Tag Archives: pubmed

New Online Tutorial for iHOP from OpenHelix

Comprehensive tutorial on the publicly available iHOP database enables researchers to quickly and effectively use this invaluable next-generation resource.

Seattle, WA,  August 10, 2009 — OpenHelix today announced the availability of a new tutorial suite for iHOP, or Information Hyperlinked Over Proteins. iHOP is a sophisticated, next generation text-mining database that provides comprehensive up-to-date information on specific genes and proteins by automatically scanning millions of PubMed abstracts each day. iHOP provides fast, accurate, comprehensive summary information on more than tens of thousands of genes, chemical compounds and Medical Subject Headings (or MeSH) terms. iHOP will selectively present only the information on genes and proteins you want. The control over the reliability and relevance of the retrieved information always remains in the hands of the user.

iHOP contains more than 15 million sentences and 80,000 different genes from over 1500 organisms and is updated daily. iHOP converts information derived from sentences in PubMed abstracts into one navigable resource using genes and proteins as hyperlinks. Superimposing this network of information on experimental interaction data makes simultaneous analysis of new and existing knowledge possible.

The iHOP tutorial suite, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contains an online, narrated, multi-media tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. The iHop tutorial will teach users:

  • to understand the four main iHOP views
  • ways of filtering your searches to optimize results to your needs
  • how to use iHOP Gene Model to keep track of interesting sentences
  • how to download data from iHOP

With OpenHelix tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others. To find out more about this and over 70 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About iHOP
iHOP was conceived and implemented by Robert Hoffmann and is maintained at the Computational Biology Center at Memorial Sloan Kettering Cancer Center headed by Chris Sander. iHOP is a free service from the academic domain, licenced under a Creative Commons Attribution-No Derivative Works 3.0 License.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

iPhone and research

Ok, so I just got my new iPhone 3Gs. I couldn’t resist. Anyway, my contract on my first generation iPhone was up. So, it was time to reconfigure and explore the huge number of apps out there for the iPhone.

I use the iPhone for a lot of things, directions, finding out what stores are in the area, keeping my grocery list, listening to music, watching shows, browsing the web, keeping my calendar and contacts and a bunch more. Oh, and to make and receive phone calls :).

I’ve read past posts on other blogs about scientific apps for the iphone, I decided it was time to check out what apps there are now.

I’ve found a few I like, some that might work (I do computational genomics now, so I haven’t tried the ones for the bench), and one that has nothing to do with biology (directly anyway), but I am in love with. Follow me below the fold.

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Tip of the Week: It's a duplicate

dejavu_thumbThere are a lot of research papers out there, more than ever. Along with the good news (increasing knowledge), comes some bad news: increasing duplication and plagiarism, more often than not going undetected. The developers of eTBLAST, which is a great tool we’ve had a tip on before, have created another tool using an eTBLAST search of Medline and other databases to find highly similar citations: Deja Vu.

These similar citations could be legitimate; a review of a previous article, an author using similar wording of an abstract from a previous paper for new research (the eTBLAST search can only search titles and abstracts), sanctioned duplications, etc, etc. as the author of the post “Deja Boo” points out. There are some real instances of duplications (authors attempting to pad their CVs) and plagiarism (stealing words and research). An earlier example (before Deja Vu) found at Panda’s Thumb is of a creationist attempting to pad a CV and look more legitimate. Errami and Gardner (two of the developers of the tool) published a paper in Nature earlier this year with many such instances of (and another in Science, reported on here with some interesting discussion) duplication and plagiarism.

Still, the database needs to be viewed with caution. Of the 74,792 ‘highly similar and duplicate citations’ found, 92% have not be verified. Of the 8% left that have been verified (this has to be done by manual curation), 65% have been found to be probably legitimate (as stated above) and 35% to be duplicates. But even the duplicates aren’t necessarily nefarious. Since full texts are not available, it is often the case that the duplication might be perfectly understandable (reusing an abstract with some minor changes for new research, etc). Still, it is a tool that, with some work, can help tremendously in that search for true duplicates and plagiarism, and perhaps even just the threat of it might lower the instances?  :D

So, with that in mind, this week’s tip of the week is a quick view of “Deja Vu.”

Swine Flu: What's the Populous to Do?

Well, as far as I can tell, read & do all the normal stuff for staying healthy (you know, all the stuff Mom used to say – wash your hands, drink plenty of liquids, eat right & get plenty of sleep.) I heard about swine flu as I woke up yesterday morning listening to NPR, and the coverage of the “outbreak” seems to be spreading more virally than the virus itself. PubMed already has a special section of their homepage dedicated to swine flu info, with links to recent PubMed articles,  a link to the swine flu sequence in NCBI’s Influenza Virus Resource, and a widget to CDC’s swine flu information page.  Through one of the PubMed references I found a resource I had not heard of before – ESNIP2 – the European Surveillance Network for Influenza in Pigs.  From the sequence report I could like to structures in NCBIsmall_world_3‘s MMDB and from there to structures in RCSB PDB.  From the CDC’s site I followed a link to an update from the World Health Organization which reported the number of cases and deaths in various world locations. I find it really cool to be able to link so freely between biological/health information resources, and be able to counter all the popular media frenzy with reports of real science. And the fear mongering seems to be just that, at least for now, because nothing that I’ve read so far indicates that swine flu is any more deadly or virulent than ‘normal’ seasonal flu – it is just a different virus than we normally see.

Yea, ok, we live in a small world where people move around and potentially spread diseases far and wide. But there is so much information at our finger tips – with an internet connection and a bit of knowledge where to look. I’ll continue to take my risks, travel, read science, and of course listen to Mom & wash my hands! :)

Addition (Trey): These are some great resources that Jennifer linked to. I’d like to include some additional general and genomic data too. I’ll add more as I find them:

Kristi at Bioinformatics@Becker (she’s here at Wash U where we are giving a seminar today) has a great post with links to many general and science links.

BioHealthBase has the swine flu strain genome details. BioHealthBase “provides a comprehensive genomic and proteomic data repository for five pathogenic organism groups that pose a threat to public health”

Effect Measure is a MUST read blog for anything public health policy and science related, and is a great read right now.

A short primer on the science of the swine flu.

Tip of the Week: Subscribing to journal updates with NCBI

NCBI RSSTwo weeks ago, I showed you how to use HubMed, an alternative search interface to PubMed, to subscribe to a feed for a specific journal, allowing you to stay up-to-date on new articles and issues of that journal. As mentioned earlier, many journals have feeds to their updates, but using PubMed and HubMed are good alternatives if you can not find a feed, want to customize it a bit or just like a single place to go to for all your feeds. This week, I’m going to show you how to do the same thing, subscribe to a feed for a specific journal, using NCBI as suggested by a commenter in the Tip of the Week a couple weeks ago.

Tip of the Week: eTBlast

etBlasteTBlast is a great tool for searching the literature, not only PubMed, but also CRISP (a database of federally funded biomedical research). Unlike PubMed or CRISP, you don’t use a few well chosen (hopefully) keywords, you can just paste in an entire paragraph or abstract and eTBlast will search and find papers similar to the entire paragraph. It saves you the time and effort of trying to narrow your search down. Just wrote that amazing research up and need to find citations for it? or granting agencies, experts in the field or the best journal to submit it to? eTBlast can help you with that. Want to do some boning up on a new field? eTBlast can help you create that reading list. This 5 minute tip shows you quickly how to use eTBlast and obtain some relevant results.

The eTBlast server site at Virginia Tech also hosts the handy ARGH search tool, allowing searches for acronyms used in biomedical contexts.

Bioinformaticist survey results

Mary wrote about this Bioinformaticist Career survey previously and now the results areblast survey out (that’s some analysis, here are the full results).

Looking through the results and discussing it briefly with others, I would say that there is nothing particularly surprising from my experience in the bioinformatics field. The survey reflects what I see today. What is notable is that many bioinformaticists in the survey have commented that they see the future of bioinformatics moving toward more integration with other fields and more cross-disciplinary needs, as illustrated by this comment by one (and many others):

“bioinformatics will be incorporated into cross-disciplinary work by scientists that will learn to use computational tools and insights as a commonplace part of their experimeweb site usents, part in silico, part wet bench”

I would agree, though of course I could well be wrong :), with that and along with that will come the need less for ‘bioinformaticists’ and more for biologists trained in bioinformatics. A quick look of some of the analysis is also not particularly surprising, BLAST is by far and away the most cited application of use (lots of alignment and phylogeny stuff there too) as can be seen by the chart (left ) on the results analysis site. Asked which web application/site they use most, it’s an interest mixture between utility sites Google Docs (hmm, maybe there’s something I should look at there :), Gmail, Twitter, WordPress and biological resources like NCBI, UCSC Genome Browser, Ensembl, BLAST, Connotea and PubMed. I think the questions here might have been designed better. Those are two entirely different categories and I would love to see the results (of course ;) for the resources if that was more explicitly asked. Perhaps next survey (btw, that those 5 biological resources made the it in the graph is no surprise to me).

It will be interesting to go through this data in some more detail!

Don't blink, PubMed adds a feature

It’s not ground breaking and you probably hadn’t noticed it yet, but it looks like something that could add some more, possibly useful, info to your PubMed searches. Last week, Pubmed announced on their technical bulletin that they’ve added a column to the right of the PubMed search summary which will contain results from other resources based on your search. Think of it as kind of an Amazon’s “you might also like” feature.

You might be forgiven for missing it because unless you are searching for one of the 200 drugs they’ve added this feature for (or read their technical bulletin), like “lovastatin,” you won’t see the column and links to the other resource. This other resource is the “Clinical Q&A” for the first implementation of this feature. It will be interesting to see how that develops and grows over time.

Tip of the Week (showcase): Firefox Biobar

biobar tipUsually, we do our own tips for the week (in fact, up till today, always) and today I was going to do one on the Firefox Biobar, an excellent Firefox addon that allows you to search and retrieve data from dozens of databases and resources at one time right on your browser bar. I just rediscovered the biobar since I’ve been using a different browser (not Firefox) for a long while and recently returned to Firefox for most of my browsing. I remember why I liked Biobar. Nice quick way to search a lot of databases from PubMed to Wormbase. Well, I was going to do a tutorial, but in my search about the BioBar, I see user Simont from Scivee already did an great tutorial on installing and using Biobar, so I’m linking to that here! Ok, so it saves me time, but why duplicate efforts? He did a fine job. Check it out.