From: John Kitchin Date: Fri, 13 Mar 2015 00:39:15 +0000 (-0400) Subject: initial conversion of pubmed.org to pubmed.el X-Git-Url: https://git.donarmstrong.com/?p=org-ref.git;a=commitdiff_plain;h=28f917ba07774b9112cbd1be49bffbca501a8f1b initial conversion of pubmed.org to pubmed.el with outshine nav. --- diff --git a/pubmed.el b/pubmed.el new file mode 100644 index 0000000..61ec861 --- /dev/null +++ b/pubmed.el @@ -0,0 +1,222 @@ +;;; pubmed.el --- Links and functions for Pubmed and NIH databases -*- lexical-binding: t; -*- + +;; Copyright (C) 2015 John Kitchin + +;; Author: John Kitchin +;; Keywords: convenience + +;; 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 3 of the License, 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. If not, see . + +;;; Commentary: + +;; * 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. +;; +;; 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]]. + +;;; Code: + +;; * 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. + +(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 "pmid:%s" 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))))) + +;; ** Get MEDLINE metadata + +;; We can get bibliographic metadata from a pmid. Here we get the MEDLINE +;; text. The website wraps the data in 
 tags.
+
+(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)))))
+
+;; ** Parse the PMID MEDLINE data
+
+;; We can parse this into a data structure.
+
+(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))
+
+;; ** 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.
+
+(defun pubmed-pmid-to-bibtex (pmid)
+  "Convert a PMID to a bibtex entry."
+  (let* ((data (pubmed-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)))))
+
+;; And we probably want to be able to insert a bibtex entry
+
+(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)))
+
+;; ** 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.
+
+(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)))))
+
+;; * 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.
+
+(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 "pmcid:%s" keyword keyword))
+    ((eq format 'latex)
+     (format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/%s}" keyword)))))
+
+;; * 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.
+
+(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 "nihmsid:%s" keyword keyword))
+    ((eq format 'latex)
+     ;; write out the latex command
+     (format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}" keyword)))))
+
+
+(provide 'pubmed)
+;;; pubmed.el ends here