Probably the main reason it rarely happens is that most people aren't in the habit of thinking about it (yet). I do see this as slowly changing, however, as is the case with citing datasets; the speed will vary by discipline.

Theoretically anyone *can* cite anything already; but for the citations to be most useful (eg for people to then be able to play programmatically with reference lists) you need some agreed upon standards. Standards for citing data are still in active development - you could get some ideas from eg  I haven't heard anything about standards for citing code though I haven't really been looking.

A permanent url is pretty vital, and a DOI certainly adds a lot of cachet for scientists who are new to all this: it makes it *look* Official even though it doesn't actually guarantee permanence or credibility. You might be interested in - it's a recent proof of concept integration between a GitHub repo and Figshare to get a DOI for the repo.

Deborah Fitchett
Digital Access Coordinator
Library, Teaching and Learning
Lincoln University, Te Whare Wānaka o Aoraki
New Zealand's specialist land-based university

-----Original Message-----
From: Code for Libraries [mailto:[log in to unmask]] On Behalf Of Heather Claxton-Douglas
Sent: Thursday, 7 November 2013 12:02 p.m.
To: [log in to unmask]
Subject: [CODE4LIB] Citing source code in high-profile academic journals


I need some advice about referencing source code in an academic journal.  I rarely see it happen and I don’t know why.

I’m building a website that connects academic researchers with software developers interested in helping scientists write code.  My goal is for these researchers to be able to reference any  new source code in the articles they publish -- much like a “gene accession number” or a “PDB code”.

Unfortunately, I don’t see any code repositories referenced in high profile journals like Science or PNAS.  I’m guessing it’s because the code in the repositories isn’t permanent and may be deleted anytime? Or perhaps a DOI needs to be assigned?

So my question to the group is:
What criteria is necessary for a code repository or database to be eligible for referencing in scientific academic journals?

Some ideas I have based on looking at the Protein Databank and Genbank are:
1) The entry is permanent -- we can’t delete articles once they’ve been published, same is true for entries in the PDB and Genbank
2) The entry gives credit to all authors and contributors
3) The entry has a DOI
4) The entry has a simple accession number - PDB is a four character code,  Genebank number is six characters.

Is there anything I’m missing?  Any advice would be greatly appreciated.

Thank you
Heather Claxton-Douglas, PhD

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