Which Of The 2011 Nar Database Submissions Are Fully Accessible?

Question

[Jeremy Leipzig]

Out of curiosity I would like to classify the databases in the 2011 NAR Database Issue by accessibility, specifically which ones offer:

1. A complete download of the data
2. A web service (REST or SOAP) which allows automated queries from robots
3. A bookmarkable website that allows links (i.e. the GET protocol) to individual records without necessarily going through a search form

For example,

Database  Complete Download?  Web Service?   Bookmarkable?   If yes, provide example:
COMBREX   No                  No             Yes             http://combrex.bu.edu/DAI?command=SciBay&fun=proteinCluster&pClusterID=419683

But I can't do this alone.

So if you are interested please visit one of the databases and report your findings (or corrections) here. I'll compile the responses into a spreadsheet and report.

Here is a Google Docs Spreadsheet if you wish to edit it directly (it's wide open): https://spreadsheets.google.com/ccc?key=tZQGRMg24BHKgO4vUjYT5TA&hl=en#gid=0

Per Andra's suggestion, I have decided to put this up on Amazon mturk:

https://www.mturk.com/mturk/searchbar?selectedSearchType=hitgroups&searchWords=nar&minReward=0.00&x=0&y=0&=%2Fsearchbar#

[Pierre Lindenbaum]

Jeremy wouldn't it be better to create a shared Google-Spreadsheet for this ?

[Casbon]

You should check for an open data licence as well. More here: http://www.isitopendata.org/

[Michael Kuhn]

I agree with Pierre. The first step IMHO would be to extract all the URLs from the abstracts (the abstract should have an URL according to the NAR DB issue guidelines) and dump them into a Google Spreadsheet.

[Jeremy Leipzig]

Yep I just wanted to keep things in this forum.

[Pierre Lindenbaum]

I've just added a row for each article...

[Pierre Lindenbaum]

Jeremy, I've suggested to create an article for each DB in wikipedia: http://goo.gl/5jUoK . The infobox would contain the information about the web services.

[Jeremy Leipzig]

Shocking how many broken links (404) and busted webapps (500) I've encountered already

[Egon Willighagen]

In the 2011 issue?? Wow!

[Pierre Lindenbaum]

Thanks Jeremy ! I didn't understand what was exactly Amazon mturk until now :-)

[Istvan Albert]

Hey Jeremy - it is a fun question

[Dan]

Did you make the data available?

[Jeremy Leipzig]

I was not able to make the MTurk thing work for some reason - i don't even know if that is still a thing.

The spreadsheet link is still active.

Answer 1

[Andra Waagmeester]

I am using amazon's mturk (http://www.mturk.com) for these kind of tasks. I am constantly looking for curated databases that contain citations to pubmed. Going through NAR (and Pathguide.org) manually is not doable. In mturk you can ask so called workers to do specific tasks for which they will be rewarded based on the complexity of the questions asked. For a question like this I would pay between a penny and 5ct for each evaluated website. I will run a new mturk task soon. I will see if I can manage to incorporate your question and will report here.

Answer 2

[Jeremy Leipzig]

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Download: no

Web service: no

Bookmarkable: no

This one is odd because it is PHP-driven and non-AJAX, so the search results could have just as easily been bookmarkable

Records are accessed post-hoc job style like in NCBI BLAST so I don't think these are permanent: http://t.caspur.it/ASPicDB/newresults.php?organism=human&job=list1507/job1