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The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis marcowanger Literature Watch 5 11-15-2011 06:48 PM
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis marcowanger Wiki Discussion 1 11-15-2011 08:58 AM
500 errors on the wiki... dan Wiki Discussion 3 08-14-2011 07:35 AM
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Old 08-12-2011, 05:56 AM   #1
dan
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Smile Better reference system for the wiki?

Currently adding a reference to a page in the wiki, you have to:

1) find the PMID for the reference you want (using PubMed),
2) type the PMID into the form field and click 'Add',
3) arrive at another form where you have to manually fill in the details of the reference
4) then save, and
5) then click to go back to the page you were on
6) to finally see the reference listed there.


Here is the use case I envision:

1) Click to "add a reference",
2) a search form 'pops up', and you enter a search term,
3) the results of the search are presented, and
4) a selection is made.


Popup forms are already implemented in Semantic Forms, so we're already half way there (conceptually). However, I only dimly remember a tool (RefHelper) which allows you to query PubMed and make a selection from the results... I know there are lots of wiki tools out there in this area, but I've never seen a 'complete solution' for the above...

Also, it would be great to not limit ourselves to PubMed, but perhaps query the Mendeley API or similar.


Anybody know of any killer apps in this area? Anyone want to help code it up?

Here are a few of the tools that I know about:

* The RefHelper extension
* http://reganmian.net/wiki/researchr:start
* http://www.mediawiki.org/wiki/Extension:Cite
* http://www.mediawiki.org/wiki/Extension:Pubmed
* http://www.mediawiki.org/wiki/Extens.../bibtex_format
* http://www.mediawiki.org/wiki/ExtensionBLP_Import
* ...
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Old 08-12-2011, 07:50 AM   #2
Joann
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Default PMID or no PMID

Although I lack specific programming skills, my suggestion as a user/reader is to enable a PMID route for papers having the ID--plus an alternate route (very simple) to record papers not in the PubMed system. There is plentiful scientific literature, and growing, outside PubMed's database and the international users of this forum can provide a wonderful referral source to capture and database this literature.

Also, in scanning the Scirus search engine results, I noticed many positive referrals and outright links to SEQanswers appearing on the web pages of professional sequencing centers. National and international. So it would perhaps be a good idea to invite centers to link up to SEQanswers on recommendation of their peer centers.
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Old 08-12-2011, 09:50 AM   #3
marcowanger
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i am not sure how to integrate python into the wiki

How about using a python script?

http://www.joemartaganna.com/bioinfo...le-app-engine/
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Old 08-17-2011, 07:35 AM   #4
marcowanger
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how about using NCBI's eutilities to fetch abstract from PMID.

http://seqanswers.com/forums/showpos...&postcount=107
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Old 08-17-2011, 07:37 AM   #5
dan
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That's the easy part. This is what the citation Pubmed does already, see links above.

The hard part is doing a search, and displaying the set of results for selection, then saving the selection to the page. And integrating this all with SMW.
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Old 08-17-2011, 09:00 AM   #6
krobison
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Even something that took a PMID (when available) and filled in the form would be a great gain. Perhaps you could shave off that smaller use case now, and tackle the bigger version later.
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Old 08-17-2011, 09:20 AM   #7
dan
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Quote:
Originally Posted by krobison View Post
Even something that took a PMID (when available) and filled in the form would be a great gain. Perhaps you could shave off that smaller use case now, and tackle the bigger version later.
That's a good point.

OK, the only issue now is getting the Pubmed extension to add semantic annotation to the results it presents. That should be relatively easy. In this case we won't need a separate form at all. Do you find any advantage in having a separate page per reference?
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