The OpenHelix Blog

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Not me–and not one of the press embargoes.  I’m talking about a data embargo.   While on the way to a workshop this week I was reading my paper issue of Science on the flight.  And I was intrigued by the story of what happened when a data embargo was broken.  The story is: Paper Retracted Following Genome Data Breach, and it is the story of data from dbGaP being published before the authors were permitted to publish on it.

The scientist who helped to develop our dbGaP tutorial had alerted me to this story (hat tip to Cyndy ), because she knew how the dbGaP data access system worked.  In fact, let me quote part of our tutorial that explains it very clearly on slide 12 :

Next is the linked study title, followed by the Embargo Release date for each study. Investigators contributing data to dbGaP may retain the exclusive right to publish analyses of their datasets for a defined period of time. Prior to the Embargo Release date, other investigators may be granted access to download and analyze data, but they may not seek publication of their results until after this time.

There’s a great and risky feature of these large-scale data projects.  Investigators are asked by the NIH data sharing rules to submit data to the appropriate repository even before they’ve had a chance to publish on it.  The risk is people will scoop the submitters.  And that’s apparently what happened in this case.

We’ve also spoken to data embargo issues in the context of the ENCODE project.  In fact, one segment of our tutorial on ENCODE covers that issue.  As more and more “big data” projects roll out in this manner, there’s likely to be more of these issues cropping up.  I think PNAS had a good idea–adding an item to their author checklist that specifies whether data is under embargo rules.  (Oh, and they retracted the paper and you can see the stub here.) But I think it’s also up to the projects and databases to explain the data embargoes clearly.  The people associated with the big data projects understand the rules, but I don’t know that it has percolated through the scientific end-user community fully.   We’re trying to help get the word out with ENCODE and dbGaP in our training materials, but I know the process varies by project.  I think this episode offers a nice “teachable moment” for this.  I’ll be referring to it in future workshops, for sure.

So keep an eye out for this as you use “big data” resources.  But use them–don’t let this dissuade you. Just keep an eye on the calendar.

dbGaP: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap

UCSC Genome Browser (with ENCODE data): http://genome.ucsc.edu/ and http://genome.ucsc.edu/ENCODE/

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

OpenHelix just opened our new web site. We will still be offering the tutorials we’ve always offered (80 and growing!), but now we have a new search engine and database of many more resources. And it’s publicly available and free.

There are now thousands of databases and analysis tools for the researcher to use when doing research in biology and genomics. The first problem the researcher has is just finding those resources, finding the right one. In another step toward helping that happen, we’ve put together a highly relevant, curated database of genomics and biological resources available to the researcher and a search engine to find them based the context of the keyword found at the resource site, tutorials and even our blogs posts that mention the database. You will find that your searches will lead you to resources relevant to your needs. Today’s tip introduces this new search.

We strongly believe this is the best method available now for the researcher not only to find relevant resources, but to find training on how to use those resources. And check back, our database of resources will be growing, as will our features.

The first time I was joking about a gene-based diet plan someone pointed out to me that there already was a book on this, done by what appears to be a sequential peddler of woo.  I’m not going to link to that book, but you can find the details in my previous post on this topic.

So when I saw coverage of a new gene-based weight-loss program on my local TV the other night I just cringed.  The story and video are available on their site.

Dieting Success May Be In Your Genes reports on a woman who succeeded in losing weight after taking the DNA test from Interleukin Genetics.  At the end of the story they say that others experts (who wouldn’t go on camera) were skeptical. But that clearly wasn’t the main point of the story.  The main point was 1 woman (anecdote) lost weight after taking a DNA test.  For $150 dollars.  At least the book was cheaper….

It looks like they have a series of tests for the “worried well” to alter their diets.  And that will be able to drive parents nuts.  At least they do offer something that describes what SNPs they are testing. I’ll be taking a closer look at that literature to see if it corresponds to their claims.

On we go, marching to genorexia nervosa.

Reactome has long been one of our favorite resources for looking at pathways and interactions.  The data quality is very high, and there are some very fun tools to use.   In fact, they were one of the earliest tutorials we did years back (but of course we have updated since).

If you aren’t already familiar with it, you should check it out: Reactome.org And even if you do know about this, you may not know that it also comes in green!  I did that as a Tip of the Week once–and check out Arabidopsis Reactome.  Of course, you’ll also find Reactome data in other places–like Entrez Gene, PID, and more.

And you should also help them out by answering their survey.  Here’s the request from the Reactome team:

Reactome Pathway Database User Survey

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools.  With this in mind, we are actively soliciting comments from the research community in order to assess community needs.  We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq

Thank you for taking part.

Robin Haw
Manager of Reactome Outreach

C’mon: you know the grant agencies and developers really want this kind of feedback. Help them out.

Royal Society and Académie des sciences Microsoft Award was won by Peer Bork this year. The award is funded by Microsoft (250,000 euro) and is given to

recognise and reward scientists working in Europe who have made a major contribution to the advancement of science through the use of computational methods.

It was awarded to Peer Bork for his work on the human microbiome. Peer definitely deserves it, as does his lab.The science and scientists that come from the Bork group are stellar. Ok, so I have a personal interest in this: I worked in his lab for 4 years, from 1999-2003. It was one of the best experiences (science and personal) of my life. Also, BioByte Solutions, started by a Bork lab researcher, has helped put together our new free database and resource search (which we’ll be introducing next week).

Congratulations Peer! Now, what is he going to do with that 368,000 dollars?!

And let me use this opportunity to point out some of the great tools and databases developed by the Bork group:
STRING: Analysis of known and predicted protein-protein interactions in all known genomes (OpenHelix Tutorial, by subscription)
STITCH: Database of known and predicted interactions of chemicals and proteins.
SMART: Domain analysis (OpenHelix Tutorial, by subscription)
iTOL: an online tool for the display and manipulation of phylogenetic trees.
XplorMed: Dataming in MedLine (OpenHelix Tutorial, by subscription)

And a whole lot more

There’s a Symposium tomorrow at Boston University for any of you in the area.  It is a celebration of “Temple Smith’s retirement and emeritus appointment” officially, but it’s a nice series of talks with a variety of perspectives for those of us in the cheap (= free) seats.

Looking forward to an informative day.

The details can be found here: http://www.bu.edu/dbin/bme/smithsymp/

I’ll be taking notes, and I hope to have new resources and tidbits on the topics next week.