What Is The Most Appropriate Uri For A Journal Article?

Question

[Dave Bridges]

PubMed ID or DOI? And which is easier to extract metadata from given that identifier?

Answer 1

[Casey Bergman]

why choose when there are pmid2doi look-up services:

• http://labs.crossref.org/styled-3/pmid2doi.html
• http://www.myexperiment.org/workflows/5.html

[Dave Bridges]

that looks good, but it seems like the database is not updated past 2010

[Larry_Parnell]

Thank you, Casey. I knew you'd have a good solution to this.

[Casey Bergman]

I asked CrossRef about updating this service and their reply was "@CrossRefNews: @caseybergman Actually this service appears to be brought to you by the Netherlands Bioinformatics Service." https://twitter.com/#!/CrossRefNews/status/157098241660436480

Answer 2

[Larry_Parnell]

One obvious answer is to use the DOI so that you can extract from more than PubMed entries.

[Michael Schubert]

For a pure "ID 2 metadata" approach, I would say that PMIDs are easier, as there is URLAPI and the Bio* Wrappers for NCBI services in general. I don't know about anything comparable for DOIs. That is, given that the set of articles can be described by both (ie., are in Pubmed).

Answer 3

[Simon Cockell]

Neither is perfect by any means.

Let's take the example of one of my papers An integrated dataset for in silico drug discovery.

Assuming we have the 2 identifiers:

• DOI: 10.2390/biecoll-jib-2010-116
• PMID: 20375448

And we want the full text and metadata for the article.

Full text first, let's use the PMID, and visit the PubMed entry for the paper, here: http://pubmed.org/20375448.

Lo and behold, there is no link through to the article at all. We've hit a dead end.

So let's try the DOI: http://dx.doi.org/10.2390/biecoll-jib-2010-116.

Hurrah, at least there is a link to the full text, even if the DOI doesn't take us through to the actual article itself, but still... success!

OK, now metadata. The DOI gave us success with the article, so let's try that first. Search the CrossRef metadata here: http://api.labs.crossref.org/search?q=10.2390%2Fbiecoll-jib-2010-116.

Hmmm, nothing about my paper at all in that list (this is because the CrossRef database is curiously free of information about that paper, despite the DOI resolving to the paper).

So, back to the PMID, and etuils, here: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=20375448.

Yay, that looks like suitable metadata (even if it is in a completely different format to that we would get back from CrossRef, so any parser we write to consume CrossRef metadata will break). But why could we not retrieve this with the DOI?

I'm not for a second suggesting that the situation is this poor for every article (mostly it depends on the publisher and what they submit to the various databases), but the proportion of articles like this is significant enough for it to be problematic.

Publishers should be providing good enough metadata on the articles themselves for this ad hoc system of arbitrary third party identifiers to be completely unnecessary.

[Chris Maloney]

I may be wrong, but I think that the reason that there's no metadata for your article in CrossRef is that the journal, "Journal of Integrative Bioinformatics", didn't submit that for you. It's the same reason the CrossRef URL is resolving to your institutional repository, instead of the journal page, http://journal.imbio.de/article.php?aid=116.

Answer 4

[Marc]

Or the http://www.pmid2doi.org/

[Casey Bergman]

+1 Marc - hadn't seen this yet. Another timely offering from NBIC.

[Casey Bergman]

Based on the reply from Crossref (see above/below) it looks like this is the same project as http://labs.crossref.org/styled-3/pmid2doi.html

[xiaoronglv]

hi, Marc, does the data of this site update timely?

Answer 5

[Steve Moss]

I'd say DOI, but it might be worth talking to Rod Page about bioGUID and bioStor and his experience in gathering metadata! Also some of the people at Mendeley or Zotero etc may be willing to help :-)

Check out Rod's blog, iPhylo, for some interesting posts too!