Mmm, can't +1 you for the update :(
Question: Is the NAR database list available in a computer readable format? |
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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. |
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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: 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: [?]http://plindenbaum.blogspot.com/2011/04/404-not-found-database-of-non.html[?] |
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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" :-) See also the answers to this newer question about Bioinformatics services in general that are no longer accessible: http://biostar.stackexchange.com/questions/7547/dead-links-and-unmaintained-broken-web-services | ||
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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. |
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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 :-)
Deleted my answer since it seemed out of scope. Sorry for the inconvenience.