Can any librarians tell me what this thing does?

June 5, 2015 2:52 PM

In some National Library of Medicine sites (I noticed it in TOXNET) that link back to PubMed, there's this one key-value pair in the query string that's appended to the PubMed URL:

http://www.​ncbi.nlm.nih.gov​/pubmed/18333769?​dopt=Abstract

Does anyone know why it's there, or what it does?

I've searched (but not exactly perused) NLM's PubMed documentation and can't find anything. Removing it seems to have no effect--PubMed PMID links (always?) deliver you to the abstract page anyway, so these two links, at least for me, behave in exactly the same way:

http://www.ncbi.nlm.nih.gov/pubmed/18333769?dopt=Abstract

http://www.ncbi.nlm.nih.gov/pubmed/18333769

Though I suppose it could be sending some information over for use by MyNCBI that I don't know about--I am not a MyNCBI superuser.

I just realized that this might be a bad example because this particular article doesn't have an abstract in PubMed, but links to articles with abstracts are the same:

http://www.ncbi.nlm.nih.gov/pubmed/19965920?dopt=Abstract

http://www.ncbi.nlm.nih.gov/pubmed/19965920

posted by pullayup to Computers & Internet (7 answers total)

IAAL, but I don't think this is a librarian question, unless you're talking systems librarians, or librarianship merely in the sense that I could even figure out this much from a 1-minute Google.

It looks like it's an XML variable. You can see an example in the raw code here. Also here is a Google Books excerpt which may make it clear as mud. I haven't done much with XML since library school so literally all I know about it is you can define your own elements which is why it's useful. Hopefully someone else who knows about this stuff will chime in soon.
posted by rabbitrabbit at 3:02 PM on June 5, 2015

I'd bet that dopt stands for "display option" or something similar. It's a url parameter to tell PubMed what type of information to display. Since the abstract is the default display option, you get it even if you don't specify a dopt parameter at all. This is quite common when building web applications.

As an experiment, I tried various options from the little "format selector" at the top of the page (the one that says "Abstract"):

http://www.ncbi.nlm.nih.gov/pubmed/18333769?dopt=Abstract&report=medline&format=text
http://www.ncbi.nlm.nih.gov/pubmed/18333769?dopt=Abstract&report=xml&format=text

This gives you the same information, but in medline or xml formats instead. Conveniently enough, these options also work in the dopt parameter, so these urls do the same thing:

http://www.ncbi.nlm.nih.gov/pubmed/18333769?dopt=medline
http://www.ncbi.nlm.nih.gov/pubmed/18333769?dopt=xml

I suspect that this is somewhat a product of legacy behavior; they may have used to use the dopt parameter for everything, then added the report and format options to allow more flexibility later, but the original dopt parameter is still around.
posted by zachlipton at 3:10 PM on June 5, 2015

Quick clarification:

I guess my question is not "what is this" but "what is PubMed using this variable for"--I should have been more explicit about this in the question.

I'm aware of other variables that are covered in the PubMed documentation, e.g the ones used to specify an institution's Outside Tool (otool=) or Linkout (holding=), but I can't find anything about this one. Of course, it could be entirely internal and not present in any of the public-facing documentation, but I figured it was worth a try.
posted by pullayup at 3:11 PM on June 5, 2015

Looks like it is an NLM thing, not a PubMed thing. Found this site explaining how to create a custom url that works with their Entrez database system. Scroll down and you'll spot it - it's the display option.
posted by Athanassiel at 4:51 PM on June 5, 2015

zachlipton had it:

A THIRD LINE, DOPT (display option), can be added to the query 
to specify the desired record format.  If no DOPT line is 
included, default display options are used.  For TERM searches, 
the default is 'document summary' format, which shows titles only
(DOPT d).  For UID searches, the default depends on the database
being searched.  MEDLINE records are shown in 'Citation report' 
format, which shows the citation, title, abstract, and MeSH indexing 
terms (DOPT r).  Nucleotide and protein records are shown in
GenBank/GenPept format (DOPT g).  (section 4.4.1) 

That's from documentation dated 1999.

Weirdly the option doesn't seem to appear anywhere in current documentation for Entrez, the NLM system(s), even in a passing mention of how it's a legacy option that's still supported for whatever option values were defined in the 1999 version of the system. It does show up in example URLs in a current citation style guide, but the URLs themselves were unexplained. And the behavior you've seen indicates that Dopt=Abstract is indeed the default display option since you get the same display either way.
posted by fedward at 7:04 PM on June 5, 2015

Yes, your initial suspicion is right: it's to support MyNCBI's option to customize your view of PubMed, including viewing the abstract within a page of results. So when I log in to my customized MyNCBI account and search, I don't see citation, citation, citation...I see citation & abstract, citation & abstract, etc. It is super handy for when you need to do lots of searching or are looking for needles in haystacks.

There are also several other ways to customize your MyNCBI settings to show different aspects of the record (like MeSH terms; highlight search terms in results; add frequently-used limits; display whole record in text only; indexing status; genes/substances discussed; and more). Feel free to PM me or post here if you have further qs on getting this set up and selecting the customizing options for MyNCBI. I'm a medical librarian and I like helping people use information resources more effectively, and MyNCBI is one of the most powerful customizing & saving tools out there, so it's worthwhile to learn about if you spend more than an hour or so a week on PubMed.
posted by holyrood at 8:15 PM on June 5, 2015

Thanks, everyone, Ask Metafilter continues to be incredible.
posted by pullayup at 5:27 AM on June 10, 2015