How Can You Cite Literature When Curating Databases?

Question

[Andra Waagmeester]

When I am entering literature knowledge I try to cite with either the PMID or DOI. I have seen other examples, such as in free text (just typing the reference in some bibliographic style) or an URL. Are there other possibilities to cite literature when curating biological databases?

[Chris Evelo]

Are you looking for the best way to do it yourself? Or do you want to know what people actually use so you can for instance find those references?

[Andra Waagmeester]

@Chris Indeed I an wondering how people cite in databases so that I can find them

Answer 1

[Pierre Lindenbaum]

• You could use (the now defunct ?)(Has it ever been used for the scientific literature ?) Life Science Identifier LSID: http://en.wikipedia.org/wiki/LSID
• a Publisher Item Identifier (PII) http://en.wikipedia.org/wiki/Publisher_Item_Identifier (you can find it in some pubmed records)
• a Pubmed central identifier ( http://www.nlm.nih.gov/pubs/techbull/ma08/ma08_pmcid.html )
• you could also imagine to put a RDF fragment describing your annotation (that would contain the date when the paper was read, who read the paper, etc... ).

[Pierre Lindenbaum]

because they were already cited in Andra's question. He's looking for the "other possibilities". Of course, PMID would be my first choice.

[Chris Evelo]

The disadvantage of a PMID based link to Pubmed is that it does not directly go to the article itself while a DOI dx.doi.org) link or Pubmed central ID based link do take you to the full text if that is available. Which is why I prefer those. DOI's are more general applicable and cover for instance also the chemistry field.

[Dave Bridges]

Why not DOI/PMID Pierre?

[Andra Waagmeester]

@Chris that is partly true. Pubmed/Medline often captures more then one url, which direct to the full text. This is a clear benefit over DOI. But I am really only looking for different ways people cite the literature, not what the best way of citing is.

[Chris Evelo]

Not sure I understand. Do you mean that if you follow the link to Pubmed you can follow the links to full text (both Pubmed Central and publisher sites) from there? Yes, true, but that is at least 2 clicks or 2 steps when mining through the links. The comment was meant as a response to Pierre's choice for Pubmed IDs over DOI's

[Pierre Lindenbaum]

Chris, as I said in another comment, not all DOI are resolvable: e.g: twitter.com/#!/bmljenny/status/51218949181935616

Answer 2

[Melanie]

I once defined an RDF scheme for capturing metadata about biological objects. I liked the OMG's Bibliographic Query Service's data model for references. (http://www.omg.org/spec/BQS/)

It has been many years since I looked at this, but I remember thinking it had the flexibility to handle pretty much anything that we'd come across. You could look at it for ideas of what you might see.

One downside for using a PubMed identifier alone is that there are some useful papers published in things that PubMed doesn't index. Even working primarily with biology, I occasionally come across a chemistry paper or a crystallography paper that is in a journal PubMed doesn't cover.

Answer 3

[Joachim]

I would go for DOI, because you can immediately tell from its appearance what it is: a DOI.

With PubMed IDs or Pubmed Central IDs you are sometimes just presented with a number (e.g., 123456 instead of PMC123456), which can be confusing. The conversion between Pubmed Central IDs and Pubmed IDs (http://www.ncbi.nlm.nih.gov/sites/pmctopmid) is also not that straightforward, because not all Pubmed Central IDs resolve to Pubmed IDs immediately (you might have to wait until the mappings are updated).

So, DOIs seem attractive due to their easily identifiable notation and their functionality as a link (as Chris said). They are also ubiquitous in the sense that they are also applied outside Pubmed Central / Pubmed covered areas.

[Pierre Lindenbaum]

The problem is that not all DOI are resolvable. e.g: https://twitter.com/#!/bmljenny/status/51218949181935616

[Joachim]

I noticed that too, but I think DOIs are a step in the right direction. Having a unified system for reference IDs seems more appealing to me than having a fool-proof system of otherwise incomparable "vendor"-specific identifiers.