README.md



Input article collection

We used list of PMIDs from article collections delivered by curators (Víctor, Soco, Paloma).
DRIVE (https://docs.google.com/spreadsheets/d/1OayfQ7ODgnU4d5PQ3SUAmFX3Tc27PocCHZ6flPXwLKc/edit?usp=sharing)
Asana (https://app.asana.com/0/1200927210854847/1203428992254399/f)


Download PDFs

We used Pubmed-Batch-Download tool to download PDF files. 


Installation

(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg$ git clone https://github.com/billgreenwald/Pubmed-Batch-Download.git
Cloning into 'Pubmed-Batch-Download'...
remote: Enumerating objects: 202, done.
remote: Counting objects: 100% (12/12), done.
remote: Compressing objects: 100% (12/12), done.
remote: Total 202 (delta 5), reused 0 (delta 0), pack-reused 190
Receiving objects: 100% (202/202), 31.23 MiB | 1.09 MiB/s, done.
Resolving deltas: 100% (102/102), done.
(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg$ mv Pubmed-Batch-Download/ github-Pubmed-Batch-Download
(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg$ cd github-Pubmed-Batch-Download/
(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ ls -l
total 52
-rw-rw-r-- 1 cmendezc cmendezc    72 ene  5 11:31 example_pmf.tsv
-rw-rw-r-- 1 cmendezc cmendezc 11430 ene  5 11:31 fetch_pdfs.py
-rw-rw-r-- 1 cmendezc cmendezc 18711 ene  5 11:31 fetch_pdfs_toScript.ipynb
-rw-rw-r-- 1 cmendezc cmendezc   551 ene  5 11:31 pubmed-batch-downloader-py3-windows.yml
-rw-rw-r-- 1 cmendezc cmendezc   895 ene  5 11:31 pubmed-batch-downloader-py3.yml
-rw-rw-r-- 1 cmendezc cmendezc  3667 ene  5 11:31 README.md
drwxrwxr-x 2 cmendezc cmendezc  4096 ene  5 11:31 ruby_version
-rw-rw-r-- 1 cmendezc cmendezc     0 ene  5 11:31 unfetched_pmids.tsv
(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ conda env create -f pubmed-batch-downloader-py3.yml


Testing

Error!

(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ conda activate pubmed-batch-downloader-py3
(pubmed-batch-downloader-py3) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ python fetch_pdfs.py -pmf example_pmf.tsv
Traceback (most recent call last):
  File "fetch_pdfs.py", line 64, in <module>
    from bs4 import BeautifulSoup
ModuleNotFoundError: No module named 'bs4'


Fix 1: Install bs4

(pubmed-batch-downloader-py3) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ pip install bs4
Collecting bs4
  Using cached https://files.pythonhosted.org/packages/10/ed/7e8b97591f6f456174139ec089c769f89a94a1a4025fe967691de971f314/bs4-0.0.1.tar.gz
Collecting beautifulsoup4 (from bs4)
  Using cached https://files.pythonhosted.org/packages/9c/d8/909c4089dbe4ade9f9705f143c9f13f065049a9d5e7d34c828aefdd0a97c/beautifulsoup4-4.11.1-py3-none-any.whl
Collecting soupsieve>1.2 (from beautifulsoup4->bs4)
  Using cached https://files.pythonhosted.org/packages/16/e3/4ad79882b92617e3a4a0df1960d6bce08edfb637737ac5c3f3ba29022e25/soupsieve-2.3.2.post1-py3-none-any.whl
Building wheels for collected packages: bs4
  Building wheel for bs4 (setup.py) ... done
  Stored in directory: /home/cmendezc/.cache/pip/wheels/a0/b0/b2/4f80b9456b87abedbc0bf2d52235414c3467d8889be38dd472
Successfully built bs4
Installing collected packages: soupsieve, beautifulsoup4, bs4
Successfully installed beautifulsoup4-4.11.1 bs4-0.0.1 soupsieve-2.3.2.post1


Error!

(pubmed-batch-downloader-py3) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ python fetch_pdfs.py -pmf example_pmf.tsv
Output directory of fetched_pdfs did not exist.  Created the directory.
Trying to fetch pmid 27547345
** fetching of reprint 27547345 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 22610656
** fetching of reprint 22610656 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 23858657
** fetching of reprint 23858657 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 24998529
** fetching of reprint 24998529 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 27859194
** fetching of reprint 27859194 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 26991916
** fetching of reprint 26991916 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 26742956
** fetching of reprint 26742956 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?
Trying to fetch pmid 28388874
** fetching of reprint 28388874 failed from error Couldn't find a tree builder with the features you requested: lxml. Do you need to install a parser library?


Fix 2: Install 

(pubmed-batch-downloader-py3) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ pip install lxml
Collecting lxml
  Downloading https://files.pythonhosted.org/packages/4b/24/300d0fd5130cf55e5bbab2c53d339728370cb4ac12ca80a4f421c2e228eb/lxml-4.9.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (5.8MB)
     |████████████████████████████████| 5.8MB 2.7MB/s 
Installing collected packages: lxml
Successfully installed lxml-4.9.2


It runs, but it didn't fetch all files. See unfetch_pmids.tsv


Run

(base) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ conda activate pubmed-batch-downloader-py3
(pubmed-batch-downloader-py3) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/github-Pubmed-Batch-Download$ cd /home/cmendezc/Documents/ccg/gitlab-automatic-extraction-growth-conditions/extraction-literature/input/pdfs
(pubmed-batch-downloader-py3) cmendezc@cmendezc-Latitude-7400:~/Documents/ccg/gitlab-automatic-extraction-growth-conditions/extraction-literature/input/pdfs$ python /home/cmendezc/Documents/ccg/github-Pubmed-Batch-Download/fetch_pdfs.py -pmf ../list_of_PMIDs.txt
Output directory of fetched_pdfs did not exist.  Created the directory.
Trying to fetch pmid 21097887
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 21097887 succeeded
Trying to fetch pmid 23818864
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 23818864 failed from error list index out of range
Trying to fetch pmid 24947454
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 24947454 succeeded
Trying to fetch pmid 25222563
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 25222563 succeeded
Trying to fetch pmid 25275371
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 25275371 succeeded
Trying to fetch pmid 25735747
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 25735747 succeeded
Trying to fetch pmid 26258987
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 26258987 succeeded
Trying to fetch pmid 26279566
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
Trying direct_pdf_link
** Reprint 26279566 could not be fetched with the current finders.
Trying to fetch pmid 26670385
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 26670385 failed from error Invalid URL 'f680gMuZlnwT4304lwsG531xpi4vbk83nDntGZ4l27M-1672941516-0-AdC4bMbcOc9cCSwDp4lsqirHOW3zv1msNUw8lijeZIxdN3BDTBUy983qf_LAfBVEhkt4k2Xwu_NYMJeaq3oG4LTyfDBxN2Ra-cmmTDVIK66GtTB9oyyn4GqMem1PTBwVEFtzEYcB4AOoR8EGbwWrEZa1jPMupBq_gJ0JlxuIGbBJw3SuuioKmRlQT_TDXNREjT2Av3DHrrz6C008shr-pgrTtAoM5aZ0N4clcoBQ1FWX04MZm-nPOxI-2zbxcHUYXqV91lbH7iWkztZWPcv6-Q3ePiFD6_-C7pdY_Mf0Y670kOKyhoqlZ0m3PqPm64-37r-nzxrcd2Z0MWJUMC8Jx1b1OA1e53TJy62F2K5ws3U82zktr4gEDS11A13r8DIn1wRCEH2dk8jI02NQoIp3JBTvUixhiNkWib01Zl7l7iAFLOJtWlVbeUsOwCh6imfV5m-2No7-SiGaur5Ip6Zf3ACDki_CjXifHxtGVh1TbvnYsBeUdoaWV3TsXdGvF7AVr_ytXg4-JiIHhaZ-SdCzpe65bWZmvwrIpCfZOEBOC-gNTm3tq5h1_2iQzVTinGQonsXdwLCYSKQeZRQ-qEFf7y4PpesHamAXmw1OZlZJtKlFgXx9MoCBp0Irx8ChWyIo5RhSBoa9j1_JW8AX1x7KDY3UX32ItW7-a2Qw5IEL_FRS6cyXOg1FLeHlanntIl11kKWmXyJ86bsvEQBn2Q9-1kMvisDZaM0LrfNT9KcghdkLgdpzsDEf-B4_MKdkVAhkBQ': No schema supplied. Perhaps you meant http://f680gMuZlnwT4304lwsG531xpi4vbk83nDntGZ4l27M-1672941516-0-AdC4bMbcOc9cCSwDp4lsqirHOW3zv1msNUw8lijeZIxdN3BDTBUy983qf_LAfBVEhkt4k2Xwu_NYMJeaq3oG4LTyfDBxN2Ra-cmmTDVIK66GtTB9oyyn4GqMem1PTBwVEFtzEYcB4AOoR8EGbwWrEZa1jPMupBq_gJ0JlxuIGbBJw3SuuioKmRlQT_TDXNREjT2Av3DHrrz6C008shr-pgrTtAoM5aZ0N4clcoBQ1FWX04MZm-nPOxI-2zbxcHUYXqV91lbH7iWkztZWPcv6-Q3ePiFD6_-C7pdY_Mf0Y670kOKyhoqlZ0m3PqPm64-37r-nzxrcd2Z0MWJUMC8Jx1b1OA1e53TJy62F2K5ws3U82zktr4gEDS11A13r8DIn1wRCEH2dk8jI02NQoIp3JBTvUixhiNkWib01Zl7l7iAFLOJtWlVbeUsOwCh6imfV5m-2No7-SiGaur5Ip6Zf3ACDki_CjXifHxtGVh1TbvnYsBeUdoaWV3TsXdGvF7AVr_ytXg4-JiIHhaZ-SdCzpe65bWZmvwrIpCfZOEBOC-gNTm3tq5h1_2iQzVTinGQonsXdwLCYSKQeZRQ-qEFf7y4PpesHamAXmw1OZlZJtKlFgXx9MoCBp0Irx8ChWyIo5RhSBoa9j1_JW8AX1x7KDY3UX32ItW7-a2Qw5IEL_FRS6cyXOg1FLeHlanntIl11kKWmXyJ86bsvEQBn2Q9-1kMvisDZaM0LrfNT9KcghdkLgdpzsDEf-B4_MKdkVAhkBQ?
Trying to fetch pmid 26673755
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 26673755 succeeded
Trying to fetch pmid 28061857
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 28061857 succeeded
Trying to fetch pmid 28526842
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 28526842 succeeded
Trying to fetch pmid 29394395
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 29394395 succeeded
Trying to fetch pmid 30137486
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 30137486 succeeded
Trying to fetch pmid 30389436
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
Trying direct_pdf_link
** Reprint 30389436 could not be fetched with the current finders.
Trying to fetch pmid 30420454
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 30420454 failed from error Invalid URL 'Ldk64CcSIXJkCs8pPt2YjpLkZJhaKs_m0pmekzL5SOY-1672941544-0-AaBQfP_66yID5nRb-xUznbW2FVXAWeiOcKnTosB_FUSxeeNSucukyHbo7OxAcJttrfA4pKDGasC8MvQz6o0cFBZv0VU_RfYXUn7Z6iVg5eVp7n_O4P9Zzk0IiE132EMNR-Xn0_gEfYM8DMCX5lS4yEgrs9hwhdJIWzS6N3fsDsa3kDjIH9oELTaDEbTbFvUXEkx3212-4NJ6SwCvfUzhtolsD7xJoswFQHjNBFrmUgScEORQpIWTWxzHPvpGTxepQMUPuAEbgNNykNbdp9oyLMDwmUnIqU7hSmeCkYU1RWlbxh95rcgH-yvV9mm3RQnIXT3WfcUE9lM5crnbBcplVCA4jbLP7kk1tu_BFbh-6gstCr0B24gEE5zJ41WGxwTbABhAmK7aAeHbH7V55EBpLOQcpkYhWZNiMMbVsG314TM_tE9UGM8B99FmrWUqCqwMcsGwDDWK7B-uHcDD5nJxQhgV5SlMnS0IVE18Bdu4zqIzT3ZS2sgGf9Drti4P5Qkso3v1pW_fBzq-Mrd6_O7cvwF7FlRc95tOXSjjS0Woc70HGNBNd1kc0ZR9NuwV9TnvPRWbuoYu3HXz65DeWmbGaLOFdHAOUARr1fD9DL9LRDmeAHOGkYkplz9pSbWXR6vYkIInqFnvQKuwhnVOltaWa6_VG3BH0oc9T4xAZdH83DsG6eHtJlitVhH8Sx_PBfukG4x0S1qsmIWUPDwZhwUe55ly0I5ISELLL8Z3tAJpq3zrdyV6CbwOjF7-nPF7aRNuxg': No schema supplied. Perhaps you meant http://Ldk64CcSIXJkCs8pPt2YjpLkZJhaKs_m0pmekzL5SOY-1672941544-0-AaBQfP_66yID5nRb-xUznbW2FVXAWeiOcKnTosB_FUSxeeNSucukyHbo7OxAcJttrfA4pKDGasC8MvQz6o0cFBZv0VU_RfYXUn7Z6iVg5eVp7n_O4P9Zzk0IiE132EMNR-Xn0_gEfYM8DMCX5lS4yEgrs9hwhdJIWzS6N3fsDsa3kDjIH9oELTaDEbTbFvUXEkx3212-4NJ6SwCvfUzhtolsD7xJoswFQHjNBFrmUgScEORQpIWTWxzHPvpGTxepQMUPuAEbgNNykNbdp9oyLMDwmUnIqU7hSmeCkYU1RWlbxh95rcgH-yvV9mm3RQnIXT3WfcUE9lM5crnbBcplVCA4jbLP7kk1tu_BFbh-6gstCr0B24gEE5zJ41WGxwTbABhAmK7aAeHbH7V55EBpLOQcpkYhWZNiMMbVsG314TM_tE9UGM8B99FmrWUqCqwMcsGwDDWK7B-uHcDD5nJxQhgV5SlMnS0IVE18Bdu4zqIzT3ZS2sgGf9Drti4P5Qkso3v1pW_fBzq-Mrd6_O7cvwF7FlRc95tOXSjjS0Woc70HGNBNd1kc0ZR9NuwV9TnvPRWbuoYu3HXz65DeWmbGaLOFdHAOUARr1fD9DL9LRDmeAHOGkYkplz9pSbWXR6vYkIInqFnvQKuwhnVOltaWa6_VG3BH0oc9T4xAZdH83DsG6eHtJlitVhH8Sx_PBfukG4x0S1qsmIWUPDwZhwUe55ly0I5ISELLL8Z3tAJpq3zrdyV6CbwOjF7-nPF7aRNuxg?
Trying to fetch pmid 33172971
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 33172971 failed from error Invalid URL 'cIp5BepthG7srw3ecaG_06Qhx8PrpoP6WpFwlAopfrE-1672941545-0-AXmWkR9H8dN8IxbsllbsHZ1SigvIVLyZ0euRPz15XW6nX_MsA3Y9dPoL0MovKxj_yUNiDnSYrVSmYNzVo-LEANJZq45ZpzDVv1GFU1qNu0PpI-0YxuWHz4dSudrD_soFz3LsTCtgLamU66ZDSsrVNGTaqqbajetYgnnhu4K-BeYnLmpOxzcMzYU9mgynHjFv0NnrdUU75kJPeOIRpgrUlqm8JRnkMq0SEvI2IPTDW0ToohbWs4bLvLX0GNKGVT_v5to_am4hEVPC9jmkfkkNOLoMmfbnZC-L2EGAKufwZgz17d89HWfaK61no8EW8y5ysZ5A9yTRfN__C_LpTG6FWw2HWyR9FgIvz799f4ysIoz52azp4a7w3G3AHCWdUBUDy6gabo_psIE4mu3dCHLcDzGNO148UT5wzxTfrQV3aatPAWjnaK6-Re0XOkABNINniMLfF6Ti-0WgY-cHyLH2RgKISy_89MeNrVJy22GToy2c_LQwZN3RT3M8M2TFXLXmi9xEE4Z_4kSRA_aRnvRjKJdMJfxhc-BYW1G-dn2SDAetNZZL7HcJW6cGlAIjNWQqTD9ieGfLxGJe0OCLysFkeY3XwRY5vTHQ-xVI-gGKBY0A9gS70DH5t_pS53fBTQZ1pK667ct-BCo5aysuQHLcXrlE9coo8k8vtQKrmQ5-Fxp2ZNV_MKLY5yqBj5yAWJI5b_O-Mp5TyE9Zzyte_cTXqYtO14DAr1ev8TwqZP3YNbunHBcvIO20uVjbNxc4m--ARi5MMuxcDg4Kvju8Dbf3YKM': No schema supplied. Perhaps you meant http://cIp5BepthG7srw3ecaG_06Qhx8PrpoP6WpFwlAopfrE-1672941545-0-AXmWkR9H8dN8IxbsllbsHZ1SigvIVLyZ0euRPz15XW6nX_MsA3Y9dPoL0MovKxj_yUNiDnSYrVSmYNzVo-LEANJZq45ZpzDVv1GFU1qNu0PpI-0YxuWHz4dSudrD_soFz3LsTCtgLamU66ZDSsrVNGTaqqbajetYgnnhu4K-BeYnLmpOxzcMzYU9mgynHjFv0NnrdUU75kJPeOIRpgrUlqm8JRnkMq0SEvI2IPTDW0ToohbWs4bLvLX0GNKGVT_v5to_am4hEVPC9jmkfkkNOLoMmfbnZC-L2EGAKufwZgz17d89HWfaK61no8EW8y5ysZ5A9yTRfN__C_LpTG6FWw2HWyR9FgIvz799f4ysIoz52azp4a7w3G3AHCWdUBUDy6gabo_psIE4mu3dCHLcDzGNO148UT5wzxTfrQV3aatPAWjnaK6-Re0XOkABNINniMLfF6Ti-0WgY-cHyLH2RgKISy_89MeNrVJy22GToy2c_LQwZN3RT3M8M2TFXLXmi9xEE4Z_4kSRA_aRnvRjKJdMJfxhc-BYW1G-dn2SDAetNZZL7HcJW6cGlAIjNWQqTD9ieGfLxGJe0OCLysFkeY3XwRY5vTHQ-xVI-gGKBY0A9gS70DH5t_pS53fBTQZ1pK667ct-BCo5aysuQHLcXrlE9coo8k8vtQKrmQ5-Fxp2ZNV_MKLY5yqBj5yAWJI5b_O-Mp5TyE9Zzyte_cTXqYtO14DAr1ev8TwqZP3YNbunHBcvIO20uVjbNxc4m--ARi5MMuxcDg4Kvju8Dbf3YKM?
Trying to fetch pmid 34428301
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 34428301 succeeded
Trying to fetch pmid 34791440
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 34791440 succeeded
Trying to fetch pmid 9140061
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 9140061 failed from error Invalid URL 'jcZKP5wy_U5fZwQzMnXsls3TZuFKtLfM.TRt.Bh4d9k-1672941556-0-ARg_NFIhKoWkMSTkM9K0NNsEvXccNV6TpzvRoQ-2vYjK8XkBbOYBTbXDk7ayo2JehzHWQXv5Q_R2fac_6YNLMbXVLvOx_MPE2G55FZnUH5eyYoAVkc294_DbWF4BkOBr9bbRZ77KShHUYqJjAOi2O7mvSeGRhr8aCrq258YcVJ0FBdP8Q5tuy2CNWxi_udpInouGKC_Bnbb4D6LtrmOH2qchHRdKNei5ina55N2xPiH6jVDZ21jK0SkCSagtetSHnT7A-CfaFwqG5cz5lnOs1l1bBFEcOFdNNkmvz5yGZK-RR1-gynCmgS1ixfHapDjmCyogIfAxI1oumhPQoHCCg8-OqSgMSXHbgJdPWvc5L68Unmk5BAZNeFU2F_-xInoVtpYPwJNkeyldxj98PbHPAYg-SqmRtv0MyKm9qcEZJIULlfwTZ2ZGAm_uAwcQ7fW_O9VfUNBlbt2SohoYWfCtILAc2Imgon6vNbdisaxRkf70SZuD0G-Fj2SCsAYhkQrqPCdJAEEfWJ1QiddGb32kTSnXCoupFAWbX441Xj4nOj5OaRem_6JScd2AJp-YxSNI0Nm4IrB8s5O_lG1o_BDYlplFwbKozatP9ckn0jeXx38wInIuKOjUgl9B_T2Xvkg6sCNxXUWsHXiHMkhQ3x2AEh47zf4T6vQoTi0wNMkUVtkNTh8gOviKKl74Pi4m3yyq1ICnA9L9D6E6MLuE_ZOfmVBM79sVEgN8jsDBojevmYv96r09rQaQ_9c5cFZk7E25jQ': No schema supplied. Perhaps you meant http://jcZKP5wy_U5fZwQzMnXsls3TZuFKtLfM.TRt.Bh4d9k-1672941556-0-ARg_NFIhKoWkMSTkM9K0NNsEvXccNV6TpzvRoQ-2vYjK8XkBbOYBTbXDk7ayo2JehzHWQXv5Q_R2fac_6YNLMbXVLvOx_MPE2G55FZnUH5eyYoAVkc294_DbWF4BkOBr9bbRZ77KShHUYqJjAOi2O7mvSeGRhr8aCrq258YcVJ0FBdP8Q5tuy2CNWxi_udpInouGKC_Bnbb4D6LtrmOH2qchHRdKNei5ina55N2xPiH6jVDZ21jK0SkCSagtetSHnT7A-CfaFwqG5cz5lnOs1l1bBFEcOFdNNkmvz5yGZK-RR1-gynCmgS1ixfHapDjmCyogIfAxI1oumhPQoHCCg8-OqSgMSXHbgJdPWvc5L68Unmk5BAZNeFU2F_-xInoVtpYPwJNkeyldxj98PbHPAYg-SqmRtv0MyKm9qcEZJIULlfwTZ2ZGAm_uAwcQ7fW_O9VfUNBlbt2SohoYWfCtILAc2Imgon6vNbdisaxRkf70SZuD0G-Fj2SCsAYhkQrqPCdJAEEfWJ1QiddGb32kTSnXCoupFAWbX441Xj4nOj5OaRem_6JScd2AJp-YxSNI0Nm4IrB8s5O_lG1o_BDYlplFwbKozatP9ckn0jeXx38wInIuKOjUgl9B_T2Xvkg6sCNxXUWsHXiHMkhQ3x2AEh47zf4T6vQoTi0wNMkUVtkNTh8gOviKKl74Pi4m3yyq1ICnA9L9D6E6MLuE_ZOfmVBM79sVEgN8jsDBojevmYv96r09rQaQ_9c5cFZk7E25jQ?
Trying to fetch pmid 32662815
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 32662815 succeeded
Trying to fetch pmid 32817380
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 32817380 failed from error Invalid URL '12Kdq1Gu6s3H_c9wV7MWTwYP1d4sz7FRpWv08o2fehs-1672941561-0-AQzKoSKCDX92o3mW4XorQJa2qF1s8dsMn24r1239tDd-OxIEJ-xofWlfZb7cmDWmkZ-d4uCYOdMgyimJ9BwqBkuJKbRguJ_HaG4KzuT0CwTAflqmSgiP6oaZRbxRIMOl3LAnhQXawFffYKLbyEKG9hEWBeEbs31LlzwG7k7IbodBBPNfYicYC2QJy8RZ5xHWPTXxcwshhdG__QByEK9fJ6RYaR8LVhOwXo-m6nKcnmcvdFAubYorAvVvggpPCiIA0EYouK_-KA_Et9mXMtoRPVhEKeO03k9LAejSpvDDd8praPe4uYMGyBe4ruFtFbjqOdJgmlwSt_hPsHu_iFLkl6eW-V_dW5iwEQOE9z1jSjKf1ZHznUnde5Nzlh3v0wV2po1Y1QuFKuy8_IO-DB4iU3MlzHKgWqCsAeLorSaui7KqJAGzqmM3Keurq7J4URVd8khAGmHXMZHt3u96krRlFp3Nsc1_jwJEKKLxr44FVFla7XnqlQIHXdzj9FffjdPd1R_p3G-UEYGLzL32dFulkql4INTbOR625BrjoAvw74XDQRcNE_P72PYyCRUSIarPTtFTQBMSfpxRaOprcTZfMR_U5zdY0uGixU3srbPeduCUA7tQOFiCiLoTD_odsa75NYCv9o_me1vJSA823Md4hCV947suGwjybNaQP-R-yrffAfni7dQRYMt-mjEHk5LtnebhpJi1G44UN_WFSDpOkB6lvKO7Qc-eoUXnm4DbeysVDTRAmVi94HkcG9tc1U7BeSVyXNUfq3C1Vr_1jJXCgUI': No schema supplied. Perhaps you meant http://12Kdq1Gu6s3H_c9wV7MWTwYP1d4sz7FRpWv08o2fehs-1672941561-0-AQzKoSKCDX92o3mW4XorQJa2qF1s8dsMn24r1239tDd-OxIEJ-xofWlfZb7cmDWmkZ-d4uCYOdMgyimJ9BwqBkuJKbRguJ_HaG4KzuT0CwTAflqmSgiP6oaZRbxRIMOl3LAnhQXawFffYKLbyEKG9hEWBeEbs31LlzwG7k7IbodBBPNfYicYC2QJy8RZ5xHWPTXxcwshhdG__QByEK9fJ6RYaR8LVhOwXo-m6nKcnmcvdFAubYorAvVvggpPCiIA0EYouK_-KA_Et9mXMtoRPVhEKeO03k9LAejSpvDDd8praPe4uYMGyBe4ruFtFbjqOdJgmlwSt_hPsHu_iFLkl6eW-V_dW5iwEQOE9z1jSjKf1ZHznUnde5Nzlh3v0wV2po1Y1QuFKuy8_IO-DB4iU3MlzHKgWqCsAeLorSaui7KqJAGzqmM3Keurq7J4URVd8khAGmHXMZHt3u96krRlFp3Nsc1_jwJEKKLxr44FVFla7XnqlQIHXdzj9FffjdPd1R_p3G-UEYGLzL32dFulkql4INTbOR625BrjoAvw74XDQRcNE_P72PYyCRUSIarPTtFTQBMSfpxRaOprcTZfMR_U5zdY0uGixU3srbPeduCUA7tQOFiCiLoTD_odsa75NYCv9o_me1vJSA823Md4hCV947suGwjybNaQP-R-yrffAfni7dQRYMt-mjEHk5LtnebhpJi1G44UN_WFSDpOkB6lvKO7Qc-eoUXnm4DbeysVDTRAmVi94HkcG9tc1U7BeSVyXNUfq3C1Vr_1jJXCgUI?
Trying to fetch pmid 32849447
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 32849447 succeeded
Trying to fetch pmid 33068046
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 33068046 failed from error Invalid URL 'Ca2tz3FARdmZBsByuyNuWeiql2uee1VreT.kVjY7yrk-1672941567-0-AexEfZqeSZGpnAKuvb4N24mFbbARpMqS4Bl7rq2oJaJLQy4XNqEXY1SvQ53OXwzuh9s8hJpJSmZKZ90s8So4WTMitRZFt0iwKRvwq5PfF8ZF-spmYvUyZmqSAcRty7hyAnlIItHCbvd0DXymu2foqGLiY7_Azyn4oIZjqDWZgwUu4cttCsPTlTJtscKhrnIDiTC2AD-6BrcAHq2eFMQXn27imPIx1RCRlJshGeDr1vbtfjlBg89wEfvUQMpUEgz-xVlFP2tkES_AqE3RIqDBCDIDkDuwxhKZ5d-k_PxAuN3Vbx-1nlLI7WeIZH3b-qHkPWg8ifOx6RsMU_A02ZEHMrjlftm66SFQ60Wsria5dpTeLxvGd34BBngLodgDKaYoG0ztHkPImcz4lT76J7-QCgKcV7O86u_4mEpHhONMbCRBLtVhcFVAX-zAMIyOWzECJ6x0Sau9cAqssr2l_Q1VT-f4uCaFA5KpmuC3IHUZQABkrvM9nh0uOhB2e7ln9OfxBG89KhjhGPRhio2LRDY4yprcBdzS-dNl1pedPEXENepuOg0R645bq0poGP4uKeYHuQ': No schema supplied. Perhaps you meant http://Ca2tz3FARdmZBsByuyNuWeiql2uee1VreT.kVjY7yrk-1672941567-0-AexEfZqeSZGpnAKuvb4N24mFbbARpMqS4Bl7rq2oJaJLQy4XNqEXY1SvQ53OXwzuh9s8hJpJSmZKZ90s8So4WTMitRZFt0iwKRvwq5PfF8ZF-spmYvUyZmqSAcRty7hyAnlIItHCbvd0DXymu2foqGLiY7_Azyn4oIZjqDWZgwUu4cttCsPTlTJtscKhrnIDiTC2AD-6BrcAHq2eFMQXn27imPIx1RCRlJshGeDr1vbtfjlBg89wEfvUQMpUEgz-xVlFP2tkES_AqE3RIqDBCDIDkDuwxhKZ5d-k_PxAuN3Vbx-1nlLI7WeIZH3b-qHkPWg8ifOx6RsMU_A02ZEHMrjlftm66SFQ60Wsria5dpTeLxvGd34BBngLodgDKaYoG0ztHkPImcz4lT76J7-QCgKcV7O86u_4mEpHhONMbCRBLtVhcFVAX-zAMIyOWzECJ6x0Sau9cAqssr2l_Q1VT-f4uCaFA5KpmuC3IHUZQABkrvM9nh0uOhB2e7ln9OfxBG89KhjhGPRhio2LRDY4yprcBdzS-dNl1pedPEXENepuOg0R645bq0poGP4uKeYHuQ?
Trying to fetch pmid 33072717
Trying genericCitationLabelled
Trying pubmed_central_v2
** fetching reprint using the 'pubmed central' finder...
** fetching of reprint 33072717 succeeded
Trying to fetch pmid 33136147
Trying genericCitationLabelled
** fetching reprint using the 'generic citation labelled' finder...
** fetching of reprint 33136147 succeeded
Trying to fetch pmid 33318048
Trying genericCitationLabelled
Trying pubmed_central_v2
Trying acsPublications
Trying uchicagoPress
Trying nejm
Trying futureMedicine
Trying science_direct
** fetching of reprint 33318048 failed from error Invalid URL 'H_HDOMjPFqBRBn9CIvFp3.MLyt6.Cr1yqjPqy7_.dNo-1672941585-0-ASGJyet_JMjh-n9RCjZP1usTaU-rAh_oVPlNBV8Ox06oZLjLmr4nLazOPGibTSzbDun4wRRfxjJD1cl8pFLvWgZNLCwgScfdMEuTEYcHelG8wh84ZPO7-PimWyY4a-Ax_JW2wfMsWOrdcFRmKRfdjpL4MFDyEGVMcjhzP9y84LW4EnDyNZqVSkX_y8VAxIbmaMeuS-EiSakyeV1RnV4_bKjzzuQXXLtk8wIhc-rF2VoAiFgTRP3-kR7Y02rLN1opo-OYhoQ29Xy2fAHIKm2pS-qBW0XNRWiOU6q8_YMmMZrWbskiukxzgyZO5MutUF8ygYDuzaZDjX0BtuezjJEtcKWslPbaM1gXj1L8Yy3U7YCwi-_CPUjNOrvFnW0EEm5jeKDUVwwIeY1-sd54wUjlnn86c6qAqpaI4unKjLk4makfoIUlKr4B62VwsTRnrfbZxbqDTyl5jZjFIGiHmrmzPXxt1QG7SrQwApYoGQYFiijEUTw-7IM3t7bXcwRYTMVfbXUEhv8JrzvShSa8x1fDEwHgU2fUnY6BoCOrpC9hZShy1xlZSOOpw4AHgCW272GoFIr2PJ-Zy1UNze2TXebaUegtUpleiM-BhsDhqCAaGxAj9SQsD153z7wtiM6kCMnHOz9IhaKIkgYpKYgXwcQmuzLZUWgWJFJ0lqYeSgvlKAgHjzRY_3Jt2gPT3L2GcgUZQXWWRx4Hs4jL2tUvAiOuqPfvPWSFVjGTZPjZCd3VVFrqpcZCh2v85PiksdgNk05aMA': No schema supplied. Perhaps you meant http://H_HDOMjPFqBRBn9CIvFp3.MLyt6.Cr1yqjPqy7_.dNo-1672941585-0-ASGJyet_JMjh-n9RCjZP1usTaU-rAh_oVPlNBV8Ox06oZLjLmr4nLazOPGibTSzbDun4wRRfxjJD1cl8pFLvWgZNLCwgScfdMEuTEYcHelG8wh84ZPO7-PimWyY4a-Ax_JW2wfMsWOrdcFRmKRfdjpL4MFDyEGVMcjhzP9y84LW4EnDyNZqVSkX_y8VAxIbmaMeuS-EiSakyeV1RnV4_bKjzzuQXXLtk8wIhc-rF2VoAiFgTRP3-kR7Y02rLN1opo-OYhoQ29Xy2fAHIKm2pS-qBW0XNRWiOU6q8_YMmMZrWbskiukxzgyZO5MutUF8ygYDuzaZDjX0BtuezjJEtcKWslPbaM1gXj1L8Yy3U7YCwi-_CPUjNOrvFnW0EEm5jeKDUVwwIeY1-sd54wUjlnn86c6qAqpaI4unKjLk4makfoIUlKr4B62VwsTRnrfbZxbqDTyl5jZjFIGiHmrmzPXxt1QG7SrQwApYoGQYFiijEUTw-7IM3t7bXcwRYTMVfbXUEhv8JrzvShSa8x1fDEwHgU2fUnY6BoCOrpC9hZShy1xlZSOOpw4AHgCW272GoFIr2PJ-Zy1UNze2TXebaUegtUpleiM-BhsDhqCAaGxAj9SQsD153z7wtiM6kCMnHOz9IhaKIkgYpKYgXwcQmuzLZUWgWJFJ0lqYeSgvlKAgHjzRY_3Jt2gPT3L2GcgUZQXWWRx4Hs4jL2tUvAiOuqPfvPWSFVjGTZPjZCd3VVFrqpcZCh2v85PiksdgNk05aMA?


Text extraction from PDF

We sent PDf files to Lisen&Curate team for extracting text.