1 #+TITLE: DOI utilities for making bibtex entries and downloading pdfs
3 This package provides functionality to download PDFs and bibtex entries from a DOI, as well as to update a bibtex entry from a DOI. It depends slightly on org-ref, to determine where to save pdf files too, and where to insert bibtex entries in the default bibliography.
5 The principle commands you will use from here are:
7 - doi-utils-get-bibtex-entry-pdf with the cursor in a bibtex entry.
8 - doi-utils-insert-bibtex-entry-from-doi to insert a bibtex entry at your cursor, clean it and try to get a pdf.
9 - doi-utils-add-bibtex-entry-from-doi to add an entry to your default bibliography (cleaned with pdf if possible).
10 - doi-utils-add-bibtex-entry-from-region to add an entry from a highlighed doi to your default bibliography.
11 - doi-utils-update-bibtex-entry-from-doi with cursor in an entry to update its fields.
14 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
15 ;;; doi-utils.el --- get bibtex entries and pdfs from a DOI
17 ;; Copyright(C) 2014 John Kitchin
19 ;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
20 ;; This file is not currently part of GNU Emacs.
22 ;; This program is free software; you can redistribute it and/or
23 ;; modify it under the terms of the GNU General Public License as
24 ;; published by the Free Software Foundation; either version 2, or (at
25 ;; your option) any later version.
27 ;; This program is distributed in the hope that it will be useful, but
28 ;; WITHOUT ANY WARRANTY; without even the implied warranty of
29 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
30 ;; General Public License for more details.
32 ;; You should have received a copy of the GNU General Public License
33 ;; along with this program ; see the file COPYING. If not, write to
34 ;; the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
35 ;; Boston, MA 02111-1307, USA.
39 ;; Lisp code to generate and update bibtex entries from a DOI, and to
40 ;; download pdfs from publisher websites from a DOI.
42 ;; Package-Requires: ((org-ref))
47 * Getting pdf files from a DOI
48 The idea here is simple. When you visit http://dx.doi.org/doi, you get redirected to the journal site. Once you have the url for the article, you can usually compute the url to the pdf, or find it in the page. Then you simply download it.
50 There are some subtleties in doing this that are described here. To get the redirect, we have to use url-retrieve, and a callback function. The callback does not return anything, so we communicate through global variables. url-retrieve is asynchronous, so we have to make sure to wait for it to finish.
52 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
53 (defvar *doi-utils-waiting* t
54 "stores waiting state for url retrieval.")
56 (defvar *doi-utils-redirect* nil
57 "stores redirect url from a callback function")
59 (defun doi-utils-redirect-callback (&optional status)
60 "callback for url-retrieve to set the redirect"
61 (when (plist-get status :error)
62 (signal (car (plist-get status :error)) (cdr(plist-get status :error))))
63 (when (plist-get status :redirect) ; is nil if there none
64 (message "redirects = %s" (plist-get status :redirect))
65 (message "*doi-utils-redirect* set to %s"
66 (setq *doi-utils-redirect* (plist-get status :redirect))))
67 ;; we have done our job, so we are not waiting any more.
68 (setq *doi-utils-waiting* nil))
71 To actually get the redirect we use url-retrieve like this.
73 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
74 (defun doi-utils-get-redirect (doi)
75 "get redirect url from dx.doi.org/doi"
76 ;; we are going to wait until the url-retrieve is done
77 (setq *doi-utils-waiting* t)
78 ;; start with no redirect. it will be set in the callback.
79 (setq *doi-utils-redirect* nil)
81 (format "http://dx.doi.org/%s" doi)
82 'doi-utils-redirect-callback)
83 ; I suspect we need to wait here for the asynchronous process to
84 ; finish. we loop and sleep until the callback says it is done via
85 ; `*doi-utils-waiting*'. this works as far as i can tell. Before I
86 ; had to run this a few times to get it to work, which i suspect
87 ; just gave the first one enough time to finish.
88 (while *doi-utils-waiting* (sleep-for 0.1)))
91 Once we have a redirect for a particular doi, we need to compute the url to the pdf. We do this with a series of functions. Each function takes a single argument, the redirect url. If it knows how to compute the pdf url it does, and returns it. We store the functions in a variable:
93 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
94 (defvar doi-utils-pdf-url-functions nil
95 "list of functions that return a url to a pdf from a redirect url. Each function takes one argument, the redirect url. The function must return a pdf-url, or nil.")
99 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
100 (defun aps-pdf-url (*doi-utils-redirect*)
101 (when (string-match "^http://journals.aps.org" *doi-utils-redirect*)
102 (replace-regexp-in-string "/abstract/" "/pdf/" *doi-utils-redirect*)))
106 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
107 (defun science-pdf-url (*doi-utils-redirect*)
108 (when (string-match "^http://www.sciencemag.org" *doi-utils-redirect*)
109 (concat *doi-utils-redirect* ".full.pdf")))
113 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
114 (defun nature-pdf-url (*doi-utils-redirect*)
115 (when (string-match "^http://www.nature.com" *doi-utils-redirect*)
116 (let ((result *doi-utils-redirect*))
117 (setq result (replace-regexp-in-string "/full/" "/pdf/" result))
118 (replace-regexp-in-string "\.html$" "\.pdf" result))))
122 http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/abstract
123 http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/pdf
125 It appears that it is not enough to use the pdf url above. That takes you to an html page. The actual link to teh pdf is embedded in that page. This is how ScienceDirect does things too.
127 This is where the link is hidden:
129 <iframe id="pdfDocument" src="http://onlinelibrary.wiley.com/store/10.1002/anie.201402680/asset/6397_ftp.pdf?v=1&t=hwut2142&s=d4bb3cd4ad20eb733836717f42346ffb34017831" width="100%" height="675px"></iframe>
133 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
134 (defun doi-utils-get-wiley-pdf-url (redirect-url)
135 "wileyscience direct hides the pdf url in html. we get it out here"
136 (setq *doi-utils-waiting* t)
137 (url-retrieve redirect-url
139 (beginning-of-buffer)
140 (re-search-forward "<iframe id=\"pdfDocument\" src=\"\\([^\"]*\\)\"" nil)
141 (setq *doi-utils-pdf-url* (match-string 1)
142 ,*doi-utils-waiting* nil)))
143 (while *doi-utils-waiting* (sleep-for 0.1))
144 ,*doi-utils-pdf-url*)
146 (defun wiley-pdf-url (*doi-utils-redirect*)
147 (when (string-match "^http://onlinelibrary.wiley.com" *doi-utils-redirect*)
148 (doi-utils-get-wiley-pdf-url (replace-regexp-in-string "/abstract" "/pdf" *doi-utils-redirect*))
149 ,*doi-utils-pdf-url*))
153 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
154 (defun springer-pdf-url (*doi-utils-redirect*)
155 (when (string-match "^http://link.springer.com" *doi-utils-redirect*)
156 (replace-regexp-in-string "/article/" "/content/pdf/" (concat *doi-utils-redirect* ".pdf"))))
160 here is a typical url http://pubs.acs.org/doi/abs/10.1021/nl500037x
161 the pdf is found at http://pubs.acs.org/doi/pdf/10.1021/nl500037x
163 we just change /abs/ to /pdf/.
165 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
166 (defun acs-pdf-url (*doi-utils-redirect*)
167 (when (string-match "^http://pubs.acs.org" *doi-utils-redirect*)
168 (replace-regexp-in-string "/abs/" "/pdf/" *doi-utils-redirect*)))
171 #+BEGIN_SRC emacs-lisp :tangle no
172 (acs-pdf-url "http://pubs.acs.org/doi/abs/10.1021/nl500037x")
176 : http://pubs.acs.org/doi/pdf/10.1021/nl500037x
179 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
180 (defun iop-pdf-url (*doi-utils-redirect*)
181 (when (string-match "^http://iopscience.iop.org" *doi-utils-redirect*)
182 (let ((tail (replace-regexp-in-string "^http://iopscience.iop.org" "" *doi-utils-redirect*)))
183 (concat "http://iopscience.iop.org" tail "/pdf" (replace-regexp-in-string "/" "_" tail) ".pdf"))))
187 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
188 (defun jstor-pdf-url (*doi-utils-redirect*)
189 (when (string-match "^http://www.jstor.org" *doi-utils-redirect*)
190 (concat (replace-regexp-in-string "/stable/" "/stable/pdfplus/" *doi-utils-redirect*) ".pdf")))
194 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
195 (defun aip-pdf-url (*doi-utils-redirect*)
196 (when (string-match "^http://scitation.aip.org" *doi-utils-redirect*)
197 ;; get stuff after content
199 (setq p2 (replace-regexp-in-string "^http://scitation.aip.org/" "" *doi-utils-redirect*))
200 (setq s (split-string p2 "/"))
201 (setq p1 (mapconcat 'identity (-remove-at-indices '(0 6) s) "/"))
202 (setq p3 (concat "/" (nth 0 s) (nth 1 s) "/" (nth 2 s) "/" (nth 3 s)))
203 (format "http://scitation.aip.org/deliver/fulltext/%s.pdf?itemId=/%s&mimeType=pdf&containerItemId=%s"
207 ** Taylor and Francis
208 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
209 (defun tandfonline-pdf-url (*doi-utils-redirect*)
210 (when (string-match "^http://www.tandfonline.com" *doi-utils-redirect*)
211 (replace-regexp-in-string "/abs/\\|/full/" "/pdf/" *doi-utils-redirect*)))
214 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
215 (defun ecs-pdf-url (*doi-utils-redirect*)
216 (when (string-match "^http://jes.ecsdl.org" *doi-utils-redirect*)
217 (replace-regexp-in-string "\.abstract$" ".full.pdf" *doi-utils-redirect*)))
220 http://ecst.ecsdl.org/content/25/2/2769
221 http://ecst.ecsdl.org/content/25/2/2769.full.pdf
223 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
224 (defun ecst-pdf-url (*doi-utils-redirect*)
225 (when (string-match "^http://ecst.ecsdl.org" *doi-utils-redirect*)
226 (concat *doi-utils-redirect* ".full.pdf")))
231 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
232 (defun rsc-pdf-url (*doi-utils-redirect*)
233 (when (string-match "^http://pubs.rsc.org" *doi-utils-redirect*)
234 (let ((url (downcase *doi-utils-redirect*)))
235 (setq url (replace-regexp-in-string "articlelanding" "articlepdf" url))
239 ** Elsevier/ScienceDirect
240 You cannot compute these pdf links; they are embedded in the redirected pages.
242 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
243 (defvar *doi-utils-pdf-url* nil
244 "stores url to pdf download from a callback function")
246 (defun doi-utils-get-science-direct-pdf-url (redirect-url)
247 "science direct hides the pdf url in html. we get it out here"
248 (setq *doi-utils-waiting* t)
249 (url-retrieve redirect-url
251 (beginning-of-buffer)
252 (re-search-forward "pdfurl=\"\\([^\"]*\\)\"" nil t)
253 (setq *doi-utils-pdf-url* (match-string 1)
254 ,*doi-utils-waiting* nil)))
255 (while *doi-utils-waiting* (sleep-for 0.1))
256 ,*doi-utils-pdf-url*)
259 (defun science-direct-pdf-url (*doi-utils-redirect*)
260 (when (string-match "^http://www.sciencedirect.com" *doi-utils-redirect*)
261 (doi-utils-get-science-direct-pdf-url *doi-utils-redirect*)
262 ,*doi-utils-pdf-url*))
265 ;; http://linkinghub.elsevier.com/retrieve/pii/S0927025609004558
266 ;; which actually redirect to
267 ;; http://www.sciencedirect.com/science/article/pii/S0927025609004558
268 (defun linkinghub-elsevier-pdf-url (*doi-utils-redirect*)
269 (when (string-match "^http://linkinghub.elsevier.com/retrieve" *doi-utils-redirect*)
270 (let ((second-redirect (replace-regexp-in-string
271 "http://linkinghub.elsevier.com/retrieve"
272 "http://www.sciencedirect.com/science/article"
273 ,*doi-utils-redirect*)))
274 (message "getting pdf url from %s" second-redirect)
275 ;(doi-utils-get-science-direct-pdf-url second-redirect)
276 ,*doi-utils-pdf-url*)))
280 http://www.pnas.org/content/early/2014/05/08/1319030111
281 http://www.pnas.org/content/early/2014/05/08/1319030111.full.pdf
284 http://www.pnas.org/content/early/2014/05/08/1319030111.full.pdf+html?with-ds=yes
285 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
286 (defun pnas-pdf-url (*doi-utils-redirect*)
287 (when (string-match "^http://www.pnas.org" *doi-utils-redirect*)
288 (concat *doi-utils-redirect* ".full.pdf?with-ds=yes")))
292 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
293 (setq doi-utils-pdf-url-functions
304 'science-direct-pdf-url
305 'linkinghub-elsevier-pdf-url
313 ** Get the pdf url for a doi
314 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
315 (defun doi-utils-get-pdf-url (doi)
316 "returns a url to a pdf for the doi if one can be
317 calculated. Loops through the functions in `doi-utils-pdf-url-functions'
319 (doi-utils-get-redirect doi)
321 (unless *doi-utils-redirect*
322 (error "No redirect found for %s" doi))
323 (message "applying functions")
325 (dolist (func doi-utils-pdf-url-functions)
326 (message "calling %s" func)
327 (let ((this-pdf-url (funcall func *doi-utils-redirect*)))
328 (message "t: %s" this-pdf-url)
330 (message "found pdf url: %s" this-pdf-url)
331 (throw 'pdf-url this-pdf-url))))))
335 : doi-utils-get-pdf-url
338 #+BEGIN_SRC emacs-lisp :tangle no
339 (doi-utils-get-pdf-url "10.1126/science.1158722")
343 : http://www.sciencemag.org/content/321/5890/792.full.pdf
345 #+BEGIN_SRC emacs-lisp :tangle no
346 (doi-utils-get-pdf-url "10.1021/nl500037x")
350 : http://pubs.acs.org/doi/pdf/10.1021/nl500037x
353 #+BEGIN_SRC emacs-lisp :tangle no
354 (doi-utils-get-pdf-url "10.1002/anie.201402680")
358 : http://onlinelibrary.wiley.com/doi/10.1002/anie.201402680/pdf
360 ** Finally, download the pdf
361 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
362 (defun doi-utils-get-bibtex-entry-pdf ()
363 "download pdf for entry at point if the pdf does not already
364 exist locally. The entry must have a doi. The pdf will be saved
365 to `org-ref-pdf-directory', by the name %s.pdf where %s is the
366 bibtex label. Files will not be overwritten. The pdf will be
367 checked to make sure it is a pdf, and not some html failure
368 page. you must have permission to access the pdf. We open the pdf
372 (bibtex-beginning-of-entry)
373 (let (;; get doi, removing http://dx.doi.org/ if it is there.
374 (doi (replace-regexp-in-string
375 "http://dx.doi.org/" ""
376 (bibtex-autokey-get-field "doi")))
381 ;; get the key and build pdf filename.
382 (re-search-forward bibtex-entry-maybe-empty-head)
383 (setq key (match-string bibtex-key-in-head))
384 (setq pdf-file (concat org-ref-pdf-directory key ".pdf"))
386 ;; now get file if needed.
387 (when (and doi (not (file-exists-p pdf-file)))
388 (setq pdf-url (doi-utils-get-pdf-url doi))
391 (url-copy-file pdf-url pdf-file)
392 ;; now check if we got a pdf
394 (insert-file-contents pdf-file)
395 ;; PDFS start with %PDF-1.x as the first few characters.
396 (if (not (string= (buffer-substring 1 6) "%PDF-"))
398 (message "%s" (buffer-string))
399 (delete-file pdf-file))
400 (message "%s saved" pdf-file)))
402 (when (file-exists-p pdf-file)
403 (org-open-file pdf-file)))
404 (message "No pdf-url found for %s at %s" doi *doi-utils-redirect* ))
408 * Getting bibtex entries from a DOI
410 I [[http://homepages.see.leeds.ac.uk/~eeaol/notes/2013/02/doi-metadata/][found]] you can download metadata about a DOI from http://dx.doi.org. You just have to construct the right http request to get it. Here is a function that gets the metadata as a plist in emacs.
412 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
413 (defun doi-utils-get-json-metadata (doi)
414 "Try to get json metadata for DOI. Open the DOI in a browser if we do not get it."
415 (let ((url-request-method "GET")
416 (url-mime-accept-string "application/citeproc+json")
417 (json-object-type 'plist)
420 (url-retrieve-synchronously
421 (concat "http://dx.doi.org/" doi))
422 (setq json-data (buffer-substring url-http-end-of-headers (point-max)))
423 (if (string-match "Resource not found" json-data)
425 (browse-url (concat "http://dx.doi.org/" doi))
426 (error "Resource not found. Opening website."))
427 (json-read-from-string json-data)))))
431 : doi-utils-get-json-metadata
434 #+BEGIN_SRC emacs-lisp :tangle no
435 (doi-utils-get-json-metadata "10.1103/PhysRevLett.99.016105")
439 | :member | http://id.crossref.org/member/16 | :volume | 99 | :indexed | (:timestamp 1423435577602 :date-parts [[2015 2 8]]) | :publisher | American Physical Society (APS) | :source | CrossRef | :URL | http://dx.doi.org/10.1103/PhysRevLett.99.016105 | :ISSN | [0031-9007 1079-7114] | :DOI | 10.1103/physrevlett.99.016105 | :type | journal-article | :title | Scaling Properties of Adsorption Energies for Hydrogen-Containing Molecules on Transition-Metal Surfaces | :issue | 1 | :deposited | (:timestamp 1313712000000 :date-parts [[2011 8 19]]) | :reference-count | 26 | :container-title | Phys. Rev. Lett. | :author | [(:given F. :family Abild-Pedersen) (:given J. :family Greeley) (:given F. :family Studt) (:given J. :family Rossmeisl) (:given T. :family Munter) (:given P. :family Moses) (:given E. :family Skúlason) (:given T. :family Bligaard) (:given J. :family Nørskov)] | :prefix | http://id.crossref.org/prefix/10.1103 | :score | 1.0 | :issued | (:date-parts [[2007 7]]) | :subject | [Physics and Astronomy(all)] | :subtitle | [] |
442 #+BEGIN_SRC emacs-lisp :tangle no
443 (doi-utils-get-json-metadata "10.1007/978-1-4612-4968-9")
447 | :member | nil | :indexed | (:timestamp 1423773021494 :date-parts [[2015 2 12]]) | :publisher | Springer New York | :source | CrossRef | :URL | http://dx.doi.org/10.1007/978-1-4612-4968-9 | :ISBN | [http://id.crossref.org/isbn/978-0-387-96347-1 http://id.crossref.org/isbn/978-1-4612-4968-9] | :ISSN | [0172-6056] | :DOI | 10.1007/978-1-4612-4968-9 | :type | book | :title | Constructive Combinatorics | :deposited | (:timestamp 1378684800000 :date-parts [[2013 9 9]]) | :reference-count | 0 | :container-title | Undergraduate Texts in Mathematics | :author | [(:given Dennis :family Stanton) (:given Dennis :family White)] | :prefix | none | :score | 1.0 | :issued | (:date-parts [[1986]]) | :subtitle | [] |
449 We can use that data to construct a bibtex entry. We do that by defining a template, and filling it in. I wrote this template expansion code which makes it easy to substitute values like %{} in emacs lisp.
451 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
452 (defun doi-utils-expand-template (s)
453 "expand a template containing %{} with the eval of its contents"
454 (replace-regexp-in-string "%{\\([^}]+\\)}"
456 (let ((sexp (substring arg 2 -1)))
457 (format "%s" (eval (read sexp))))) s))
460 Now we define a function that fills in that template from the metadata.
462 As different bibtex types share common keys, it is advantageous to separate data extraction from json, and the formatting of the bibtex entry.
464 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
465 (setq doi-utils-json-metadata-extract
466 '((type (plist-get results :type))
467 (author (mapconcat (lambda (x) (concat (plist-get x :given) " " (plist-get x :family)))
468 (plist-get results :author) " and "))
469 (title (plist-get results :title))
470 (subtitle (plist-get results :subtitle))
471 (journal (plist-get results :container-title))
472 (series (plist-get results :container-title))
473 (publisher (plist-get results :publisher))
474 (volume (plist-get results :volume))
475 (issue (plist-get results :issue))
476 (number (plist-get results :issue))
477 (year (elt (elt (plist-get (plist-get results :issued) :date-parts) 0) 0))
478 (month (elt (elt (plist-get (plist-get results :issued) :date-parts) 0) 1))
479 (pages (plist-get results :page))
480 (doi (plist-get results :DOI))
481 (url (plist-get results :URL))
482 (booktitle (plist-get results :container-title))))
485 Next, we need to define the different bibtex types. Each type has a bibtex type (for output) and the type as provided in the doi record. Finally, we have to declare the fields we want to output.
487 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el :results none
488 (setq doi-utils-bibtex-type-generators nil)
490 (defun doi-utils-concat-prepare (lst &optional acc)
491 "Given a list `lst' of strings and other expressions, which are
492 intented to passed to `concat', concat any subsequent strings,
493 minimising the number of arguments being passed to `concat'
494 without changing the results."
495 (cond ((null lst) (nreverse acc))
496 ((and (stringp (car lst))
498 (doi-utils-concat-prepare (cdr lst) (cons (concat (car acc) (car lst))
500 (t (doi-utils-concat-prepare (cdr lst) (cons (car lst) acc)))))
502 (defmacro doi-utils-def-bibtex-type (name matching-types &rest fields)
503 "Define a BibTeX type identified by (symbol) `name' with
504 `fields' (given as symbols), matching to retrieval expressions in
505 `doi-utils-json-metadata-extract'. This type will only be used
506 when the `:type' parameter in the JSON metadata is contained in
507 `matching-types' - a list of strings."
508 `(push (lambda (type results)
509 (when (or ,@(mapcar (lambda (match-type) `(string= type ,match-type)) matching-types))
510 (let ,(mapcar (lambda (field)
511 (let ((field-expr (assoc field doi-utils-json-metadata-extract)))
513 ;; need to convert to string first
514 `(,(car field-expr) (format "%s" ,(cadr field-expr)))
515 (error "unknown bibtex field type %s" field))))
518 ,@(doi-utils-concat-prepare
520 (list (concat "@" (symbol-name name) "{,\n")
521 ;; there seems to be some bug with mapcan,
522 ;; so we fall back to flatten
523 (mapcar (lambda (field)
524 `(" " ,(symbol-name field) " = {" ,field "},\n"))
527 doi-utils-bibtex-type-generators))
529 (doi-utils-def-bibtex-type article ("journal-article" "article-journal")
530 author title journal year volume number pages doi url)
532 (doi-utils-def-bibtex-type inproceedings ("proceedings-article")
533 author title booktitle year month pages doi url)
535 (doi-utils-def-bibtex-type book ("book")
536 author title series publisher year pages doi url)
538 (doi-utils-def-bibtex-type inbook ("book-chapter")
539 author title booktitle series publisher year pages doi url)
543 With the code generating the bibtex entry in place, we can glue it to the json retrieval code.
544 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
545 (defun doi-utils-doi-to-bibtex-string (doi)
546 "return a bibtex entry as a string for the doi. Not all types are supported yet."
547 (let* ((results (doi-utils-get-json-metadata doi))
548 (type (plist-get results :type)))
549 ;(format "%s" results) ; json-data
550 (or (some (lambda (g) (funcall g type results)) doi-utils-bibtex-type-generators)
551 (message "%s not supported yet\n%S." type results))))
555 : doi-utils-doi-to-bibtex-string
557 To see that in action:
558 #+BEGIN_SRC emacs-lisp :tangle no
559 (doi-utils-doi-to-bibtex-string "10.1103/PhysRevLett.99.016105")
565 author = {F. Abild-Pedersen and J. Greeley and F. Studt and J. Rossmeisl and T. Munter and P. Moses and E. Skúlason and T. Bligaard and J. Nørskov},
566 title = {Scaling Properties of Adsorption Energies for Hydrogen-Containing Molecules on Transition-Metal Surfaces},
567 journal = {Phys. Rev. Lett.},
572 doi = {10.1103/physrevlett.99.016105},
573 url = {http://dx.doi.org/10.1103/PhysRevLett.99.016105},
579 #+BEGIN_SRC emacs-lisp :tangle no
580 (doi-utils-doi-to-bibtex-string "10.1007/978-1-4612-4968-9")
586 author = {Dennis Stanton and Dennis White},
587 title = {Constructive Combinatorics},
588 series = {Undergraduate Texts in Mathematics},
589 publisher = {Springer New York},
592 doi = {10.1007/978-1-4612-4968-9},
593 url = {http://dx.doi.org/10.1007/978-1-4612-4968-9},
597 That is just the string for the entry. To be useful, we need a function that inserts the string into a buffer. This function will insert the string at the cursor, clean the entry, try to get the pdf, and create a notes entry for you.
599 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
600 (defun doi-utils-insert-bibtex-entry-from-doi (doi)
601 "insert bibtex entry from a doi. Also cleans entry using
602 org-ref, and tries to download the corresponding pdf."
603 (interactive "sDOI :")
604 (insert (doi-utils-doi-to-bibtex-string doi))
606 (if (bibtex-key-in-head nil)
607 (org-ref-clean-bibtex-entry t)
608 (org-ref-clean-bibtex-entry))
610 (doi-utils-get-bibtex-entry-pdf)
611 (save-selected-window
612 (org-ref-open-bibtex-notes)))
615 It may be you are in some other place when you want to add a bibtex entry. This next function will open the first entry in org-ref-default-bibliography go to the end, and add the entry. You can sort it later.
617 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
618 (defun doi-utils-add-bibtex-entry-from-doi (doi bibfile)
619 "Add entry to end of a file in in the current directory ending
620 with .bib or in `org-ref-default-bibliography'. If you have an
621 active region that starts like a DOI, that will be the initial
622 prompt. If no region is selected and the first entry of the
623 kill-ring starts like a DOI, then that is the intial
624 prompt. Otherwise, you have to type or pste in a DOI."
626 (list (read-input "DOI: "
627 ;; now set initial input
629 ;; If region is active and it starts like a doi we want it.
630 ((and (region-active-p)
631 (s-match "^10" (buffer-substring
634 (buffer-substring (region-beginning) (region-end)))
635 ;; if the first entry in the kill-ring looks
636 ;; like a DOI, let's use it.
637 ((if (s-match "^10" (car kill-ring))
639 ;; otherwise, we have no initial input. You
640 ;; will have to type it in.
643 ;; now get the bibfile to add it to
646 (append (f-entries "." (lambda (f) (f-ext? f "bib")))
647 org-ref-default-bibliography))))
648 ;; Wrap in save-window-excursion to restore your window arrangement after this
650 (save-window-excursion
652 ;; Check if the doi already exists
653 (goto-char (point-min))
654 (if (search-forward doi nil t)
655 (message "%s is already in this file" doi)
658 (doi-utils-insert-bibtex-entry-from-doi doi)
663 * Updating bibtex entries
664 I wrote this code because it is pretty common for me to copy bibtex entries from ASAP articles that are incomplete, e.g. no page numbers because it is not in print yet. I wanted a convenient way to update an entry from its DOI. Basically, we get the metadata, and update the fields in the entry.
666 There is not bibtex set field function, so I wrote this one.
668 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
669 (defun bibtex-set-field (field value &optional nodelim)
670 "set field to value in bibtex file. create field if it does not exist"
671 (interactive "sfield: \nsvalue: ")
672 (bibtex-beginning-of-entry)
674 (if (setq found (bibtex-search-forward-field field t))
677 (goto-char (car (cdr found)))
680 (bibtex-make-field field nil nil nodelim)
684 (message "new field being made")
685 (bibtex-beginning-of-entry)
686 (forward-line) (beginning-of-line)
687 (bibtex-next-field nil)
689 (bibtex-make-field field nil nil nodelim)
694 The updating function looks like this. We get all the keys from the json plist metadata, and update the fields if they exist.
696 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
697 (defun plist-get-keys (plist)
698 "return keys in a plist"
700 for key in results by #'cddr collect key))
702 (defun doi-utils-update-bibtex-entry-from-doi (doi)
703 "update fields in a bibtex entry from the doi. Every field will be updated, so previous changes will be lost."
705 (or (replace-regexp-in-string "http://dx.doi.org/" "" (bibtex-autokey-get-field "doi"))
706 (read-string "DOI: "))))
707 (let* ((results (doi-utils-get-json-metadata doi))
708 (type (plist-get results :type))
710 (lambda (x) (concat (plist-get x :given)
711 " " (plist-get x :family)))
712 (plist-get results :author) " and "))
713 (title (plist-get results :title))
714 (journal (plist-get results :container-title))
719 (plist-get results :issued) :date-parts) 0) 0)))
720 (volume (plist-get results :volume))
721 (number (or (plist-get results :issue) ""))
722 (pages (or (plist-get results :page) ""))
723 (url (or (plist-get results :URL) ""))
724 (doi (plist-get results :DOI)))
726 ;; map the json fields to bibtex fields. The code each field is mapped to is evaluated.
727 (setq mapping '((:author . (bibtex-set-field "author" author))
728 (:title . (bibtex-set-field "title" title))
729 (:container-title . (bibtex-set-field "journal" journal))
730 (:issued . (bibtex-set-field "year" year))
731 (:volume . (bibtex-set-field "volume" volume))
732 (:issue . (bibtex-set-field "number" number))
733 (:page . (bibtex-set-field "pages" pages))
734 (:DOI . (bibtex-set-field "doi" doi))
735 (:URL . (bibtex-set-field "url" url))))
737 ;; now we have code to run for each entry. we map over them and evaluate the code
740 (eval (cdr (assoc key mapping))))
741 (plist-get-keys results)))
743 ; reclean entry, but keep key if it exists.
744 (if (bibtex-key-in-head)
745 (org-ref-clean-bibtex-entry t)
746 (org-ref-clean-bibtex-entry)))
748 * DOI functions for WOS
749 I came across this API http://wokinfo.com/media/pdf/OpenURL-guide.pdf to make links to the things I am interested in here. Based on that document, here are three links based on a doi:10.1021/jp047349j that take you to different Web Of Science (WOS) pages.
752 1. go to article in WOS: http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:doi/10.1021/jp047349j
753 2. citing articles: http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F10.1021/jp047349j&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.citing=yes
754 3. related articles: http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F10.1021/jp047349j&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.related=yes
756 These are pretty easy to construct, so we can write functions that will create them and open the url in our browser. There are some other options that could be considered, but since we usually have a doi, it seems like the best way to go for creating the links. Here are the functions.
758 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
759 (defun doi-utils-wos (doi)
760 "Open Web of Science entry for DOI"
761 (interactive "sDOI: ")
764 "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info:doi/%s" doi)))
766 (defun doi-utils-wos-citing (doi)
767 "Open Web of Science citing articles entry. May be empty if none are found"
768 (interactive "sDOI: ")
771 "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F"
773 "&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.citing=yes")))
775 (defun doi-utils-wos-related (doi)
776 "Open Web of Science related articles page."
777 (interactive "sDOI: ")
779 (concat "http://ws.isiknowledge.com/cps/openurl/service?url_ver=Z39.88-2004&rft_id=info%3Adoi%2F"
781 "&svc_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Asch_svc&svc.related=yes")))
785 * A new doi link for org-mode
786 The idea is to add a menu to the doi link, so rather than just clicking to open the article, you can do other things.
789 3. open citing articles
790 4. open related articles
794 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el :results silent
795 (defun doi-utils-open (doi)
796 (interactive "sDOI: ")
797 (browse-url (concat "http://dx.doi.org/" doi)))
800 (defun doi-utils-open-bibtex (doi)
801 "Search through `reftex-default-bibliography' for DOI."
802 (interactive "sDOI: ")
804 (dolist (f reftex-default-bibliography)
806 (when (search-forward doi (point-max) t)
807 (bibtex-beginning-of-entry)
811 (defun doi-utils-crossref (doi)
812 "Search DOI in CrossRef."
813 (interactive "sDOI: ")
816 "http://search.crossref.org/?q=%s" doi)))
819 (defun doi-utils-google-scholar (doi)
820 "Google scholar the word at point or selection."
821 (interactive "sDOI: ")
824 "http://scholar.google.com/scholar?q=%s" doi)))
827 (defun doi-utils-pubmed (doi)
828 "Pubmed the word at point or selection."
829 (interactive "sDOI: ")
832 "http://www.ncbi.nlm.nih.gov/pubmed/?term=%s"
833 (url-hexify-string doi))))
836 (defvar doi-link-menu-funcs '()
837 "Functions to run in doi menu. Each entry is a list of (key menu-name function).
838 The function must take one argument, the doi.")
840 (setq doi-link-menu-funcs
841 '(("o" "pen" doi-utils-open)
842 ("w" "os" doi-utils-wos)
843 ("c" "iting articles" doi-utils-wos-citing)
844 ("r" "elated articles" doi-utils-wos-related)
845 ("s" "Google Scholar" doi-utils-google-scholar)
846 ("f" "CrossRef" doi-utils-crossref)
847 ("p" "ubmed" doi-utils-pubmed)
848 ("b" "open in bibtex" doi-utils-open-bibtex)
849 ("g" "et bibtex entry" doi-utils-add-bibtex-entry-from-doi)))
852 (defun doi-link-menu (link-string)
853 "Generate the link menu message, get choice and execute it.
854 Options are stored in `doi-link-menu-funcs'."
860 (concat "[" (elt tup 0) "]"
862 doi-link-menu-funcs "") ": "))
863 (let* ((input (read-char-exclusive))
865 (char-to-string input) doi-link-menu-funcs)))
878 doi:10.1021/jp047349j
881 * Getting a doi for a bibtex entry missing one
882 Some bibtex entries do not have a DOI, maybe because they were entered by hand, or copied from a source that did not have it available. Here we develop some functions to help you find the DOI using Crossref.
884 Here is our example bibtex entry.
886 @article{deml-2014-oxide,
887 author = {Ann M. Deml and Vladan Stevanovi{\'c} and
888 Christopher L. Muhich and Charles B. Musgrave and
890 title = {Oxide Enthalpy of Formation and Band Gap Energy As
891 Accurate Descriptors of Oxygen Vacancy Formation
893 journal = {Energy Environ. Sci.},
898 doi = {10.1039/c3ee43874k,
899 url = {http://dx.doi.org/10.1039/c3ee43874k}},
906 The idea is to query Crossref in a way that is likely to give us a hit relevant to the entry.
908 According to http://search.crossref.org/help/api we can send a query with a free form citation that may give us something back. We do this to get a list of candidates, and run a helm command to get the doi.
911 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
912 (defun doi-utils-crossref-citation-query ()
913 "Query Crossref with the title of the bibtex entry at point to
914 get a list of possible matches. This opens a helm buffer to
915 select an entry. The default action inserts a doi and url field
916 in the bibtex entry at point. The second action opens the doi
917 url. If there is already a doi field, the function raises an
920 (bibtex-beginning-of-entry)
921 (let* ((entry (bibtex-parse-entry))
925 (unless (string= ""(reftex-get-bib-field "doi" entry))
926 (error "Entry already has a doi field"))
929 (url-retrieve-synchronously
931 "http://search.crossref.org/dois?q="
932 (url-hexify-string (org-ref-bib-citation))))
933 (setq json-string (buffer-substring url-http-end-of-headers (point-max)))
934 (setq json-data (json-read-from-string json-string)))
936 (let* ((name (format "Crossref hits for %s" (org-ref-bib-citation)))
937 (helm-candidates (mapcar (lambda (x)
940 (cdr (assoc 'fullCitation x))
942 (cdr (assoc 'doi x)))
943 (cdr (assoc 'doi x))))
945 (source `((name . ,name)
946 (candidates . ,helm-candidates)
947 ;; just return the candidate
948 (action . (("Insert doi and url field" . (lambda (doi)
949 (bibtex-make-field "doi")
951 ;; crossref returns doi url, but I prefer only a doi for the doi field
952 (insert (replace-regexp-in-string "^http://dx.doi.org/" "" doi))
953 (when (string= ""(reftex-get-bib-field "url" entry))
954 (bibtex-make-field "url")
957 ("Open url" . (lambda (doi)
958 (browse-url doi))))))))
959 (helm :sources '(source)))))
963 : doi-utils-crossref-citation-query
967 * Adding a bibtex entry from a crossref query
968 The idea here is to perform a query on Crossref, get a helm buffer of candidates, and select the entry(ies) you want to add to your bibtex file. You can select a region, e.g. a free form citation, or set of words, or you can type the query in by hand.
970 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
971 (defun doi-utils-add-entry-from-crossref-query (query bibtex-file)
975 ;; now set initial input
977 ;; If region is active assume we want it
979 (replace-regexp-in-string
981 (buffer-substring (region-beginning) (region-end))))
982 ;; type or paste it in
987 (append (f-entries "." (lambda (f) (f-ext? f "bib")))
988 org-ref-default-bibliography))))
994 (url-retrieve-synchronously
996 "http://search.crossref.org/dois?q="
997 (url-hexify-string query)))
998 (setq json-string (buffer-substring url-http-end-of-headers (point-max)))
999 (setq json-data (json-read-from-string json-string)))
1001 (let* ((name (format "Crossref hits for %s"
1002 ;; remove carriage returns. they cause problems in helm.
1003 (replace-regexp-in-string "\n" " " query)))
1004 (helm-candidates (mapcar (lambda (x)
1007 (cdr (assoc 'fullCitation x))
1009 (cdr (assoc 'doi x)))
1010 (cdr (assoc 'doi x))))
1012 (source `((name . ,name)
1013 (candidates . ,helm-candidates)
1014 ;; just return the candidate
1015 (action . (("Insert bibtex entry" . (lambda (doi)
1016 (doi-utils-add-bibtex-entry-from-doi
1017 (replace-regexp-in-string "^http://dx.doi.org/" "" doi) ,bibtex-file)))
1018 ("Open url" . (lambda (doi)
1019 (browse-url doi))))))))
1020 (helm :sources '(source)))))
1029 "doi": "http://dx.doi.org/10.1039/c3ee43874k",
1031 "normalizedScore": 100,
1032 "title": "Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics",
1033 "fullCitation": "Ann M. Deml, Vladan Stevanović, Christopher L. Muhich, Charles B. Musgrave, Ryan O'Hayre, 2014, 'Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics', <i>Energy & Environmental Science</i>, vol. 7, no. 6, p. 1996",
1034 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1039%2Fc3ee43874k&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxide+enthalpy+of+formation+and+band+gap+energy+as+accurate+descriptors+of+oxygen+vacancy+formation+energetics&rft.jtitle=Energy+%26+Environmental+Science&rft.date=2014&rft.volume=7&rft.issue=6&rft.spage=1996&rft.aufirst=Ann+M.&rft.aulast=Deml&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Ann+M.+Deml&rft.au=+Vladan+Stevanovi%C4%87&rft.au=+Christopher+L.+Muhich&rft.au=+Charles+B.+Musgrave&rft.au=+Ryan+O%27Hayre",
1038 "doi": "http://dx.doi.org/10.1103/physrevb.86.085123",
1040 "normalizedScore": 24,
1041 "title": "Composition-dependent oxygen vacancy formation in multicomponent wide-band-gap oxides",
1042 "fullCitation": "Altynbek Murat, Julia E. Medvedeva, 2012, 'Composition-dependent oxygen vacancy formation in multicomponent wide-band-gap oxides', <i>Physical Review B</i>, vol. 86, no. 8",
1043 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1103%2Fphysrevb.86.085123&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Composition-dependent+oxygen+vacancy+formation+in+multicomponent+wide-band-gap+oxides&rft.jtitle=Physical+Review+B&rft.date=2012&rft.volume=86&rft.issue=8&rft.aufirst=Altynbek&rft.aulast=Murat&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Altynbek+Murat&rft.au=+Julia+E.+Medvedeva",
1047 "doi": "http://dx.doi.org/10.1021/cm5033755",
1048 "score": 0.94063884,
1049 "normalizedScore": 20,
1050 "title": " Tunable Oxygen Vacancy Formation Energetics in the Complex Perovskite Oxide Sr x La 1– x Mn y Al 1– y O 3 ",
1051 "fullCitation": "Ann M. Deml, Vladan Stevanović, Aaron M. Holder, Michael Sanders, Ryan O’Hayre, Charles B. Musgrave, 2014, ' Tunable Oxygen Vacancy Formation Energetics in the Complex Perovskite Oxide Sr x La 1– x Mn y Al 1– y O 3 ', <i>Chemistry of Materials</i>, vol. 26, no. 22, pp. 6595-6602",
1052 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1021%2Fcm5033755&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=+Tunable+Oxygen+Vacancy+Formation+Energetics+in+the+Complex+Perovskite+Oxide+Sr++x++La++1%E2%80%93+x++Mn++y++Al++1%E2%80%93+y++O+3+&rft.jtitle=Chemistry+of+Materials&rft.date=2014&rft.volume=26&rft.issue=22&rft.spage=6595&rft.epage=6602&rft.aufirst=Ann+M.&rft.aulast=Deml&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Ann+M.+Deml&rft.au=+Vladan+Stevanovi%C4%87&rft.au=+Aaron+M.+Holder&rft.au=+Michael+Sanders&rft.au=+Ryan+O%E2%80%99Hayre&rft.au=+Charles+B.+Musgrave",
1056 "doi": "http://dx.doi.org/10.1103/physrevb.37.5905",
1058 "normalizedScore": 17,
1059 "title": "Oxygen-vacancy-formation enthalpy in YBa_{2}(Cu_{0.985}Fe_{0.015})_{3}O_{7-δ} oxide superconductor",
1060 "fullCitation": "Chuck Blue, Khaled Elgaid, Ivan Zitkovsky, P. Boolchand, Darl McDaniel, W. Joiner, Jean Oostens, Warren Huff, 1988, 'Oxygen-vacancy-formation enthalpy in YBa_{2}(Cu_{0.985}Fe_{0.015})_{3}O_{7-δ} oxide superconductor', <i>Physical Review B</i>, vol. 37, no. 10, pp. 5905-5908",
1061 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1103%2Fphysrevb.37.5905&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxygen-vacancy-formation+enthalpy+in+YBa_%7B2%7D%28Cu_%7B0.985%7DFe_%7B0.015%7D%29_%7B3%7DO_%7B7-%CE%B4%7D+oxide+superconductor&rft.jtitle=Physical+Review+B&rft.date=1988&rft.volume=37&rft.issue=10&rft.spage=5905&rft.epage=5908&rft.aufirst=Chuck&rft.aulast=Blue&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Chuck+Blue&rft.au=+Khaled+Elgaid&rft.au=+Ivan+Zitkovsky&rft.au=+P.+Boolchand&rft.au=+Darl+McDaniel&rft.au=+W.+Joiner&rft.au=+Jean+Oostens&rft.au=+Warren+Huff",
1065 "doi": "http://dx.doi.org/10.1063/1.1732384",
1067 "normalizedScore": 16,
1068 "title": "Enthalpy of Formation of Oxygen Vacancies in Barium Oxide",
1069 "fullCitation": "H. Holloway, 1962, 'Enthalpy of Formation of Oxygen Vacancies in Barium Oxide', <i>The Journal of Chemical Physics</i>, vol. 36, no. 11, p. 2820",
1070 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1063%2F1.1732384&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Enthalpy+of+Formation+of+Oxygen+Vacancies+in+Barium+Oxide&rft.jtitle=The+Journal+of+Chemical+Physics&rft.date=1962&rft.volume=36&rft.issue=11&rft.spage=2820&rft.aufirst=H.&rft.aulast=Holloway&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=H.+Holloway",
1074 "doi": "http://dx.doi.org/10.1002/crat.2170221219",
1075 "score": 0.73206276,
1076 "normalizedScore": 15,
1077 "title": "Vacancy formation enthalpy in AgZn alloys",
1078 "fullCitation": "St. Chabik, 1987, 'Vacancy formation enthalpy in AgZn alloys', <i>Crystal Research and Technology</i>, vol. 22, no. 12, pp. 1523-1527",
1079 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1002%2Fcrat.2170221219&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Vacancy+formation+enthalpy+in+AgZn+alloys&rft.jtitle=Crystal+Research+and+Technology&rft.date=1987&rft.volume=22&rft.issue=12&rft.spage=1523&rft.epage=1527&rft.aufirst=St.&rft.aulast=Chabik&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=St.+Chabik",
1083 "doi": "http://dx.doi.org/10.1007/s10562-013-0985-7",
1085 "normalizedScore": 14,
1086 "title": "Methane Oxidation by Lanthanum Oxide Doped with Cu, Zn, Mg, Fe, Nb, Ti, Zr, or Ta: The Connection Between the Activation Energy and the Energy of Oxygen-Vacancy Formation",
1087 "fullCitation": "Alan R. Derk, Bo Li, Sudhanshu Sharma, George M. Moore, Eric W. McFarland, Horia Metiu, 2013, 'Methane Oxidation by Lanthanum Oxide Doped with Cu, Zn, Mg, Fe, Nb, Ti, Zr, or Ta: The Connection Between the Activation Energy and the Energy of Oxygen-Vacancy Formation', <i>Catalysis Letters</i>, vol. 143, no. 5, pp. 406-410",
1088 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1007%2Fs10562-013-0985-7&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Methane+Oxidation+by+Lanthanum+Oxide+Doped+with+Cu%2C+Zn%2C+Mg%2C+Fe%2C+Nb%2C+Ti%2C+Zr%2C+or+Ta%3A+The+Connection+Between+the+Activation+Energy+and+the+Energy+of+Oxygen-Vacancy+Formation&rft.jtitle=Catalysis+Letters&rft.date=2013&rft.volume=143&rft.issue=5&rft.spage=406&rft.epage=410&rft.aufirst=Alan+R.&rft.aulast=Derk&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Alan+R.+Derk&rft.au=+Bo+Li&rft.au=+Sudhanshu+Sharma&rft.au=+George+M.+Moore&rft.au=+Eric+W.+McFarland&rft.au=+Horia+Metiu",
1092 "doi": "http://dx.doi.org/10.1039/c3cp55214d",
1094 "normalizedScore": 14,
1095 "title": "Oxygen vacancy formation and annihilation in lanthanum cerium oxide as a metal reactive oxide on 4H-silicon carbide",
1096 "fullCitation": "Way Foong Lim, Kuan Yew Cheong, 2014, 'Oxygen vacancy formation and annihilation in lanthanum cerium oxide as a metal reactive oxide on 4H-silicon carbide', <i>Physical Chemistry Chemical Physics</i>, vol. 16, no. 15, p. 7015",
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1101 "doi": "http://dx.doi.org/10.1021/cm052543j",
1103 "normalizedScore": 13,
1104 "title": "Energetics of Bulk and Nano-Akaganeite, β-FeOOH: Enthalpy of Formation, Surface Enthalpy, and Enthalpy of Water Adsorption",
1105 "fullCitation": "Lena Mazeina, Suraj Deore, Alexandra Navrotsky, 2006, 'Energetics of Bulk and Nano-Akaganeite, β-FeOOH: Enthalpy of Formation, Surface Enthalpy, and Enthalpy of Water Adsorption', <i>Chemistry of Materials</i>, vol. 18, no. 7, pp. 1830-1838",
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1110 "doi": "http://dx.doi.org/10.1063/1.1677897",
1112 "normalizedScore": 13,
1113 "title": "Thermochemical and Theoretical Investigations of the Sodium-Oxygen System. I. The Standard Enthalpy of Formation of Sodium Oxide (Na2O)",
1114 "fullCitation": "P. A. G. O'Hare, 1972, 'Thermochemical and Theoretical Investigations of the Sodium-Oxygen System. I. The Standard Enthalpy of Formation of Sodium Oxide (Na2O)', <i>The Journal of Chemical Physics</i>, vol. 56, no. 9, p. 4513",
1115 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1063%2F1.1677897&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Thermochemical+and+Theoretical+Investigations+of+the+Sodium-Oxygen+System.+I.+The+Standard+Enthalpy+of+Formation+of+Sodium+Oxide+%28Na2O%29&rft.jtitle=The+Journal+of+Chemical+Physics&rft.date=1972&rft.volume=56&rft.issue=9&rft.spage=4513&rft.aufirst=P.+A.+G.&rft.aulast=O%27Hare&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=P.+A.+G.+O%27Hare",
1119 "doi": "http://dx.doi.org/10.1063/1.1679492",
1121 "normalizedScore": 13,
1122 "title": "Erratum: Thermochemical and theoretical investigations of the sodium-oxygen system. I. The standard enthalpy of formation of sodium oxide (Na2O)",
1123 "fullCitation": "P. A. G. O'Hare, 1973, 'Erratum: Thermochemical and theoretical investigations of the sodium-oxygen system. I. The standard enthalpy of formation of sodium oxide (Na2O)', <i>The Journal of Chemical Physics</i>, vol. 58, no. 5, p. 2196",
1124 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1063%2F1.1679492&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Erratum%3A+Thermochemical+and+theoretical+investigations+of+the+sodium-oxygen+system.+I.+The+standard+enthalpy+of+formation+of+sodium+oxide+%28Na2O%29&rft.jtitle=The+Journal+of+Chemical+Physics&rft.date=1973&rft.volume=58&rft.issue=5&rft.spage=2196&rft.aufirst=P.+A.+G.&rft.aulast=O%27Hare&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=P.+A.+G.+O%27Hare",
1128 "doi": "http://dx.doi.org/10.1002/pssb.19680250249",
1129 "score": 0.62748235,
1130 "normalizedScore": 13,
1131 "title": "On enthalpy calculation of vacancy formation in inorganic substances",
1132 "fullCitation": "B. N. Oshcherin, 1968, 'On enthalpy calculation of vacancy formation in inorganic substances', <i>Physica Status Solidi (b)</i>, vol. 25, no. 2, pp. K123-K125",
1133 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1002%2Fpssb.19680250249&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=On+enthalpy+calculation+of+vacancy+formation+in+inorganic+substances&rft.jtitle=Physica+Status+Solidi+%28b%29&rft.date=1968&rft.volume=25&rft.issue=2&rft.spage=K123&rft.epage=K125&rft.aufirst=B.+N.&rft.aulast=Oshcherin&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=B.+N.+Oshcherin",
1137 "doi": "http://dx.doi.org/10.1002/pssb.2221040224",
1138 "score": 0.62748235,
1139 "normalizedScore": 13,
1140 "title": "Vacancy Formation Enthalpy in Cadmium by Positron Lifetime Measurements",
1141 "fullCitation": "P. Mascher, L. Breitenhuber, W. Puff, 1981, 'Vacancy Formation Enthalpy in Cadmium by Positron Lifetime Measurements', <i>physica status solidi (b)</i>, vol. 104, no. 2, pp. 601-605",
1142 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1002%2Fpssb.2221040224&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Vacancy+Formation+Enthalpy+in+Cadmium+by+Positron+Lifetime+Measurements&rft.jtitle=physica+status+solidi+%28b%29&rft.date=1981&rft.volume=104&rft.issue=2&rft.spage=601&rft.epage=605&rft.aufirst=P.&rft.aulast=Mascher&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=P.+Mascher&rft.au=+L.+Breitenhuber&rft.au=+W.+Puff",
1146 "doi": "http://dx.doi.org/10.1016/0375-9601(79)90707-2",
1147 "score": 0.62748235,
1148 "normalizedScore": 13,
1149 "title": "Vacancy formation enthalpy in γ cerium from positron annihilation",
1150 "fullCitation": "M. Boidron, R. Paulin, 1979, 'Vacancy formation enthalpy in γ cerium from positron annihilation', <i>Physics Letters A</i>, vol. 73, no. 3, pp. 200-202",
1151 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1016%2F0375-9601%2879%2990707-2&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Vacancy+formation+enthalpy+in+%CE%B3+cerium+from+positron+annihilation&rft.jtitle=Physics+Letters+A&rft.date=1979&rft.volume=73&rft.issue=3&rft.spage=200&rft.epage=202&rft.aufirst=M.&rft.aulast=Boidron&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=M.+Boidron&rft.au=+R.+Paulin",
1155 "doi": "http://dx.doi.org/10.1016/0036-9748(83)90449-0",
1156 "score": 0.62748235,
1157 "normalizedScore": 13,
1158 "title": "Estimation of the vacancy formation enthalpy of metals",
1159 "fullCitation": "Alcides R. Patete, Joachim P. Neumann, 1983, 'Estimation of the vacancy formation enthalpy of metals', <i>Scripta Metallurgica</i>, vol. 17, no. 8, pp. 1047-1048",
1160 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1016%2F0036-9748%2883%2990449-0&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Estimation+of+the+vacancy+formation+enthalpy+of+metals&rft.jtitle=Scripta+Metallurgica&rft.date=1983&rft.volume=17&rft.issue=8&rft.spage=1047&rft.epage=1048&rft.aufirst=Alcides+R.&rft.aulast=Patete&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Alcides+R.+Patete&rft.au=+Joachim+P.+Neumann",
1164 "doi": "http://dx.doi.org/10.1039/c3ja50034a",
1165 "score": 0.62469214,
1166 "normalizedScore": 13,
1167 "title": "Formation of an oxygen vacancy-dinitrogen complex in nitrogen-doped hafnium oxide",
1168 "fullCitation": "Mino Yang, Jee-Hwan Bae, Cheol-Woong Yang, Anass Benayad, Hionsuck Baik, 2013, 'Formation of an oxygen vacancy-dinitrogen complex in nitrogen-doped hafnium oxide', <i>Journal of Analytical Atomic Spectrometry</i>, vol. 28, no. 4, p. 482",
1169 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1039%2Fc3ja50034a&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Formation+of+an+oxygen+vacancy-dinitrogen+complex+in+nitrogen-doped+hafnium+oxide&rft.jtitle=Journal+of+Analytical+Atomic+Spectrometry&rft.date=2013&rft.volume=28&rft.issue=4&rft.spage=482&rft.aufirst=Mino&rft.aulast=Yang&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Mino+Yang&rft.au=+Jee-Hwan+Bae&rft.au=+Cheol-Woong+Yang&rft.au=+Anass+Benayad&rft.au=+Hionsuck+Baik",
1173 "doi": "http://dx.doi.org/10.1016/0021-9517(81)90023-3",
1174 "score": 0.62469214,
1175 "normalizedScore": 13,
1176 "title": "SCF-SW-X$alpha; calculations of the removal of oxygen from oxide surfaces by vacancy formation and crystallographic shear mechanisms",
1177 "fullCitation": "E BROCAWIK, 1981, 'SCF-SW-X$alpha; calculations of the removal of oxygen from oxide surfaces by vacancy formation and crystallographic shear mechanisms', <i>Journal of Catalysis</i>, vol. 72, no. 2, pp. 379-382",
1178 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1016%2F0021-9517%2881%2990023-3&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=SCF-SW-X%24alpha%3B+calculations+of+the+removal+of+oxygen+from+oxide+surfaces+by+vacancy+formation+and+crystallographic+shear+mechanisms&rft.jtitle=Journal+of+Catalysis&rft.date=1981&rft.volume=72&rft.issue=2&rft.spage=379&rft.epage=382&rft.aufirst=E&rft.aulast=BROCAWIK&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=E+BROCAWIK",
1182 "doi": "http://dx.doi.org/10.1063/1.2335842",
1183 "score": 0.62469214,
1184 "normalizedScore": 13,
1185 "title": "Bulk and surface oxygen vacancy formation and diffusion in single crystals, ultrathin films, and metal grown oxide structures",
1186 "fullCitation": "J. Carrasco, N. Lopez, F. Illas, H.-J. Freund, 2006, 'Bulk and surface oxygen vacancy formation and diffusion in single crystals, ultrathin films, and metal grown oxide structures', <i>The Journal of Chemical Physics</i>, vol. 125, no. 7, p. 074711",
1187 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1063%2F1.2335842&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Bulk+and+surface+oxygen+vacancy+formation+and+diffusion+in+single+crystals%2C+ultrathin+films%2C+and+metal+grown+oxide+structures&rft.jtitle=The+Journal+of+Chemical+Physics&rft.date=2006&rft.volume=125&rft.issue=7&rft.spage=074711&rft.aufirst=J.&rft.aulast=Carrasco&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=J.+Carrasco&rft.au=+N.+Lopez&rft.au=+F.+Illas&rft.au=+H.-J.+Freund",
1191 "doi": "http://dx.doi.org/10.1016/j.ijhydene.2011.12.079",
1193 "normalizedScore": 13,
1194 "title": "Oxygen vacancy formation on the Ni/Ce0.75Zr0.25O2(111) surface. A DFT+U study",
1195 "fullCitation": "Delfina GarcÃa Pintos, Alfredo Juan, Beatriz Irigoyen, 2012, 'Oxygen vacancy formation on the Ni/Ce0.75Zr0.25O2(111) surface. A DFT+U study', <i>International Journal of Hydrogen Energy</i>, vol. 37, no. 19, pp. 14937-14944",
1196 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.ijhydene.2011.12.079&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxygen+vacancy+formation+on+the+Ni%2FCe0.75Zr0.25O2%28111%29+surface.+A+DFT%2BU+study&rft.jtitle=International+Journal+of+Hydrogen+Energy&rft.date=2012&rft.volume=37&rft.issue=19&rft.spage=14937&rft.epage=14944&rft.aufirst=Delfina&rft.aulast=Garc%C3%ADa+Pintos&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Delfina+Garc%C3%ADa+Pintos&rft.au=+Alfredo+Juan&rft.au=+Beatriz+Irigoyen",
1200 "doi": "http://dx.doi.org/10.1103/physrevb.90.144105",
1202 "normalizedScore": 13,
1203 "title": "Vacancy formation enthalpy of filled <span class=\"aps-inline-formula\"><math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mi>d</mi></math></span>-band noble metals by hybrid functionals",
1204 "fullCitation": "Weiwei Xing, Peitao Liu, Xiyue Cheng, Haiyang Niu, Hui Ma, Dianzhong Li, Yiyi Li, Xing-Qiu Chen, 2014, 'Vacancy formation enthalpy of filled <span class="aps-inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML"><mi>d</mi></math></span>-band noble metals by hybrid functionals', <i>Physical Review B</i>, vol. 90, no. 14",
1205 "coins": "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1103%2Fphysrevb.90.144105&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Vacancy+formation+enthalpy+of+filled+%3Cspan+class%3D%22aps-inline-formula%22%3E%3Cmath+xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F1998%2FMath%2FMathML%22%3E%3Cmi%3Ed%3C%2Fmi%3E%3C%2Fmath%3E%3C%2Fspan%3E-band+noble+metals+by+hybrid+functionals&rft.jtitle=Physical+Review+B&rft.date=2014&rft.volume=90&rft.issue=14&rft.aufirst=Weiwei&rft.aulast=Xing&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Weiwei+Xing&rft.au=+Peitao+Liu&rft.au=+Xiyue+Cheng&rft.au=+Haiyang+Niu&rft.au=+Hui+Ma&rft.au=+Dianzhong+Li&rft.au=+Yiyi+Li&rft.au=+Xing-Qiu+Chen",
1212 #+BEGIN_SRC emacs-lisp :var data=json :results value raw :tangle no
1213 (let ((json-object-type 'plist)
1214 (json (json-read-from-string data)))
1219 ((year . 2014) (coins . ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1039%2Fc3ee43874k&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxide+enthalpy+of+formation+and+band+gap+energy+as+accurate+descriptors+of+oxygen+vacancy+formation+energetics&rft.jtitle=Energy+%26+Environmental+Science&rft.date=2014&rft.volume=7&rft.issue=6&rft.spage=1996&rft.aufirst=Ann+M.&rft.aulast=Deml&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Ann+M.+Deml&rft.au=+Vladan+Stevanovi%C4%87&rft.au=+Christopher+L.+Muhich&rft.au=+Charles+B.+Musgrave&rft.au=+Ryan+O%27Hayre) (fullCitation . Ann M. Deml, Vladan Stevanovi\304\207, Christopher L. Muhich, Charles B. Musgrave, Ryan O'Hayre, 2014, 'Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics', <i>Energy & Environmental Science</i>, vol. 7, no. 6, p. 1996) (title . Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics) (normalizedScore . 100) (score . 4.7002907) (doi . http://dx.doi.org/10.1039/c3ee43874k))
1223 Here is a list of helm candidates
1224 #+BEGIN_SRC emacs-lisp :var data=json :results code :tangle no
1225 (let (;(json-object-type 'plist)
1226 (json (json-read-from-string data)))
1227 (mapcar (lambda (x) (cons (assoc 'fullCitation x) x)) json))
1231 #+BEGIN_SRC emacs-lisp :tangle no
1233 (((fullCitation . "Ann M. Deml, Vladan Stevanovi\304\207, Christopher L. Muhich, Charles B. Musgrave, Ryan O'Hayre, 2014, 'Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics', <i>Energy & Environmental Science</i>, vol. 7, no. 6, p. 1996")
1235 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1039%2Fc3ee43874k&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxide+enthalpy+of+formation+and+band+gap+energy+as+accurate+descriptors+of+oxygen+vacancy+formation+energetics&rft.jtitle=Energy+%26+Environmental+Science&rft.date=2014&rft.volume=7&rft.issue=6&rft.spage=1996&rft.aufirst=Ann+M.&rft.aulast=Deml&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Ann+M.+Deml&rft.au=+Vladan+Stevanovi%C4%87&rft.au=+Christopher+L.+Muhich&rft.au=+Charles+B.+Musgrave&rft.au=+Ryan+O%27Hayre")
1236 (fullCitation . "Ann M. Deml, Vladan Stevanovi\304\207, Christopher L. Muhich, Charles B. Musgrave, Ryan O'Hayre, 2014, 'Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics', <i>Energy & Environmental Science</i>, vol. 7, no. 6, p. 1996")
1237 (title . "Oxide enthalpy of formation and band gap energy as accurate descriptors of oxygen vacancy formation energetics")
1238 (normalizedScore . 100)
1240 (doi . "http://dx.doi.org/10.1039/c3ee43874k"))
1241 ((fullCitation . "Altynbek Murat, Julia E. Medvedeva, 2012, 'Composition-dependent oxygen vacancy formation in multicomponent wide-band-gap oxides', <i>Physical Review B</i>, vol. 86, no. 8")
1243 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1103%2Fphysrevb.86.085123&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Composition-dependent+oxygen+vacancy+formation+in+multicomponent+wide-band-gap+oxides&rft.jtitle=Physical+Review+B&rft.date=2012&rft.volume=86&rft.issue=8&rft.aufirst=Altynbek&rft.aulast=Murat&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Altynbek+Murat&rft.au=+Julia+E.+Medvedeva")
1244 (fullCitation . "Altynbek Murat, Julia E. Medvedeva, 2012, 'Composition-dependent oxygen vacancy formation in multicomponent wide-band-gap oxides', <i>Physical Review B</i>, vol. 86, no. 8")
1245 (title . "Composition-dependent oxygen vacancy formation in multicomponent wide-band-gap oxides")
1246 (normalizedScore . 24)
1248 (doi . "http://dx.doi.org/10.1103/physrevb.86.085123"))
1249 ((fullCitation . "Ann M. Deml, Vladan Stevanovi\304\207, Aaron M. Holder, Michael Sanders, Ryan O\342\200\231Hayre, Charles B. Musgrave, 2014, ' Tunable Oxygen Vacancy Formation Energetics in the Complex Perovskite Oxide Sr x La 1\342\200\223 x Mn y Al 1\342\200\223 y O 3 ', <i>Chemistry of Materials</i>, vol. 26, no. 22, pp. 6595-6602")
1251 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1021%2Fcm5033755&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=+Tunable+Oxygen+Vacancy+Formation+Energetics+in+the+Complex+Perovskite+Oxide+Sr++x++La++1%E2%80%93+x++Mn++y++Al++1%E2%80%93+y++O+3+&rft.jtitle=Chemistry+of+Materials&rft.date=2014&rft.volume=26&rft.issue=22&rft.spage=6595&rft.epage=6602&rft.aufirst=Ann+M.&rft.aulast=Deml&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Ann+M.+Deml&rft.au=+Vladan+Stevanovi%C4%87&rft.au=+Aaron+M.+Holder&rft.au=+Michael+Sanders&rft.au=+Ryan+O%E2%80%99Hayre&rft.au=+Charles+B.+Musgrave")
1252 (fullCitation . "Ann M. Deml, Vladan Stevanovi\304\207, Aaron M. Holder, Michael Sanders, Ryan O\342\200\231Hayre, Charles B. Musgrave, 2014, ' Tunable Oxygen Vacancy Formation Energetics in the Complex Perovskite Oxide Sr x La 1\342\200\223 x Mn y Al 1\342\200\223 y O 3 ', <i>Chemistry of Materials</i>, vol. 26, no. 22, pp. 6595-6602")
1253 (title . " Tunable Oxygen Vacancy Formation Energetics in the Complex Perovskite Oxide Sr x La 1\342\200\223 x Mn y Al 1\342\200\223 y O 3 ")
1254 (normalizedScore . 20)
1255 (score . 0.94063884)
1256 (doi . "http://dx.doi.org/10.1021/cm5033755"))
1257 ((fullCitation . "Chuck Blue, Khaled Elgaid, Ivan Zitkovsky, P. Boolchand, Darl McDaniel, W. Joiner, Jean Oostens, Warren Huff, 1988, 'Oxygen-vacancy-formation enthalpy in YBa_{2}(Cu_{0.985}Fe_{0.015})_{3}O_{7-\316\264} oxide superconductor', <i>Physical Review B</i>, vol. 37, no. 10, pp. 5905-5908")
1259 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1103%2Fphysrevb.37.5905&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxygen-vacancy-formation+enthalpy+in+YBa_%7B2%7D%28Cu_%7B0.985%7DFe_%7B0.015%7D%29_%7B3%7DO_%7B7-%CE%B4%7D+oxide+superconductor&rft.jtitle=Physical+Review+B&rft.date=1988&rft.volume=37&rft.issue=10&rft.spage=5905&rft.epage=5908&rft.aufirst=Chuck&rft.aulast=Blue&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Chuck+Blue&rft.au=+Khaled+Elgaid&rft.au=+Ivan+Zitkovsky&rft.au=+P.+Boolchand&rft.au=+Darl+McDaniel&rft.au=+W.+Joiner&rft.au=+Jean+Oostens&rft.au=+Warren+Huff")
1260 (fullCitation . "Chuck Blue, Khaled Elgaid, Ivan Zitkovsky, P. Boolchand, Darl McDaniel, W. Joiner, Jean Oostens, Warren Huff, 1988, 'Oxygen-vacancy-formation enthalpy in YBa_{2}(Cu_{0.985}Fe_{0.015})_{3}O_{7-\316\264} oxide superconductor', <i>Physical Review B</i>, vol. 37, no. 10, pp. 5905-5908")
1261 (title . "Oxygen-vacancy-formation enthalpy in YBa_{2}(Cu_{0.985}Fe_{0.015})_{3}O_{7-\316\264} oxide superconductor")
1262 (normalizedScore . 17)
1264 (doi . "http://dx.doi.org/10.1103/physrevb.37.5905"))
1265 ((fullCitation . "H. Holloway, 1962, 'Enthalpy of Formation of Oxygen Vacancies in Barium Oxide', <i>The Journal of Chemical Physics</i>, vol. 36, no. 11, p. 2820")
1267 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1063%2F1.1732384&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Enthalpy+of+Formation+of+Oxygen+Vacancies+in+Barium+Oxide&rft.jtitle=The+Journal+of+Chemical+Physics&rft.date=1962&rft.volume=36&rft.issue=11&rft.spage=2820&rft.aufirst=H.&rft.aulast=Holloway&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=H.+Holloway")
1268 (fullCitation . "H. Holloway, 1962, 'Enthalpy of Formation of Oxygen Vacancies in Barium Oxide', <i>The Journal of Chemical Physics</i>, vol. 36, no. 11, p. 2820")
1269 (title . "Enthalpy of Formation of Oxygen Vacancies in Barium Oxide")
1270 (normalizedScore . 16)
1272 (doi . "http://dx.doi.org/10.1063/1.1732384"))
1273 ((fullCitation . "St. Chabik, 1987, 'Vacancy formation enthalpy in AgZn alloys', <i>Crystal Research and Technology</i>, vol. 22, no. 12, pp. 1523-1527")
1275 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1002%2Fcrat.2170221219&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Vacancy+formation+enthalpy+in+AgZn+alloys&rft.jtitle=Crystal+Research+and+Technology&rft.date=1987&rft.volume=22&rft.issue=12&rft.spage=1523&rft.epage=1527&rft.aufirst=St.&rft.aulast=Chabik&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=St.+Chabik")
1276 (fullCitation . "St. Chabik, 1987, 'Vacancy formation enthalpy in AgZn alloys', <i>Crystal Research and Technology</i>, vol. 22, no. 12, pp. 1523-1527")
1277 (title . "Vacancy formation enthalpy in AgZn alloys")
1278 (normalizedScore . 15)
1279 (score . 0.73206276)
1280 (doi . "http://dx.doi.org/10.1002/crat.2170221219"))
1281 ((fullCitation . "Alan R. Derk, Bo Li, Sudhanshu Sharma, George M. Moore, Eric W. McFarland, Horia Metiu, 2013, 'Methane Oxidation by Lanthanum Oxide Doped with Cu, Zn, Mg, Fe, Nb, Ti, Zr, or Ta: The Connection Between the Activation Energy and the Energy of Oxygen-Vacancy Formation', <i>Catalysis Letters</i>, vol. 143, no. 5, pp. 406-410")
1283 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1007%2Fs10562-013-0985-7&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Methane+Oxidation+by+Lanthanum+Oxide+Doped+with+Cu%2C+Zn%2C+Mg%2C+Fe%2C+Nb%2C+Ti%2C+Zr%2C+or+Ta%3A+The+Connection+Between+the+Activation+Energy+and+the+Energy+of+Oxygen-Vacancy+Formation&rft.jtitle=Catalysis+Letters&rft.date=2013&rft.volume=143&rft.issue=5&rft.spage=406&rft.epage=410&rft.aufirst=Alan+R.&rft.aulast=Derk&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Alan+R.+Derk&rft.au=+Bo+Li&rft.au=+Sudhanshu+Sharma&rft.au=+George+M.+Moore&rft.au=+Eric+W.+McFarland&rft.au=+Horia+Metiu")
1284 (fullCitation . "Alan R. Derk, Bo Li, Sudhanshu Sharma, George M. Moore, Eric W. McFarland, Horia Metiu, 2013, 'Methane Oxidation by Lanthanum Oxide Doped with Cu, Zn, Mg, Fe, Nb, Ti, Zr, or Ta: The Connection Between the Activation Energy and the Energy of Oxygen-Vacancy Formation', <i>Catalysis Letters</i>, vol. 143, no. 5, pp. 406-410")
1285 (title . "Methane Oxidation by Lanthanum Oxide Doped with Cu, Zn, Mg, Fe, Nb, Ti, Zr, or Ta: The Connection Between the Activation Energy and the Energy of Oxygen-Vacancy Formation")
1286 (normalizedScore . 14)
1288 (doi . "http://dx.doi.org/10.1007/s10562-013-0985-7"))
1289 ((fullCitation . "Way Foong Lim, Kuan Yew Cheong, 2014, 'Oxygen vacancy formation and annihilation in lanthanum cerium oxide as a metal reactive oxide on 4H-silicon carbide', <i>Physical Chemistry Chemical Physics</i>, vol. 16, no. 15, p. 7015")
1291 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1039%2Fc3cp55214d&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Oxygen+vacancy+formation+and+annihilation+in+lanthanum+cerium+oxide+as+a+metal+reactive+oxide+on+4H-silicon+carbide&rft.jtitle=Physical+Chemistry+Chemical+Physics&rft.date=2014&rft.volume=16&rft.issue=15&rft.spage=7015&rft.aufirst=Way+Foong&rft.aulast=Lim&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Way+Foong+Lim&rft.au=+Kuan+Yew+Cheong")
1292 (fullCitation . "Way Foong Lim, Kuan Yew Cheong, 2014, 'Oxygen vacancy formation and annihilation in lanthanum cerium oxide as a metal reactive oxide on 4H-silicon carbide', <i>Physical Chemistry Chemical Physics</i>, vol. 16, no. 15, p. 7015")
1293 (title . "Oxygen vacancy formation and annihilation in lanthanum cerium oxide as a metal reactive oxide on 4H-silicon carbide")
1294 (normalizedScore . 14)
1296 (doi . "http://dx.doi.org/10.1039/c3cp55214d"))
1297 ((fullCitation . "Lena Mazeina, Suraj Deore, Alexandra Navrotsky, 2006, 'Energetics of Bulk and Nano-Akaganeite, \316\262-FeOOH:\302\240 Enthalpy of Formation, Surface Enthalpy, and Enthalpy of Water Adsorption', <i>Chemistry of Materials</i>, vol. 18, no. 7, pp. 1830-1838")
1299 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1021%2Fcm052543j&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Energetics+of+Bulk+and+Nano-Akaganeite%2C+%CE%B2-FeOOH%3A%C2%A0+Enthalpy+of+Formation%2C+Surface+Enthalpy%2C+and+Enthalpy+of+Water+Adsorption&rft.jtitle=Chemistry+of+Materials&rft.date=2006&rft.volume=18&rft.issue=7&rft.spage=1830&rft.epage=1838&rft.aufirst=Lena&rft.aulast=Mazeina&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=Lena+Mazeina&rft.au=+Suraj+Deore&rft.au=+Alexandra+Navrotsky")
1300 (fullCitation . "Lena Mazeina, Suraj Deore, Alexandra Navrotsky, 2006, 'Energetics of Bulk and Nano-Akaganeite, \316\262-FeOOH:\302\240 Enthalpy of Formation, Surface Enthalpy, and Enthalpy of Water Adsorption', <i>Chemistry of Materials</i>, vol. 18, no. 7, pp. 1830-1838")
1301 (title . "Energetics of Bulk and Nano-Akaganeite, \316\262-FeOOH:\302\240 Enthalpy of Formation, Surface Enthalpy, and Enthalpy of Water Adsorption")
1302 (normalizedScore . 13)
1304 (doi . "http://dx.doi.org/10.1021/cm052543j"))
1305 ((fullCitation . "P. A. G. O'Hare, 1972, 'Thermochemical and Theoretical Investigations of the Sodium-Oxygen System. I. The Standard Enthalpy of Formation of Sodium Oxide (Na2O)', <i>The Journal of Chemical Physics</i>, vol. 56, no. 9, p. 4513")
1307 (coins . "ctx_ver=Z39.88-2004&rft_id=info%3Adoi%2Fhttp%3A%2F%2Fdx.doi.org%2F10.1063%2F1.1677897&rfr_id=info%3Asid%2Fcrossref.org%3Asearch&rft.atitle=Thermochemical+and+Theoretical+Investigations+of+the+Sodium-Oxygen+System.+I.+The+Standard+Enthalpy+of+Formation+of+Sodium+Oxide+%28Na2O%29&rft.jtitle=The+Journal+of+Chemical+Physics&rft.date=1972&rft.volume=56&rft.issue=9&rft.spage=4513&rft.aufirst=P.+A.+G.&rft.aulast=O%27Hare&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.au=P.+A.+G.+O%27Hare")
1308 (fullCitation . "P. A. G. O'Hare, 1972, 'Thermochemical and Theoretical Investigations of the Sodium-Oxygen System. I. The Standard Enthalpy of Formation of Sodium Oxide (Na2O)', <i>The Journal of Chemical Physics</i>, vol. 56, no. 9, p. 4513")
1309 (title . "Thermochemical and Theoretical Investigations of the Sodium-Oxygen System. I. The Standard Enthalpy of Formation of Sodium Oxide (Na2O)")
1310 (normalizedScore . 13)
1312 (doi . "http://dx.doi.org/10.1063/1.1677897"))
1318 These are not really doi utilities, but for now I am putting them here.
1320 I found this on the web. It can be handy, but the bibtex entry has a lot of stuff in it.
1322 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
1323 (defun isbn-to-bibtex-lead (isbn)
1324 "Search lead.to for ISBN bibtex entry. You have to copy the entry if it is on the page to your bibtex file."
1325 (interactive "sISBN: ")
1327 (format "http://lead.to/amazon/en/?key=%s+&si=all&op=bt&bn=&so=sa&ht=us" isbn)))
1330 Here we get isbn metadata and build a bibtex entry.
1331 http://xisbn.worldcat.org/xisbnadmin/doc/api.htm#getmetadata
1334 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
1335 (defun isbn-to-bibtex (isbn bibfile)
1336 "Get bibtex entry for ISBN and insert it into BIBFILE unless an
1337 entry with the generated key already exists in the file."
1342 ;; now set initial input
1344 ;; If region is active and it starts with a number, we use it
1345 ((and (region-active-p)
1346 (s-match "^[0-9]" (buffer-substring (region-beginning) (region-end))))
1347 (buffer-substring (region-beginning) (region-end)))
1348 ;; if first entry in kill ring starts with a number assume it is an isbn
1349 ;; and use it as the guess
1350 ((if (s-match "^[0-9]" (car kill-ring))
1352 ;; type or paste it in
1355 (ido-completing-read
1357 (append (f-entries "." (lambda (f) (f-ext? f "bib")))
1358 org-ref-default-bibliography))))
1360 (let* ((results (with-current-buffer
1361 (url-retrieve-synchronously
1363 "http://xisbn.worldcat.org/webservices/xid/isbn/%s?method=getMetadata&format=json&fl=*"
1365 (json-read-from-string
1366 (buffer-substring url-http-end-of-headers (point-max)))))
1367 (status (cdr (nth 1 results)))
1368 (metadata (aref (cdar results) 0))
1372 ;; check if we got something
1373 (unless (string= "ok" status)
1374 (error "Status is %s" status))
1376 ;; construct an alphabetically sorted bibtex entry. I assume ISBN numbers go
1377 ;; with book entries.
1379 (concat "\n@book{,\n"
1382 (loop for field in (-sort 'string-lessp (mapcar 'car metadata))
1384 (format " %s={%s}," field (cdr (assoc field metadata))))
1388 ;; build entry in temp buffer to get the key so we can check for duplicates
1389 (setq new-entry (with-temp-buffer
1391 (org-ref-clean-bibtex-entry)
1392 (setq new-key (bibtex-key-in-head))
1395 (goto-char (point-min))
1396 (when (search-forward new-key nil t)
1398 (setq new-key (read-input
1399 (format "%s already exists. Enter new key (C-g to cancel): " new-key)
1401 (goto-char (point-max))
1403 ;; set key. It is simplest to just replace it, even if it is the same.
1404 (bibtex-beginning-of-entry)
1405 (re-search-forward bibtex-entry-maybe-empty-head)
1406 (if (match-beginning bibtex-key-in-head)
1407 (delete-region (match-beginning bibtex-key-in-head)
1408 (match-end bibtex-key-in-head)))
1417 #+BEGIN_SRC emacs-lisp :tangle doi-utils.el
1418 (provide 'doi-utils)
1421 #+BEGIN_SRC emacs-lisp :tangle no
1422 (org-babel-load-file "doi-utils.org")
1426 : Loaded doi-utils.el