Online tool to convert plain text references into list of PubMed IDs or DOIs

Question

A smart researcher is using a reference manager (zotero, endnote) for citing papers. To import papers into the reference manager is a tedious task.

Is there a web based tool that could automate some of it. Consider a block of text with references below (emailed as free text by a colleague) and the tool would convert it into a list of PubMed IDs or DOIs.

•         Saxon AJ, Ling W, Hillhouse M, Thomas C, Hasson A, Ang A, Doraimani G, Tasissa G, Lokhnygina Y, Leimberger JD, Bruce RD, McCarthy J, Wiest K, McLaughlin P, Bilangi R, Cohen AJ, Woody GE, Jacobs P.  Buprenorphine/Naloxone and Methadone Effects on Laboratory Indices of Liver Health: A Randomized Trial.  Drug and Alcohol Dependence 2013;128(1-2):71-76. 
•         Woody GE, Poole SA, Subramaniam GA, Dugosh KL, Bogenschutz MP, Abbott P, Patkar AA, Publicker M, McCain K, Sharpe Potter J, Formar RF, Vetter V, McNicholas L, Blaine J, Lynch KG, Fudala P.  Extended vs. Short-Term Buprenorphine-Naloxone for Treatment of Opioid-Addicted Youth: A Randomized Trial.  JAMA 2008;300(17):2003-2011. 
•         Wu LT, Pan JJ, Blazer DG, et al. Using a latent variable approach to inform gender and racial/ethnic differences in cocaine dependence: A National Drug Abuse Treatment Clinical Trials Network study. J Subst Abuse Treat 2010; 38(Suppl. 1): S70–79. 
•         Wu LT, Blazer DG, Patkar AA, et al. Heterogeneity of stimulant dependence: A National Drug Abuse Treatment Clinical Trials Network study. Am J Addict 2009; 18(3): 206–18. 
•         Wu LT, Blazer DG, Stitzer ML, Patkar AA, Blaine JD. Infrequent illicit methadone use among stimulant-using patients in methadone maintenance treatment programs: A National Drug Abuse Treatment Clinical Trials Network study. Am J Addict 2008; 17(4): 304–11. 
•         Wu LT, Pan JJ, Blazer DG, et al. The construct and measurement equivalence of cocaine and opioid dependences: A National Drug Abuse Treatment Clinical Trials Network (CTN) study. Drug Alcohol Depend 2009; 103(3): 114–23. 
•         Wu LT, Blazer DG, Woody GE, et al. Alcohol and drug dependence symptom items as brief screeners for substance use disorders: Results from the Clinical Trials Network. J Psychiatr Res 2012; 46(3): 360–69. 

Output would be:

PMID:22921476
PMID:18984887
...

Answer 1

You could use CrossRef

Go to this link:

Paste the references into the box and supply an email: If you want PubMed IDs then click the box:

You'll get results like this:

You could then do some text manipulation to extract the doi or PMID.

Note: the tool requires to register your email.

Enter the email address you registered for use of Crossref services. If you have >not registered your email address, request an account. [link to register]

Answer 2

Another option is to use the rcrossref package in R.

Here is a complete example that returns dois and PMIDs for the references you specify. It could readily be adapted to a different set of references. You probably just want to double check that it is returning accurate results.

# install.packages(rcrosref)
library(rcrossref)

# here is a simple example of extracting one ref
ref <- " Saxon AJ, Ling W, Hillhouse M, Thomas C, Hasson A, Ang A, Doraimani G, Tasissa G, Lokhnygina Y, Leimberger JD, Bruce RD, McCarthy J, Wiest K, McLaughlin P, Bilangi R, Cohen AJ, Woody GE, Jacobs P.  Buprenorphine/Naloxone and Methadone Effects on Laboratory Indices of Liver Health: A Randomized Trial.  Drug and Alcohol Dependence 2013;128(1-2):71-76."
results <- cr_works(query = ref, limit =1)


# Save the references to a variable
# I've used scan make sure you run the empty line after the last reference to 
# let the scan function know that all references have been imported
refs <- scan(what = "character", sep = "\n")
Saxon AJ, Ling W, Hillhouse M, Thomas C, Hasson A, Ang A, Doraimani G, Tasissa G, Lokhnygina Y, Leimberger JD, Bruce RD, McCarthy J, Wiest K, McLaughlin P, Bilangi R, Cohen AJ, Woody GE, Jacobs P.  Buprenorphine/Naloxone and Methadone Effects on Laboratory Indices of Liver Health: A Randomized Trial.  Drug and Alcohol Dependence 2013;128(1-2):71-76. 
Woody GE, Poole SA, Subramaniam GA, Dugosh KL, Bogenschutz MP, Abbott P, Patkar AA, Publicker M, McCain K, Sharpe Potter J, Formar RF, Vetter V, McNicholas L, Blaine J, Lynch KG, Fudala P.  Extended vs. Short-Term Buprenorphine-Naloxone for Treatment of Opioid-Addicted Youth: A Randomized Trial.  JAMA 2008;300(17):2003-2011. 
Wu LT, Pan JJ, Blazer DG, et al. Using a latent variable approach to inform gender and racial/ethnic differences in cocaine dependence: A National Drug Abuse Treatment Clinical Trials Network study. J Subst Abuse Treat 2010; 38(Suppl. 1): S70–79. 
Wu LT, Blazer DG, Patkar AA, et al. Heterogeneity of stimulant dependence: A National Drug Abuse Treatment Clinical Trials Network study. Am J Addict 2009; 18(3): 206–18. 
Wu LT, Blazer DG, Stitzer ML, Patkar AA, Blaine JD. Infrequent illicit methadone use among stimulant-using patients in methadone maintenance treatment programs: A National Drug Abuse Treatment Clinical Trials Network study. Am J Addict 2008; 17(4): 304–11. 
Wu LT, Pan JJ, Blazer DG, et al. The construct and measurement equivalence of cocaine and opioid dependences: A National Drug Abuse Treatment Clinical Trials Network (CTN) study. Drug Alcohol Depend 2009; 103(3): 114–23. 
Wu LT, Blazer DG, Woody GE, et al. Alcohol and drug dependence symptom items as brief screeners for substance use disorders: Results from the Clinical Trials Network. J Psychiatr Res 2012; 46(3): 360–69. 


# import reference infomation from crossref
# cr_works uses the reference as the query
# limit = 1 limits returned references to 1
# I think that corresponds to the best match, but you would want to check
# this assumption
matches <- lapply(refs, function(X) try(rcrossref::cr_works(query = X, limit =1)))

# extract doi from returned object
dois <- sapply(matches, function(X) try(X$data$DOI))
dois

# Use the following function to convert doi to pubmed id
allids <- lapply(dois, function(X) try(rcrossref::id_converter(X)))
pmids <- sapply(allids, function(X) try(X$records[,"pmid"]))
pmids