--- /dev/null
+;;; pubmed.el --- Links and functions for Pubmed and NIH databases -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2015 John Kitchin
+
+;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
+;; 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 <http://www.gnu.org/licenses/>.
+
+;;; 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 "<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)))))
+
+;; ** 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.
+
+(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 "<pre>"))
+ (p2 (search-forward "</pre>")))
+ (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 <pre> 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 "<pre>"))
+ (p2 (search-forward "</pre>")))
+ (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 "<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)))))
+
+;; * 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 "<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)))))
+
+
+(provide 'pubmed)
+;;; pubmed.el ends here
projects / org-ref.git / blobdiff