Retrieving Full-Text PDFs | HubMeta Tutorial #11 — Transcript

Full transcript

1. 0:15Okay, now that we have finished
2. 0:18screening all the articles in the title
3. 0:21scan, which is equivalent to Prisma's
4. 0:24title and abstract screening, we can now
5. 0:28move on to the next step, which is
6. 0:31fetching the PDFs of these articles.
7. 0:35This is arguably one of the most
8. 0:37difficult, one of the most laborious
9. 0:39parts of the process because it's just
10. 0:43honestly
11. 0:45there are not a lot of good ways of
12. 0:48doing this. It usually takes a lot of
13. 0:50manual work involved. However, I'll show
14. 0:54you briefly how we have implemented
15. 0:58automatic PDF download inside Hub Meta.
16. 1:01So, we have a few options here. First of
17. 1:04all, know that when you are in this
18. 1:06page, as we have said here,
19. 1:09this page is only listing the papers
20. 1:12that do not have a PDF file. So, as soon
21. 1:15as a a paper
22. 1:17as soon as an article has a PDF attached
23. 1:20to it,
24. 1:21it will not be shown in this page again.
25. 1:23So, these are only articles that have
26. 1:26been voted yes after title and abstract
27. 1:30screening, but yet we do not have a PDF
28. 1:33for them. All right? So, the first step
29. 1:35that we do here is to use Hub Meta's
30. 1:38automatic find PDF function. So, the
31. 1:41first thing that we do here is to go to
32. 1:44this settings tab, and here we can add
33. 1:48institutional resolver links. And what
34. 1:51these are is sometimes libraries of the
35. 1:54institutions that we work with, they
36. 1:55will provide you with a link that, you
37. 2:00know, will
38. 2:01if you add as a resolver to software
39. 2:04like Zotero and in this case Hub Meta,
40. 2:07uh
41. 2:09then it can be used to download the PDF.
42. 2:11So, talk with your institution's library
43. 2:14and see if they have a link to a
44. 2:16resolver. And if they did, you can add
45. 2:19it here. Or or if you know there are
46. 2:21other public websites or, you know,
47. 2:24other types of uh platforms that will
48. 2:26give you uh
49. 2:28a resolver link and you put them here.
50. 2:31So, once they are added uh here, if you
51. 2:34click on this search button, what this
52. 2:37does, it
53. 2:39we have a process of going through open
54. 2:43access articles, going through those
55. 2:46resolvers that you have added, and this
56. 2:48helps you find some of the PDFs that you
57. 2:51are looking for. So, in this case, you
58. 2:52see it's uh
59. 2:54it has looked through
60. 2:56three of them so far, found one of them,
61. 2:59not found one. Usually, um you know,
62. 3:02depending on on the project and the
63. 3:05resolvers that you add, your yield could
64. 3:08be anywhere between
65. 3:10um 20 to 70%. That's that's the number.
66. 3:14The next step after this run its course
67. 3:17and downloaded the PDFs um that it could
68. 3:21download, you will download the
69. 3:23remaining articles as an RIS file. So,
70. 3:27clicking on this will give you this RIS
71. 3:29file, and what we can do with that is to
72. 3:32open this inside Zotero or inside
73. 3:37um
74. 3:38EndNote or software like that. And
75. 3:42EndNote and Zotero, each of them have
76. 3:45this function to download PDFs of your
77. 3:49articles. So, you can this is basically
78. 3:52getting help from another platform to
79. 3:54download your PDFs. This This probably
80. 3:58helps us to get another 20% of our
81. 4:01articles. So, here I will right-click
82. 4:04and use uh find full text. And
83. 4:09uh this one is trying to download
84. 4:12uh the PDFs uh for these articles.
85. 4:17All right. Now that Zotero is done, it
86. 4:19actually found around 14 files, which is
87. 4:22very good. It's usually not that
88. 4:25successful, but you know, we just got
89. 4:27lucky this time. So, here is how I
90. 4:29export from Zotero with PDFs back onto
91. 4:34Hubmed. So, again, I will right-click on
92. 4:36these articles and then pick export
93. 4:41items.
94. 4:42And make sure that this check, which is
95. 4:46export files, is also
96. 4:48uh checked. Make sure you have picked
97. 4:51RIS and hit okay. And then this will
98. 4:55create a folder. Let's just say output
99. 5:00PDFs.
100. 5:02And uh MP. This is my project. Let's uh
101. 5:07save that. And then we go back to
102. 5:10Hubmed.
103. 5:11Use this last one, which is upload.
104. 5:15And then you see there is a Zotero
105. 5:17option. And here I will
106. 5:20use the drag and drop or just click on
107. 5:24um
108. 5:25uh upload. And all I have to do is to
109. 5:27select the whole folder that we just
110. 5:30exported out of Zotero. When I click on
111. 5:33upload, it it usually gives me, you
112. 5:36know, this alert about like how many
113. 5:38files I'm uploading. That's coming from
114. 5:40your browser. So, here it says, "You
115. 5:43have 14 PDFs that are ready to upload
116. 5:47here. Are you confirming this? And then,
117. 5:50when I say yes, it will upload all of
118. 5:52them one by one.
119. 5:54And it takes a few seconds for all of
120. 5:58them to be saved in our
121. 6:01storage and our database and then be
122. 6:03processed and all.
123. 6:06And once that is done, you can see that
124. 6:10I only have just a few. Like I started
125. 6:13with 19. Most of them were downloaded
126. 6:17and now are out of my fetch page. These
127. 6:20are the final ones that I have to do
128. 6:22manually. And for them, we have this
129. 6:26icon here, which is LibKey. And LibKey
130. 6:31is
131. 6:32is an extension where you can log in to
132. 6:35your institution once. Like in this
133. 6:37case, I have logged in with University
134. 6:39of Calgary's library. So, after the
135. 6:42first time you log in, um um every time
136. 6:46after that, this page is here. It gives
137. 6:48you a direct PDF download link. You
138. 6:52click on it and
139. 6:55there we go. We have the PDF here.
140. 6:58Uh we save it and then
141. 7:01back to up meta to upload it. I will
142. 7:04click on this
143. 7:06uh
144. 7:06um
145. 7:07gray PDF icon
146. 7:10and
147. 7:11pick the file that we just downloaded.
148. 7:14And give it a second. When it is red,
149. 7:17that means it's there. So, if I refresh
150. 7:20my page, that line is all is also gone,
151. 7:24which means, you know, one less to
152. 7:28download. And then, you get the idea.
153. 7:30You download the rest and then you're
154. 7:32ready for the next step, which is
155. 7:34looking at the full text of your
156. 7:37articles. See you in the next video.
157. 7:41>> [music]
158. 7:50[music]
159. 7:54>> Mhm.