                  reflection. We propose that these methods are
+                  synergistically related and, when used together,
+                  maximize students' potential for intellectual and
+                  personal growth.},
+}
+#+END_SRC
+
+** PMID to xml
+We can also get xml of the MEDLINE data. The web page here also wraps the xml in a 
 block and escapes the <> with < and >, which we have to undo. I have not used this code for anything, so I am not sure how good the xml code is.
+
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+(defun pubmed-get-medline-xml (pmid)
+  "Get MEDLINE xml for PMID as a string."
+  (interactive)
+  (with-current-buffer
+    (url-retrieve-synchronously
+     (format "http://www.ncbi.nlm.nih.gov/pubmed/%s/?report=xml&format=text" pmid))
+    (goto-char (point-min))
+    (while (search-forward "<" nil t)
+      (replace-match "<"))
+    (goto-char (point-min))
+    (while (search-forward ">" nil t)
+      (replace-match ">"))
+    (goto-char (point-min))   
+			   
+    (let ((p1 (search-forward "
"))
+	  (p2 (search-forward "
")))
+      (buffer-substring (+ 1 p1) (- p2 6)))))
+#+END_SRC
+
+#+RESULTS:
+: pubmed-get-medline-xml
+
+#+BEGIN_SRC emacs-lisp :tangle no
+(pubmed-get-medline-xml "23162369")
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+
+    
+        23162369
+        
+            2012
+            11
+            19
+        
+        

+            
+                1040-726X
+                
+                    24
+                    4
+                    
+                        2012
+                        Dec
+                    
+                
+                Educational psychology review
+                Educ Psychol Rev
+            
+            Transformational Teaching: Theoretical Underpinnings, Basic Principles, and Core Methods.
+            
+                569-608
+            
+            
+                Approaches to classroom instruction have evolved considerably over the past 50 years. This progress has been spurred by the development of several learning principles and methods of instruction, including active learning, student-centered learning, collaborative learning, experiential learning, and problem-based learning. In the present paper, we suggest that these seemingly different strategies share important underlying characteristics and can be viewed 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 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, but do so while enhancing students' personal development and attitudes toward learning. They accomplish these goals by establishing a shared vision for a course, providing modeling and mastery experiences, challenging and encouraging students, personalizing attention and feedback, creating experiential lessons that transcend the boundaries of the classroom, and promoting ample opportunities for preflection and reflection. We propose that these methods are synergistically related and, when used together, maximize students' potential for intellectual and personal growth.
+            
+            
+                
+                    Slavich
+                    George M
+                    GM
+                    
+                        Cousins Center for Psychoneuroimmunology and Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, UCLA Medical Plaza 300, Room 3156, Los Angeles, CA 90095-7076, USA.
+                    
+                
+                
+                    Zimbardo
+                    Philip G
+                    PG
+                
+            
+            ENG
+            
+                
+                    R01 AG026364
+                    AG
+                    NIA NIH HHS
+                    United States
+                
+                
+                    T32 MH019925
+                    MH
+                    NIMH NIH HHS
+                    United States
+                
+            
+            
+                JOURNAL ARTICLE
+            
+            
+                2012
+                7
+                24
+            
+        

+        
+            Educ Psychol Rev
+            9885342
+            1040-726X
+        
+    
+    
+        
+            
+                2012
+                7
+                24
+            
+            
+                2012
+                11
+                20
+                6
+                0
+            
+            
+                2012
+                11
+                20
+                6
+                0
+            
+            
+                2012
+                11
+                20
+                6
+                0
+            
+        
+        ppublish
+        
+            10.1007/s10648-012-9199-6
+            23162369
+            PMC3498956
+            NIHMS395714
+        
+        
+    
+
+
+#+end_example
+
+* Pubmed Central (PMC) link
+A PMCID starts with PMC and is followed by numbers. The PMCID is a unique reference number or identifier that is assigned to every article that is accepted into PMC. The PMCID is also used by recipients of NIH funding to demonstrate compliance with the NIH Public Access policy. The PMCID can be found in both PMC and PubMed.
+
+Here we define a new link. Clicking on it simply opens a webpage to the article.
+
+#+BEGIN_SRC emacs-lisp :tangle pubmed.el
+(org-add-link-type
+ "pmcid"
+ ;; clicking
+ (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/%s" link-string)))
+ ;; formatting
+(lambda (keyword desc format)
+   (cond
+    ((eq format 'html)
+     (format "" keyword))
+    ((eq format 'latex)
+     (format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/%s}" keyword)))))
+#+END_SRC
+
+
+* 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
+(org-add-link-type
+ "nihmsid"
+ ;; clicking
+ (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s" link-string)))
+ ;; formatting
+(lambda (keyword desc format)
+   (cond
+    ((eq format 'html) (format "")); 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
+
+#+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
+#+BEGIN_SRC emacs-lisp :tangle org-ref.el
+(provide 'pubmed)
+#+END_SRC
+
+
+* Build								   :noexport:
+This code will tangle the elisp code out to pubmed.el and load it.
+
+[[elisp:(org-babel-load-file "pubmed.org")]]
+
+
+
-- 
2.39.2