How I Use ObsidianMD and Zotero For Academic Research — Transcript

Full transcript

1. 0:02hey hi hello guys and welcome back to
2. 0:06another video in this video i'm going to
3. 0:08be going through how i use zotero and
4. 0:13obsidian for my literature notes
5. 0:15and for organizing my literature the
6. 0:17ideas of behind this video uh came from
7. 0:20a live stream of holly's that i attended
8. 0:22where people were talking about their
9. 0:24ways of organizing literature and
10. 0:26organizing notes etc and someone was
11. 0:29saying that
12. 0:30um they're a bit scared of obsidian
13. 0:32because of the coding aspect and i want
14. 0:34to put this out there because
15. 0:36a lot of the youtube videos that exist
16. 0:38about obsidian that do have some sort of
17. 0:40code in them or are clearly made by
18. 0:43people they're not phased by code um i'm
19. 0:45absolutely terrified of code so i very
20. 0:49deliberately do not have any of that
21. 0:50going on so i think if this is a setup
22. 0:52that's all i can do
23. 0:54and i can get on with i think most
24. 0:56people will be able to get on with it as
25. 0:58well the zotero bit of this is more
26. 1:02background um i won't go into too much
27. 1:04detail about zotero but it is necessary
28. 1:07to sort of bring that in just because it
29. 1:09ties into the way i do things in
30. 1:10obsidian i won't go through any of the
31. 1:12tacky bits on how i set up my zotero i
32. 1:14will link an excellent guide in the
33. 1:16description because i quite frankly
34. 1:18don't know what i'm doing i'll leave
35. 1:20that to other more capable people uh but
36. 1:22i'll sort of take you through quickly my
37. 1:24my setup i have a little key down here
38. 1:26at the side uh i use emojis for sort of
39. 1:28statuses etc books that i have yet to
40. 1:33read
41. 1:34are
42. 1:35orange if i dnf them don't finish them
43. 1:38they're marked as red if i finish them
44. 1:40they're green if i need to find you know
45. 1:43a way to read the book whether that's a
46. 1:44pdf or a physical copy i've got the
47. 1:46stack of books
48. 1:48if it's something i think is relevant
49. 1:50enough and important enough that i want
50. 1:52to take notes on it it's marked with
51. 1:54these uh nuts
52. 1:56if it's something i don't think is
53. 1:58important enough to take notes uh on
54. 2:01at this junction then it's these brown
55. 2:03leaves and if it's something i have
56. 2:04taken notes on it is green leaves as my
57. 2:07other tags i just try to be liberal
58. 2:10tag anything that i can think of um
59. 2:13and not be too worried about it
60. 2:16for now i only have one
61. 2:19folder i also have an inbox folder where
62. 2:21if i just need to
63. 2:23cite something quickly uh and i don't
64. 2:25want to worry about how we can do the
65. 2:26metadata and like break up my workflow
66. 2:28i'll just
67. 2:29dump it in here deal with it later i use
68. 2:32two extensions for my zotero i use a
69. 2:35better bibtex nate's sop file
70. 2:38soft file i use to send a pdfs from my
71. 2:42zotero to my ipad where i will annotate
72. 2:45and highlight them in pdf expert
73. 2:49sort file then
74. 2:50syncs that pdf back to zotero so that i
75. 2:53can access my
76. 2:55highlights and my notes on the pdf in
77. 2:57zotero this was a change i made from
78. 3:01using
79. 3:02good notes and onenote because i ended
80. 3:04up having multiple versions of the same
81. 3:07article in multiple places this workflow
82. 3:10stems from wanting to have things in as
83. 3:13few places as possible that's why i use
84. 3:14stock file to to make sure that
85. 3:16everything comes back to zotero and why
86. 3:19i've linked my zotero with my obsidian
87. 3:21so that i'm not duplicating things
88. 3:23better bibtex generates this
89. 3:27citation key i think zotero has citation
90. 3:31keys otherwise as well but all the
91. 3:33guides recommended to use the better bib
92. 3:36text one so that's what i'm doing the
93. 3:38only thing you need to know about
94. 3:41this beyond the guide whatever that's
95. 3:43relevant to like my setup is that this
96. 3:46is the citation key format i use and it
97. 3:48basically means that the citation key
98. 3:51will be
99. 3:53the author last name and the year if
100. 3:56there are two authors it'll be both of
101. 3:58their last names separated by dot and
102. 4:00then the year
103. 4:01and if there are more than that it'll be
104. 4:03just the first author
105. 4:05dot l and then the year
106. 4:08and
107. 4:09i've set this up to liberty because this
108. 4:10is how i've set it up in obsidian as
109. 4:13well which is important um because they
110. 4:16link it together so that's sort of
111. 4:18briefly how my cetera is set up and i'm
112. 4:21going to take you over to obsidian so
113. 4:24this is my obsidian i've already got
114. 4:26this set up so this is not going to be a
115. 4:29solve when you first open obsidian
116. 4:31here's what you do other people have
117. 4:33done that and they've done it far better
118. 4:34than me so i'm going to leave some
119. 4:37excellent really basic introduction
120. 4:39videos linked down below just to sort of
121. 4:42get you into like how does this program
122. 4:44work and then so once you know the
123. 4:47basics this is how i've set mine up for
124. 4:50an academic purpose and
125. 4:52without using any coding let's start
126. 4:53with aesthetics the funnest bit uh the
127. 4:56biggest rabbit hole of them all as you
128. 4:58can see i'm not a dark mage person
129. 5:01currently i'm not opposed to a bit of
130. 5:02dark mode but in the minute i find a
131. 5:04like soft cream
132. 5:06light mode the way to go so i will show
133. 5:09you the
134. 5:10theme that i use um
135. 5:14it's the minimal theme which i really
136. 5:16like i think it's excellent
137. 5:18but i use the style settings
138. 5:22plugin to edit the theme
139. 5:25which is excellent i will leave all of
140. 5:28the details of how i've got mine set up
141. 5:30below
142. 5:31um i've got a little pink accent color
143. 5:34going on this is the base uh
144. 5:36color that i use
145. 5:38and then only other thing that's really
146. 5:42really important to me
147. 5:45theme wise is to have italics
148. 5:48as a standout color because i usually
149. 5:51use italic when i've got
150. 5:54some thoughts uh on an article versus
151. 5:57what was in the art so i want to be able
152. 5:59to see my notes my own notes clearly um
153. 6:03so the italic text color is really
154. 6:05important to me while we're in here
155. 6:07let's talk about the plugins that i use
156. 6:10these are the plugins that i use so all
157. 6:14of my login are
158. 6:16community or core plugins i don't have
159. 6:19any like github things going on again
160. 6:22it's a little bit advanced for me so i
161. 6:25just get my plugins from from the
162. 6:27community plugins page and these are the
163. 6:29ones that i currently have downloaded i
164. 6:31won't go through them but the only
165. 6:33plugin we're going to talk about at
166. 6:35length because it's the key to this
167. 6:36workflow is the citations plugin what
168. 6:39the citations plugin uh relies on is an
169. 6:42export of your zotero library so in
170. 6:45zotero you just go to file click export
171. 6:48library
172. 6:49exporters better double attacks again
173. 6:52that's that plugin uh i've got installed
174. 6:55and then you check keep updated then you
175. 6:57save that wherever your vault your
176. 7:00obsidian vault is saved um and you save
177. 7:03it in your obsidian role so it'll be
178. 7:05within your phd
179. 7:07within my phd vault it's the zotero file
180. 7:10and that's just what i named it keeps
181. 7:12things easy then
182. 7:14here you can create a
183. 7:16folder if you want all of your
184. 7:18literature notes to go into a folder
185. 7:20i've made mine uh literature notes and
186. 7:23whenever i create a new uh
187. 7:25note using this plugin
188. 7:27this is where it's saved then you can
189. 7:29set up a template for your literature
190. 7:30notes which i've done and i love it and
191. 7:33these are the properties that you can
192. 7:35include in your template mine's very
193. 7:38simple what i've done is uh the site key
194. 7:41just asked the title and that is this uh
195. 7:44again this is what i showed earlier with
196. 7:46the better bib text
197. 7:48why that is important and why that
198. 7:50format is important
199. 7:52is because it links through to the
200. 7:55titles uh of my literature notes then
201. 7:58for the actual template of of the the
202. 8:02note
203. 8:02uh i just have like metadata up here so
204. 8:05it gives me the title of the paper
205. 8:07the authors of the paper the year was
206. 8:09published and the link to the zotero
207. 8:13entry and then i like to have a status
208. 8:16which is the status like the emojis that
209. 8:19i showed you in zotero earlier
210. 8:21uh i tag them here and then i link it to
211. 8:24any other notes that i think might be
212. 8:27relevant as i put it in so i've got a
213. 8:28little area for links then i write
214. 8:31myself a little abstract i'll show you
215. 8:33how this looks actually in a note um but
216. 8:36i've got a heading for that and then
217. 8:38i've got heading for
218. 8:39any notes from the paper and then i've
219. 8:41got a heading for references from that
220. 8:43paper to check out but obviously this
221. 8:45looks funky if you want to replicate
222. 8:47that i can write that out in the
223. 8:48description as well but i will show you
224. 8:50how it looks so this is how i've got my
225. 8:52folder structure set up you don't need
226. 8:54folders in obsidian but i like to have
227. 8:56some level of folders just to keep it a
228. 8:58bit tidier so this is the folder that my
229. 9:01literature notes get saved into which
230. 9:03you saw
231. 9:04in the plugin setup let me show you this
232. 9:07one which i know there's plenty in so
233. 9:09this is what gets automatically
234. 9:11populated in the template like i showed
235. 9:14you with the title the author the year
236. 9:16and the zotero link
237. 9:18then i've added the relevant tags i've
238. 9:21finished the book i've taken notes and
239. 9:23then
240. 9:24this little paper clip is anything
241. 9:26literature related
242. 9:27just to keep my uh my meta bets my
243. 9:31document drafts and my daily notes
244. 9:34out of my graph you which i will show
245. 9:36you later again just a little abstract
246. 9:38not a scientific abstract at all just
247. 9:40like
248. 9:41a summary for myself
249. 9:43and then uh in this little code block i
250. 9:46just put in like how it's relevant to me
251. 9:48basically so that's the abstract bit
252. 9:51then under notes i
253. 9:53usually again
254. 9:54my own thoughts are in yellow then i
255. 9:56usually just
256. 9:58add quotes and i make sure to add the
257. 10:00page number so i can easily find them
258. 10:02again
259. 10:04um
260. 10:07so for the references to checkout
261. 10:09section we're going to move into another
262. 10:10article that's got a bit more in it um
263. 10:12and that's because this section
264. 10:17is currently basically the backbone of
265. 10:20my entire workflow so what drew me to
266. 10:23obsidian was the ability to link things
267. 10:27together obviously when you're doing a
268. 10:29literature review like it's so difficult
269. 10:30to sort of see how all of it fits
270. 10:33together how all of the different papers
271. 10:36fit together and
272. 10:37who's citing who and everything like
273. 10:39that so i wanted a way to link things
274. 10:42together
275. 10:43and i've see is coming clutch it gets a
276. 10:46little bit complicated just to explain
277. 10:48not really to understand so remember the
278. 10:50site which is generated in this format
279. 10:52because it's an easy format for me and
280. 10:55you know it looks it looks a lot like an
281. 10:57in-text citation right walker 2011. like
282. 10:59that's how you would cite something in a
283. 11:01paper uh if you're using insert in-text
284. 11:04citations right not like footnotes or
285. 11:06anything like that so it's an easy
286. 11:08intuitive thing for me to remember so
287. 11:10obviously that
288. 11:12links through to the way i got the
289. 11:15citation plugin set up and that the
290. 11:17title of the literature
291. 11:18note will just be the site key so that
292. 11:21means that if i see a citation in a
293. 11:22paper
294. 11:23say zimmerman 2015
295. 11:27and i think oh that's important okay
296. 11:29i'll write out what the paper says about
297. 11:31this and then i'll cite it like this and
298. 11:33i'll use the double square brackets
299. 11:36which in obsidian creates a link to this
300. 11:38note i'll do this for all the papers
301. 11:41that i think might be relevant i don't
302. 11:44know whether i've already read this
303. 11:46paper whether i've already cited this
304. 11:48paper whether i already have a note for
305. 11:50this paper but i don't
306. 11:52need to because this format is going to
307. 11:54be the same regardless so i'll put this
308. 11:56in and if it happens that i already have
309. 11:59a literature note
310. 12:01for this paper this will be the title of
311. 12:03that note i do actually have in it for
312. 12:05this paper already so if i click on this
313. 12:08it goes into that note which is
314. 12:10excellent because now these two papers
315. 12:13are linked together but equally if i
316. 12:16don't have a reference
317. 12:17for the paper say this one it will
318. 12:19create a new note with that title but
319. 12:22what will also happen is that when i do
320. 12:24these notes and i put these links in
321. 12:27it doesn't matter if when i do that i
322. 12:30don't have a note with this title
323. 12:33if i later add a note with this title
324. 12:35then that link will work so that's why
325. 12:38it's so important for the site key to be
326. 12:40really easy really snappy is that i can
327. 12:42write it out myself and it'll be the
328. 12:45same when the paper is generated and
329. 12:47added because that means that the links
330. 12:50that i've set up when i'm taking notes
331. 12:52from a paper initially will
332. 12:55work and will automatically links with
333. 12:57future papers that i add let me know in
334. 12:59the comments if that don't make sense
335. 13:01but i think it's more intuitive if you
336. 13:03try to do it so let me give you an
337. 13:06example of how this works so for example
338. 13:09old road 2007 i don't currently have a
339. 13:12note for him i've just
340. 13:15cited that if i'd now read albright 2007
341. 13:18i was ready to take some notes on that
342. 13:20i'm going to do the hotkey that i've set
343. 13:22up for my
344. 13:24citations plugin you manage all of that
345. 13:26in the hotkeys tab in the settings and
346. 13:28this will bring up the search bar
347. 13:32and it searches in the export of your
348. 13:34zotero library
349. 13:36that you've saved in your obsidian so
350. 13:38i'm going to search for aldride find the
351. 13:412007
352. 13:42and that
353. 13:44has now generated
354. 13:46a
355. 13:47new literature note it's that template
356. 13:49we saw earlier it's all blank ready to
357. 13:51be filled out ready to be taken notes on
358. 13:54so if we say
359. 13:56hello
360. 13:57this is an article
361. 14:01excellent great we love that
362. 14:03if we now go back to
363. 14:05this one where we initially found our
364. 14:09old 2007
365. 14:11citation
366. 14:13if i now click on that link i haven't
367. 14:15done anything to this i haven't updated
368. 14:17this link in any way i haven't indicated
369. 14:19that i've no made a note of it
370. 14:22it now links automatically to this new
371. 14:25note i hope that illustrates
372. 14:27why doing these links right is so
373. 14:29important because it means that you're
374. 14:31future proofing them so if i now if i
375. 14:34ever
376. 14:35go back and i read and take notes on any
377. 14:39of the articles that i cited in any of
378. 14:42these articles i've already done notes
379. 14:43on they will link together down here at
380. 14:46the bottom you can actually see if
381. 14:47there's any backlinks so you can see any
382. 14:50of your other notes that link to this
383. 14:52current note which is excellent and you
384. 14:54can click through and find it
385. 14:57but the way i really like seeing the
386. 15:01links
387. 15:02in practice
388. 15:03is the graph view
389. 15:06it looks a little bit insane
390. 15:10currently
391. 15:12so what is so cool about this is these
392. 15:15pink
393. 15:17dots they are
394. 15:19my
395. 15:20literature notes
396. 15:22in here and all of these little
397. 15:27sort of brown dots
398. 15:29they are
399. 15:31articles cited
400. 15:33by these articles
401. 15:35that i haven't yet created notes for if
402. 15:38i hover over any one of these i can see
403. 15:42all of the notes that
404. 15:45it links to so i can see links between 7
405. 15:482015 and any pink notes which are
406. 15:51obviously the articles i have taken
407. 15:53notes on but i can also see any articles
408. 15:54they haven't taken notes on yet so
409. 15:57this
410. 15:58one
411. 15:59this one they're all waiting to be
412. 16:01taking notes on and where this becomes
413. 16:03really useful is
414. 16:05for planning my future reading so if i
415. 16:09hover over
416. 16:10this note here it links to this note
417. 16:13over here and that links not only to
418. 16:15this note but also to this note
419. 16:18which means that i should probably read
420. 16:20this article because two articles i've
421. 16:22already read cites this article that's
422. 16:25where my little next list
423. 16:27comes in
424. 16:28uh
425. 16:29any
426. 16:30um
427. 16:31citations that i see have been made by
428. 16:33multiple articles i've read i will pop
429. 16:36on my reading list or if i've already
430. 16:38read it i'll pop it on my note taking
431. 16:39list obviously this is super like
432. 16:44excessive at this point i need to sort
433. 16:45my graph you out of it because it is a
434. 16:47little bit uh
435. 16:49insane um
436. 16:51but this is how i'm doing
437. 16:53my literature
438. 16:55search
439. 16:56basically
440. 16:57is i'm just going through and seeing
441. 17:01what
442. 17:02is connected and which notes
443. 17:05are cited by multiple papers
444. 17:08um
445. 17:12so there's a couple here that's cited by
446. 17:15uh multiple papers and this is why i
447. 17:19really like the linking feature is that
448. 17:22you can see links in the literature you
449. 17:25can also click into any one note and
450. 17:27find see the graph you just for that
451. 17:30note um
452. 17:32obviously this one's a bit excessive
453. 17:35because there's a lot of articles cited
454. 17:36and you can change uh
455. 17:39like how so
456. 17:41if it's just one then it's just the
457. 17:43notes that link to the notes you've got
458. 17:47open
459. 17:48as if you go up to two it's also any
460. 17:50notes that link two
461. 17:52notes linked to this article which is
462. 17:55obviously an easier way to see it than
463. 17:56like having all your notes from all your
464. 17:58articles
465. 18:00and it gives you more
466. 18:02of an obvious like
467. 18:04web that's easier to follow to see these
468. 18:06connections
469. 18:08so that's how i use obsidian for my
470. 18:10workflow but yeah obviously i'm still
471. 18:12working on all of this like it's not
472. 18:14done
473. 18:14by any means and i'm sure it'll change
474. 18:17uh as i work through it but this is this
475. 18:20is all i'm doing there's no coding
476. 18:22anywhere here and i think there's even
477. 18:25some uh some plugins floating around now
478. 18:29where
479. 18:30i think i saw one i'll link it below
480. 18:32which uh basically uh gives you like a
481. 18:34pop-up
482. 18:35like toolbar almost for like for rich
483. 18:38text so you don't even have to do like
484. 18:40the hashes for titles so it's definitely
485. 18:43getting like you don't have to do any
486. 18:45sort of markdown bits but yeah that's my
487. 18:48setup i hope
488. 18:49it was useful and definitely check out
489. 18:52the links in the description uh i'm
490. 18:53gonna try and absolutely overload the
491. 18:55description box with with stuff that i
492. 18:58found useful in researching obsidian and
493. 19:01everything like that there's also a
494. 19:02discord as well as the obsidian forums
495. 19:04but i just wanted to show
496. 19:07that even if you don't do the coding bit
497. 19:09it can still
498. 19:10give you some really powerful tools so
499. 19:13we're gonna leave it there like i said
500. 19:15if anything didn't make sense or if you
501. 19:16have any other questions about how i do
502. 19:18stuff definitely let me know in the
503. 19:19comments or you know ping me on
504. 19:21instagram or something and
505. 19:23i will try to explain what i do but yeah
506. 19:27i hope it's been useful i hope you can
507. 19:28take something from this uh maybe try it
508. 19:31out for yourself and yeah that is going
509. 19:34to be it for this video i will see you
510. 19:36next time i guess until then
511. 19:38take