Is The Nar Database List Available In A Computer Readable Format?

Question

[Andra Waagmeester]

NAR nicely lists all their database issues on http://www.oxfordjournals.org/nar/database/c/. Is the list also available in a downloadable format? I could write a parser to create such a list, but I am wondering if I am not reinventing the wheel.

[Neilfws]

You're wondering whether academic journals have figured out how to use the Web for effective transmission of information? I can assure you that they have not. Go write that parser :-)

[Fred Fleche]

Deleted my answer since it seemed out of scope. Sorry for the inconvenience.

Answer 1

[Pierre Lindenbaum]

Not a direct answer, but I'm currently trying to add a wikipedia article for each Database from the NAR 2011 issue: http://en.wikipedia.org/wiki/Category:Biological_databases

UPDATE: You could also use the following pubmed query to get all the articles published in NAR/Database Issue:

"Nucleic Acids Res"[JOUR] "Database issue"[ISS]

save it as XML and use XPATH/XSLT to extract the URLs of those databases. The MESH terms could help you to categorize the databases.

UPDATE: I wrote the (java) program and I blogged about it here.

[Neilfws]

Nice solution. Then write some code to check the response code returned by the URLs, save to database, throw web application on top and submit your own article - "404 not found: a database of non-functional resources in the NAR database collection" :-)

[Andra Waagmeester]

Mmm, can't +1 you for the update :(

[Chris Evelo]

See also the answers to this newer question about Bioinformatics services in general that are no longer accessible: Dead Links And Unmaintained/Broken Web-Services

Answer 2

[Andra Waagmeester]

With the suggestion from @pierre, I wrote a quick and dirty parser. I have uploaded a csv file with pmid, url: http://bit.ly/faX0fm

It surfs my purposes, but you might want to clean it. This list just lists the url's found in an pubmed abstract.