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292 lines
10 KiB
292 lines
10 KiB
;;; org-ref-pubmed.el --- Links and functions for Pubmed and NIH databases -*- lexical-binding: t; -*-
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;; Copyright (C) 2015 John Kitchin
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;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
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;; Keywords: convenience
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with this program. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;;* Introduction
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;; This document is an experiment at creating a literate program to provide
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;; functions for interacting with pubmed databases.
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;; This library provides links that go to pubmed resources, e.g.
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;; pmcid:PMC3498956
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;;
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;; pmid:23162369
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;;
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;; and nihmsid:NIHMS395714
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;;
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;; See http://www.ncbi.nlm.nih.gov/pmc/about/public-access-info/#p3 for details
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;; of these identifiers.
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;;
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;; For PMID there is one interactive function that inserts a bibtex entry:
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;; pubmed-insert-bibtex-from-pmid.
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;; This library is complementary to [[./doi-utils.org]].
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;;; Code:
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;;* PMID (from PubMed) link and functions
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;; A PMID is a number that identifies an entry in the Pubmed database. The PMID
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;; is a unique reference number for PubMed citations. The PMID is a distinctly
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;; different number from the PMCID and is used only for PubMed records.
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(require 'dash)
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(require 'org)
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(require 'org-ref-utils)
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(org-ref-link-set-parameters "pmid"
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:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pubmed/%s" link-string)))
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:export (lambda (keyword desc format)
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(cond
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((eq format 'html)
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(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s\">pmid:%s</a>" keyword (or desc keyword))) ; no output for html
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((eq format 'latex)
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;; write out the latex command
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(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}{%s}" keyword (or desc keyword))))))
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;;** Get MEDLINE metadata
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;; We can get bibliographic metadata from a pmid. Here we get the MEDLINE
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;; text. The website wraps the data in <pre></pre> tags.
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(defun pubmed-get-medline (pmid)
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"Get MEDLINE text for PMID as a string."
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(with-current-buffer
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(url-retrieve-synchronously
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(format "http://www.ncbi.nlm.nih.gov/pubmed/%s/?report=medline&format=text" pmid))
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(goto-char (point-min))
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(let ((p1 (search-forward "<pre>"))
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(p2 (search-forward "</pre>")))
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(buffer-substring (+ 1 p1) (- p2 6)))))
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;;** Parse the PMID MEDLINE data
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;; We can parse this into a data structure.
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(defun pubmed-parse-medline (pmid)
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"Parse the medline text for PMID and return a list of cons cells."
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(let ((data '())
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(p1)
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(p2)
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(tag)
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(value))
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(with-temp-buffer (insert (pubmed-get-medline pmid))
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(goto-char (point-min))
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(while (re-search-forward "\\(^[A-Z]\\{2,4\\}\\)\\s-*- "
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nil t)
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(setq tag (match-string 1))
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;; point is at end of the search
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(setq p1 (point))
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;; now go to next tag
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(re-search-forward "\\(^[A-Z]\\{2,4\\}\\)\\s-*- " nil t)
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(setq p2 (- (match-beginning 1) 1))
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(setq value (buffer-substring p1 p2))
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(setq data (append data (list (cons tag value))))
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;; now go back to last tag to get the next one
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(goto-char p1)))
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data))
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;;** PMID to bibtex entry
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;; The point of parsing the MEDLINE text is so we can make bibtex entries. We
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;; only support Journal articles for now.
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(defun pubmed-pmid-to-bibtex (pmid)
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"Convert a PMID to a bibtex entry."
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(let* ((data (pubmed-parse-medline pmid))
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(type (downcase (cdr (assoc "PT" data))))
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(title (cdr (assoc "TI" data)))
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(authors (mapconcat 'cdr
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(-filter (lambda (x)
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(string= (car x) "FAU"))
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data)
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" and "))
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(abstract (cdr (assoc "AB" data)))
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(volume (cdr (assoc "VI" data)))
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(issue (cdr (assoc "IP" data)))
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(journal (cdr (assoc "JT" data)))
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(year (cdr (assoc "DP" data)))
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(pages (cdr (assoc "PG" data)))
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(aid (cdr (assoc "AID" data))))
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(cond
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((string= type "journal article")
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(concat "@article{,
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author = {" authors "},
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title = {" title "},
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abstract = {" abstract "},
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journal = {" journal "},
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volume = {" volume "},
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number = {" issue "},
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year = {" (car (split-string year)) "},
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pages = {" pages "},
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doi = {" (replace-regexp-in-string " \\[doi\\]" "" (or aid "")) "},
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}"))
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(t
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(message "No conversion for type: %s" type)))))
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;; And we probably want to be able to insert a bibtex entry
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;;;###autoload
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(defun pubmed-insert-bibtex-from-pmid (pmid)
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"Insert a bibtex entry at point derived from PMID.
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You must clean the entry after insertion."
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(interactive "sPMID: ")
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(insert (pubmed-pmid-to-bibtex pmid)))
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;;** PMID to xml
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;; We can also get xml of the MEDLINE data. The web page here also wraps the xml
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;; in a <pre> block and escapes the <> with < and >, which we have to
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;; undo. I have not used this code for anything, so I am not sure how good the
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;; xml code is.
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;;;###autoload
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(defun pubmed-get-medline-xml (pmid)
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"Get MEDLINE xml for PMID as a string."
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(interactive)
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(with-current-buffer
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(url-retrieve-synchronously
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(format "http://www.ncbi.nlm.nih.gov/pubmed/%s/?report=xml&format=text" pmid))
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(goto-char (point-min))
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(while (search-forward "<" nil t)
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(replace-match "<"))
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(goto-char (point-min))
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(while (search-forward ">" nil t)
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(replace-match ">"))
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(goto-char (point-min))
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(let ((p1 (search-forward "<pre>"))
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(p2 (search-forward "</pre>")))
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(buffer-substring (+ 1 p1) (- p2 6)))))
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;;* Pubmed Central (PMC) link
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;; A PMCID starts with PMC and is followed by numbers. The PMCID is a unique
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;; reference number or identifier that is assigned to every article that is
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;; accepted into PMC. The PMCID is also used by recipients of NIH funding to
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;; demonstrate compliance with the NIH Public Access policy. The PMCID can be
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;; found in both PMC and PubMed.
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;; Here we define a new link. Clicking on it simply opens a webpage to the
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;; article.
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(org-ref-link-set-parameters "pmcid"
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:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/%s" link-string)))
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:export (lambda (keyword desc format)
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(cond
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((eq format 'html)
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(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/%s\">pmcid:%s</a>" keyword (or desc keyword)))
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((eq format 'latex)
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(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/%s}{%s}" keyword (or desc keyword))))))
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;;* NIHMSID
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;; The NIHMSID is a preliminary article identifier that applies only to
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;; manuscripts deposited through the NIHMS system. The NIHMSID is only valid for
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;; compliance reporting for 90 days after the publication date of an
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;; article. Once the Web version of the NIHMS submission is approved for
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;; inclusion in PMC and the corresponding citation is in PubMed, the article
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;; will also be assigned a PMCID.
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(org-ref-link-set-parameters "nihmsid"
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:follow (lambda (link-string) (browse-url (format "http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s" link-string)))
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:export (lambda (keyword desc format)
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(cond
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((eq format 'html)
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(format "<a href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/mid//%s\">nihmsid:%s</a>" keyword (or desc keyword)))
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((eq format 'latex)
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;; write out the latex command
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(format "\\url{http://www.ncbi.nlm.nih.gov/pmc/articles/mid/%s}{%s}" keyword (or desc keyword))))))
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;;* Searching pubmed
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;;;###autoload
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(defun pubmed ()
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"Open http://www.ncbi.nlm.nih.gov/pubmed in a browser."
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(interactive)
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(browse-url "http://www.ncbi.nlm.nih.gov/pubmed"))
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;;;###autoload
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(defun pubmed-advanced ()
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"Open http://www.ncbi.nlm.nih.gov/pubmed/advanced in a browser."
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(interactive)
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(browse-url "http://www.ncbi.nlm.nih.gov/pubmed/advanced"))
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;;;###autoload
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(defun pubmed-simple-search (query)
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"Open QUERY in Pubmed in a browser."
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(interactive "sQuery: ")
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(browse-url
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(format "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s" (url-hexify-string query))))
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(org-ref-link-set-parameters "pubmed-search"
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:follow (lambda (query)
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"Open QUERY in a `pubmed-simple-search'."
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(pubmed-simple-search query))
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:export (lambda (query desc format)
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(let ((url (format "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s" (url-hexify-string query))))
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(cond
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((eq format 'html)
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(format "<a href=\"%s\">%s</a>" url (or desc (concat "pubmed-search:" query))))
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((eq format 'latex)
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(format "\\href{%s}{%s}" url (or desc (concat "pubmed-search:" query))))))))
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;; ** Pubmed clinical
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;; These functions were suggested by Colin Melville <casm40@gmail.com>.
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;;;###autoload
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(defun pubmed-clinical ()
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"Open http://www.ncbi.nlm.nih.gov/pubmed/clinical in a browser."
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(interactive)
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(browse-url "http://www.ncbi.nlm.nih.gov/pubmed/clinical"))
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;;;###autoload
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(defun pubmed-clinical-search (query)
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"Open QUERY in pubmed-clinical."
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(interactive "sQuery: ")
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(browse-url
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(format "https://www.ncbi.nlm.nih.gov/pubmed/clinical?term=%s" (url-hexify-string query))))
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(org-ref-link-set-parameters "pubmed-clinical"
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:follow (lambda (query)
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"Open QUERY in a `pubmed-clinical-search'."
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(pubmed-clinical-search query))
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:export (lambda (query desc format)
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(let ((url (format "http://www.ncbi.nlm.nih.gov/pubmed/clinical?term=%s"
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(url-hexify-string query))))
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(cond
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((eq format 'html)
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(format "<a href=\"%s\">%s</a>" url
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(or desc (concat "pubmed-clinical-search:" query))))
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((eq format 'latex)
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(format "\\href{%s}{%s}" url
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(or desc (concat "pubmed-clinical-search:" query))))))))
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(provide 'org-ref-pubmed)
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;;; org-ref-pubmed.el ends here
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