What Is Your Approach In Finding, Managing And Categorizing Bioinformatics Literature?

Question

[Andra Waagmeester]

To find literature I use a set of different search engines (Pubmed, Google Scholar, ACM.org, etc). Sometimes directly at their website or through literature managers such as, Jabref and Mekentosj Papers. The latter is great, since it captures the pdf locally.

Then I use connotea, citeulike, and WikiPathways to order my collection. Recently I even started using twitter to manage literature annotations.

Still it happens, even often, that I "loose" papers. I know that I have read a paper, but I don't manage to find it again. I forgot under which label or where I had stored it, or even that I had annotated it.

With all the technology in place, I am still not able to track literature completely.

That is why I am looking for other approaches to optimize my literature management strategy.

Answer 1

[Giovanni M Dall'Olio]

My approach is to use the mendeley software to organize my collection of articles. The software is free and works very well: you can store the pdfs of the articles, write notes on them, and synchronize everything on all the computers you own.

Another alternative is Zotero, a firefox extension that enables to bookmark articles as you find them in pubmed or on the web. I have been using zotero before mendeley and I have been very happy with it.. I switched because zotero missed some feature that mendeley had, but that gap has been reduced now. The difference between these two software is that mendeley is a stand-alone program, while zotero runs within the browser.

As for searching articles, I mainly use pubmed and google/scholar. However, this article that I was reading earlier this morning on Nature Precedings could give you some ideas:

• Bajpai et al, Nat.Prec 2011. In search of the right literature search engine(s)

[David W]

A standalone zotero is being developed at the moment. Still alpha but looks exciting: http://www.zotero.org/blog/zotero-standalone-alpha-with-chrome-and-safari-support/

[Thaman]

+1 for mendeley

[Niallhaslam]

+1 for mendeley. I made the switch from citeulike (mendeley allows importing) and it makes life way easier. You can create a watch dir and when new files are added to that dir mendeley sorts them. Groups and stuff are also useful.

[Giovanni M Dall'Olio]

@david w: thanks, I'll look at the zotero standalone app.

[Michi]

zotero! and in our group we have our own webdav-server. Easy to organize, easy to share with group. And also it lets you add the pdf-files so you can access at home ;-)

Answer 2

[Thaman]

There are other search engines like:

• ScienceDirect
• oxfordjournal
• Scitation
• IEEE Xplore (Huge collection)
• Nature
• BioMedical engineering online,
• bioinformatics.fr,
• BMC Bioinformatics,
• SpringerLink,
• CiteULike

The technique of finding and searching of appropriate literature is provided in an individual sites. For managing literature

• TeXMED, a utilty to searching PubMed and returning BibTex formatted hits.
• BibTex
• EndNote - Useful tool which I use
• Zotero, a plug-in for Firefox that provides a complete reference management system that saves the database in a central site, accessible online. Mentioned by Giovanni too.
• mendeley - Great! mentioned by Goivanni

Sync/Sharing in devices

• Window Live Share
• Dropbox (Obviously the best choice)
• Box.net

[by0]

Might want to add pubtex to the list for managing literature :)

Answer 3

[Simon Cockell]

My literature management strategy has 3 generic steps, with exceptions for special cases (obviously, this is Bioinformatics after all)...

1. I have persistant searches at hubmed.org, which return an RSS feed I can import into Google Reader.
2. Articles I want to read are bookmarked in CiteULike. In general, if I can't get the full-text of an article, I don't bookmark it.
3. As a note, it is possible to send articles to CiteULike from within Google Reader.
4. PDFs are imported into Papers for local management. The Spotlight indexing of full-text by Papers means I have never lost an article I couldn't later rediscover.
5. Papers sorts PDFs logically for me (directories by year/author initial, filenames by article title), and my library is in my DropBox folder, so is available on all my computers, whether Mac or not.

Step one is obviously bypassed for papers I discover by alternative means (Twitter, Friendfeed etc etc), although it does mean I have been able to completely eliminate ToCs from cluttering my inbox.

[Carlos Villacorta]

I also use Papers in my Mac coupled with Dropbox. I wish there was an easy way of browsing the collection from my other Linux laptop.

Perhaps exporting the collection from Papers to a bibtex file that I can open in Linux. But it's a pain doing it everytime I add new articles. Any suggestion?

[Simon Cockell]

Carlos, you could use Mendeley to 'watch' your Papers directory. This would at least give you a dynamic view over the PDFs in there.

Answer 4

[Neilfws]

I subscribe to ~ 30 journal RSS feeds using Google Reader. This allows me to cycle quickly through new articles ("no, no, no, no, ah - that one maybe"). I've set up the "send to" feature, to bookmark articles in CiteULike. Then I upload the PDF to CiteULike too, either at the same time or a little later.