On 2013 Aug 16, Martin Fenner commented:

I've written a blog post about this paper, and a plugin for the Jekyll blogging platform that automatically detects database links in blog posts, currently supporting ENA/GenBank/DDBJ, Uniprot, PDB and MGI.

It is common practice in the life sciences to add tags right into the text. I don't think we necessarily need identifiers for databases, as proposed by William. Writing the tags as links would already be a major step forward, and that is why I wrote the jekyll plugin.

Even better would be to include database tags in the references of a paper. They would not only be easier to find, but we could also add metadata to the document. But we are probably a few years away from this as we have a strong community practice to have database tags right in the text.

On 2013 Aug 15, William Gunn commented:

I think what's really needed here is identifiers for databases, so we don't end up with the same problem that we have for authors and institutions, where there is so much ambiguity. Another job for ORCID?

On 2013 Jul 04, John Overington commented:

A standard for database tag structures would be really useful in general - 1ABC is a PDB code, but it's also many other things, so PDB1ABC would be more general and useful. However, as a database provider this paper highlighted several features that I didn't know and will now explore - e.g. the NLM JATS DTD.

On 2013 Jul 04, John Overington commented:

A standard for database tag structures would be really useful in general - 1ABC is a PDB code, but it's also many other things, so PDB1ABC would be more general and useful. However, as a database provider this paper highlighted several features that I didn't know and will now explore - e.g. the NLM JATS DTD.

On 2013 Aug 15, William Gunn commented:

I think what's really needed here is identifiers for databases, so we don't end up with the same problem that we have for authors and institutions, where there is so much ambiguity. Another job for ORCID?

On 2013 Aug 16, Martin Fenner commented:

I've written a blog post about this paper, and a plugin for the Jekyll blogging platform that automatically detects database links in blog posts, currently supporting ENA/GenBank/DDBJ, Uniprot, PDB and MGI.

It is common practice in the life sciences to add tags right into the text. I don't think we necessarily need identifiers for databases, as proposed by William. Writing the tags as links would already be a major step forward, and that is why I wrote the jekyll plugin.

Even better would be to include database tags in the references of a paper. They would not only be easier to find, but we could also add metadata to the document. But we are probably a few years away from this as we have a strong community practice to have database tags right in the text.