Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…
This is mostly a note to me to read this later, and check the damn variants I got from my eczema family: RT @NicholasMMurphy: Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis. http://t.co/IcUfoxVG #GWAS [Mary]
Cute, but certainly only a fraction of tools out there: RT @spitshine: RT @alexbateman1: Very neat Periodic table of Bioinformatics from @eaglegen http://t.co/w0MvWIbu Shame its missing Pf [Mary]
” provides a central location for voluntary submission of genetic test information by providers. The scope includes the test’s purpose, methodology, validity, evidence of the test’s usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.”
I’m always interested in checking out new resources from NCBI, especially when it is my turn to do a weekly tip. Initially I figured that I would check out the GTR and post a video on how to use it – but the NCBI beat me to that. You can see their YouTube tips (there are two) by clicking the link on their homepage & learn some search tips, etc. [Note, the two videos continued to loop for me & I needed to stop them after viewing them once].
But the question that I came up with is, “What will the GTR provide me with that I am not already getting from other clinical resources that I use, and that OpenHelix trains on?” I try to address that question in my video by doing the same search, for “Cystic fibrosis”, at five different clinically-related resources, and discussing what each offers and specializes in doing. Of course, in a five minute video I can’t be comprehensive – either for resources or what they cover – but I think it will give you enough of a taste for you to appreciate what the GTR offers you, or to continue the comparison on your own.
The resources that I visit in the tip movie are: the GTR, GeneTests, the Genetic Home Reference (GHR), OMIM, and Orphanet. At each resource I do a basic search for the the disease “Cystic fibrosis” and show the initial results display that resulted. I don’t have time to compare the detailed reports available at each, but lower on the post I link to a reference on the resource (if available), as well as the landing page for OpenHelix training materials on the resource – since we have a tutorial on many of these resources. I also include direct links to each resource.
I’d suggest that you read the NIH News article on the GTR release for some background on the GTR. I won’t cover everything here, but there are a couple of paragraphs that I want to point your attention to. The first explains the relationship between GeneTests and GTR, and says:
“GTR is built upon data pulled from the laboratory directory of GeneTests, a pioneering NIH-funded resource that will be phased out over the coming year. GTR is designed to contain more detailed information than its predecessor, as well as to encompass a much broader range of testing approaches, such as complex tests for genetic variations associated with common diseases and with differing responses to drugs. GeneReviews, which is the section of GeneTests that contains peer-reviewed, clinical descriptions of more than 500 conditions, is also now available through GTR.”
It seems to be another case where it was deemed easier to start a new resource (GTR) than to try and revamp an old resource (GeneTests) to handle the amazing influx of new data. Often resources aren’t retired as soon as expected, due to user feedback, but it is important to note that GTR seems to be in place to eventually replace GeneTests. I assume the GeneReviews will still be edited by & copyright to the University of Washington, Seattle, but I don’t have a reference for that. The similar transition occurred for OMIM, which was hosted at NCBI for years but now has a new URL at Johns Hopkins (watch for our new tutorial on OMIM, which is currently in the works).
The second paragraph that I found particularly interesting was the one on what the GTR contains, and will contain. It states:
“In addition to basic facts, GTR will offer detailed information on analytic validity, which assesses how accurately and reliably the test measures the genetic target; clinical validity, which assesses how consistently and accurately the test detects or predicts the outcome of interest; and information relating to the test’s clinical utility, or how likely the test is to improve patient outcomes.”
I didn’t immediately find mention of who will provide the validity or utility information in the GTR documentation, which is currently under construction. It is clear that much of the content of the database will be “voluntarily submitted by test providers”, and it is stated that “NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading.”, but I also saw that experts will input on GTR’s content regularly, as can be read here. The GTR team is also very interested in receiving input on the resource, which can be submitted through the GTR feedback form.
*OpenHelix tutorials for these resources available for individual purchase or through a subscription
For GeneTests (free from PMC) – Pagon RA (2006). GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94 (3), 343-8 PMID: 16888670
For GHR (free from PMC) – Mitchell JA, Fomous C, & Fun J (2006). Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94 (3), 336-42 PMID: 16888669
For OMIM (open access article) – Amberger, J., Bocchini, C., & Hamosh, A. (2011). A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) Human Mutation, 32 (5), 564-567 DOI: 10.1002/humu.21466
For Orphanet (full access requires subscription) - Aymé, S., & Schmidtke, J. (2007). Networking for rare diseases: a necessity for Europe Bundesgesundheitsblatt – Gesundheitsforschung – Gesundheitsschutz, 50 (12), 1477-1483 DOI: 10.1007/s00103-007-0381-9
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…
Nice video on RNA interference by Nature Reviews Genetics. You can access all of the featured RNAi multimedia links from this page, or go straight to the video on this page. [Jennifer]
Interesting, The Repertoire 10K (R10K) Project: RT @deannachurch: CG: go to http://t.co/rekf2Gkd for more information on joining the project! #AGBT [Mary]
And it’s not in the papers anymore… RT @genome_gov: Pachter: “My worst nightmare: the curse of deep sequencing” aka too much data. #AGBT [Mary]
Read a Nature Outlook on allergies from Nov. 2011 – lot of new philosophies & theories that I wasn’t aware of. Currently free full access is available to the Nature Allergy Outlook [Jennifer]
Most Wednesdays our blog features a 5 minute movie introducing you to a new resource, or a new feature at a well-established resource, or something similar. Occasionally we provide you with something much more – a full length, full feature introductory tutorial on a resource. This week is one such “full feature” tip.
For today’s tip I am offering our full introductory tutorial on the RCSB PDB, which we completely updated to cover their Top Search Bar, PDB 101 education feature, and more. Our revised materials were released at the beginning of the month, so I thought it would be great to feature as my February tip. From the suite landing page, click on the “Launch Online Tutorial” button to view the movie, or use any of the download buttons to obtain our slides (with full script), exercises, or handouts.
My mentioning downloads reminds me of a question that we get frequently, and got again in our RCSB PDB webinar that we presented last week (as you can read on our webinar follow up post here): “Can I useOpenHelix materials in a class that I am teaching?” The answer is absolutely! We would love our materials to be used as quick course materials, lab or journal club presentations, etc – anything that furthers their reach, actually. Our only request is that it not be for profit, and you don’t remove our copyright messages. We try to make it easy to use our materials too because we include the full script for our slides in the notes area of them, so there’s no guessing what information is being covered on any particular slide. And our exercise documents are designed so that you could offer your students either just the first page, to work on their own; or the full document which leads users step-by-step through each hands-on activity at the resource. So by all means, use this tip, and all of our RCSB PDB training materials for your own benefit, as well as that of your students, lab mates, etc. Enjoy!
Original RCSB PDB paper – Berman, H., & et al (2000). The Protein Data Bank Nucleic Acids Research, 28 (1), 235-242 DOI: 10.1093/nar/28.1.235
More recent RCSB PDB reference – Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J., Young, J., Yukich, B., Zardecki, C., Berman, H., & Bourne, P. (2010). The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq1021
It’s been a about a month since I attended the ScienceOnline2012 “unconference” on science communication. There have been many great posts summarizing the meeting, or specific sessions, or extending conversations started at the meeting, some of these ScienceOnline2012 posts are listed here. I’ve decided to add my voice as a set of thank yous, organized by the events that I attended.
I got to Raleigh just in time to hop the shuttle from the hotel to the McKimmon Center at NC State University. Before I even made it in the door I got to hug Bora – and no, I never did come down with nerdibacter12! I have enjoyed the intimate Sigma Xi center, which was the site for all the previous ScienceOnline conferences that I had attended. However I was immediately struck by the fact that the McKimmons Center is a REALLY nice facility! It felt like it was built for ScienceOnline, rather than allowing us to be in their building. There was a lobby area in front of two large rooms, one set up as Karyn Traphagen’s brilliant Cafe where I got coffee. The second large room was set up as a small auditorium and where I attending the keynote address, etc. On either side of the two large center rooms were conference rooms of various sizes. The whole layout of the center provided plenty of room and encouraged movement through spaces to other spaces. I think this flow and space was really essential for the success of the conference, and I thank NC State University and the staff of the McKimmon Center for hosting ScienceOnline2012. I request that you host future ScienceOnline conferences as well, if at all possible.
The keynote address was entitled “The Vain Girl’s Survival Guide to Science and the Media” and was delivered by Mireya Mayor, who told her personal story of how she got to science & how she is doing it as a mother of four. Just the other day Mary & I were discussing how new areas of science need new types of people – not just the middle-aged white guys in stuffy lab coats – and Mireya’s story is a great one of how she overcame society’s expectations of her in order to “do her own science thing”. I’m hoping to get her book “Pink Boots and a Machete” soon to learn more about her. Thanks Mireya for coming & sharing your story with the scio12 gang!
Then it was time to attend my first session & I was already torn. I chose to attend the Dealing with Data discussion with Antony Williams and Kaitlin Thaney. Their session was great, including a lot of active discussion about peoples’ willingness to use shared data, but not to share data. If there had been two of me I would have also attended the Science Scribe 2.0 hands-on workshop by Perrin Ireland. People who were in it said it was great & it is such a cool concept. After lunch I joined a very interesting Open Notebook Science discussion with Jean-Claude Bradley and was surprised that there is no great software for keeping an open notebook, even though NIH & other funding agencies are encouraging fundees to do “open science”. I then joined the Sex, Gender and Controversy: Writing to Educate, Writing to Titillate discussion with Scicurious and Kate Clancy - the discussion in this session inspired my scio13 program suggestion. Thanks to all Thursday session leaders!
Thursday evening shuttles took conference attendees to the North Carolina Museum of Natural Sciences. I’d been there before with my family but being there with finger food, beer & lots of friends & other attendees was great! One of the highlights of the evening was getting a “behind the scenes” tour of the museum’s new Nature Research Center, which is still being constructed but will open April 20th with an opening gala April 13th. With any luck I’ll be able to go back & visit the new center shortly after it opens, since it looks very cool & “hands on”. Another highlight was a brief talk by Meg Lowman, the director of the Nature Research Center. It was nice to see Meg again this year – last year she gave a great banquet talk. Thanks NC Museum of Natural Sciences for opening your doors to us!
A third highlight of the evening was enjoying delicious Kentucky Ale from Alltech & hanging out with David and Kate from Alltech. I met David last year & enjoyed catching up – Alltech is close to where I got my PhD so I caught up on favorite restaurants, etc. I just met Kate this year, but had a great time talking to her. At Kate’s suggestion I tried “branded” eggs from Eggland and in a side-by-side scrambled egg taste test my daughter & I both tasted a difference. Kate explained to me that buying particular brands of food allows you to buy food produced or grown in certain healthy ways. For example, you might choose certain meat brands because you know they don’t use hormones & do feed their animals certain foods – like Alltech’s natural livestock feed supplements. I enjoyed my evening with David & Kate (among others) enough that I’ve been talking to people at a local beer store that my neighbor runs, hoping to be able to buy Kentucky ale throughout the year! Thanks Alltech!
In the evening I attended the conference banquet and enjoyed seven stories by seven attendees. The storytellers were guided and mentored by Jeff Polish, founder and Director of The Monti (and who also looks and sounds a bit like a hip Ray Ramano). The Monti is a cool “non-profit organization that invites people from the community to tell personal stories without the use of notes.” The ScienceOnline2012 Monti stories were amazing – no description possible, just go listen to them for yourself here (note, there is some ‘over 18′ content in some of the stories). Thanks to Jeff and all the storytellers – you guys are amazing!
Thursday evening I retired to the hotel bar with a LOT of other attendees for the informally organized “scisweetup”, which was a chocolate tasting event that brought out SO much chocolate & in SO many flavors! You can see pictures of it here. Thanks to the scisweetup organizers (without whom I might have spent the night in my room sleeping) and for all the other participants – I enjoyed your chocolate & I hoped you liked mine.
In conclusion, I’d like to thank everyone involved in making this great conference happen – the sponsors, the session leaders, and especially the organizers – Anton, Bora and Karyn! It was amazing, as you can see in the short video here that captures the spirit quite well.
The February 15th “How to use the RCSB Protein Data Bank” webinar may generate some questions that we won’t have time to cover or there may be further questions that arise. So we’ll leave this blog post open for follow-up on issues that arise from our discussion. Feel free to add your questions as comments to the post.
1. We were asked about differences in what I was showing in my screenshots, and what people were seeing on RCSB PDB pages. There are two possible reasons that this might be.
The first reason is that not all structures are associated with all types of information. For example, if you compare the 2ara structure summary page to the 2arc structure summary page you will notice that the 2ara page is the apo form of the molecule and does not have a ligand, a “Ligand Chemical Component” area, or an area for External Ligand Annotation information. The 2arc structure is bound to its ligand, alpha-L-arabinose (or ARA) and so it does have both Ligand Chemical Component area and an area for External Ligand Annotation on its page. The information that you see on various RCSB PDB pages will depend on what is available for the specific entry that you are looking at.
The second reason is a bit more trivial, but equally important – RCSB PDB pages are constantly being updated, and so while the screenshots in our training materials do accurately represent the overall organization and features of resource pages, specific numbers, reference lists, etc. may change over time from what our screenshots show. We work closely with the RCSB PDB developers to keep our materials up-to-date with major software updates that would dramatically change functionality of the tools we present.
2. Another great set of questions that we got during the webinar is whether people could use our materials for their students, and where to download our free training materials on the RCSB PDB.
We would be delighted if our materials were used to teach students, or were presented as a group meeting, etc – really any non-profit use of our freely available materials is fine by us – as long as you don’t remove our copyright notices. We often “train the trainer” in our live seminars or webinars, who then go out and further the reach of our materials by using them to train others at their institutions. And we’ve heard that our materials are great to use in a classroom because not only do we offer the online modular tutorial movie that can be watched online from any browser, we also provide PowerPoint slides with the full script text, handouts for note taking, and an exercise document that can be handed out as a class assignment, or used for a classroom “walk through” discussion.
All that leads to the next part of the question, where can I download OpenHelix’s free training materials on the RCSB PDB? You can download materials free of charge, and without registering at our RCSB PDB tutorial landing page. Just click any of the buttons on the page to 1) launch the movie, 2) download any of our materials, or 3) visit the RCSB PDB resource.
We’ve all seen the discussions – on twitter, in journals, lots of places – on how to collect, store, find and use all the data that is and will be generated. Here at OpenHelix we believe that there is a gold mine of bioscience data that is being vastly underutilized, and our goal is to help make that data more accessible to researchers, clinicians, librarians, students and anyone else who is interested in science.
We go at our goal in a variety of ways, including: this blog with its weekly tips, answers and other posts; with our online tutorial materials on over 100 different biological databases and resources; and with our live trainings, many of which are sponsored by resource providers such as the UCSC Genome Browser group.
In today’s tip I will introduce you to another one of our efforts to “extend research” by showing you a glimpse of an OpenHelix app that we designed for the SciVerse platform, which Elsevier has described as an “ecosystem providing workflow solutions to improve scientist productivity and help them in their research process”. This app scans a ScienceDirect journal article for any database names or URLs that we train on, and then displays a list of such resources in the window of the app. A researcher can use this list to go from a research article to our training on how to use the resource, and to the resource itself. We believe this type of integration will help extend research by making it easier to find, access and use data associated with a paper. If you have access to articles through ScienceDirect, and you try out our app, please comment here & let us know what you think, or suggest future enhancements. Also you could consider reviewing it for the app gallery. Thanks!
References: Reference shown in Tip (subscription required): Mortensen, H., & Euling, S. (2011). Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century Toxicology and Applied Pharmacology DOI: 10.1016/j.taap.2011.01.015
OpenHelix Reference (free from PMC here): Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010). OpenHelix: bioinformatics education outside of a different box Briefings in Bioinformatics, 11 (6), 598-609 DOI: 10.1093/bib/bbq026
SciVerse Reference (subscription required): Bengtson, J. (2011). ScienceDirect Through SciVerse: A New Way To Approach Elsevier Medical Reference Services Quarterly, 30 (1), 42-49 DOI: 10.1080/02763869.2011.541346
There have been tweets asking for links to posts about ScienceOnline to be added to the ScienceOnline2012 blog and media coverage. I clicked on & read a few of the posts, including Anton’s Sixth time around – ScienceOnline2012 coming soon post. It inspired me to look back on what attending ScienceOnline has meant to OpenHelix. We are lucky enough to have attended all but one of the six ScienceOnline conferences, and in this post I thought I’d highlight some of the benefits that we’ve gained from our attendance each year.
2008: We didn’t make it to the first Science Blogging meeting, which occurred in 2007 and had about 150 attendees (as described in this post from Bora), but in 2008 Trey and I attended the second annual North Carolina Science Blogging Conference. In 2007 OpenHelix was awarded a Phase II SBIR grant to expand our training materials and as part of our outreach & communication mandate. On Dec. 20th, 2007 we began this OpenHelix Blog, with our first full post “Pinot noir genome, for your holiday contemplation” published the next day, so it was a natural fit for us to attend a blogging conference January of 2008. We learned a lot at the conference, had a lot of our blogging theories and approaches reaffirmed, and met phenomenal people & projects. Trey discussed one of those in his post “Research Blogging (Science Blogging Conference)“, and we’ve recently reached a couple of ResearchBlogging.org milestones that we are quite proud of: we now have contributed well over 100 posts and have over 60,000 views. And we see a lot of benefit from those views because people find us on the ResearchBlogging.org homepage’s recent Post List, follow links over to our blog, and end up reading & commenting. In a recent conversation with Dave Munger, we discussed one of his newer efforts ScienceSeeker.org beta, which we are already members of. I’m sure we’ll have more on that effort in the future. I also vaguely remember sitting with a table of marine biologists at the Town Hall Grill the first night, one of whom told me about tweeting while he tweeted about our chat.
2010: As odd as it sounds, my most memorable Scio10 moments were food based. One lunch I split an Only Burger burger & fries with the wonderfully cool Danielle Lee – oh my gosh that burger was good! (@DNLee5 – let me know if you wanna split another one this year if the truck shows up one lunch!) :) I also had the pleasure of sitting at a banquet table with Andrea Novicki and Lenore Ramm. As we were talking, who should join us but Anton Zuiker! I got to hear “behind the scenes” stories about the conference, such as testing SignalShare to the edge of their wifi-providing abilities – and these are the people who provide for events such as the Grammys, etc. It was fun & I have been reading & sending people to the Coconut Wireless ever since. I also learned about some blog legalities from Victoria Stodden, attended a great librarian session from Stephanie Willen Brown & Dorothea Salo, and hears about Science in the Cloud with John Hogenesch. #scio10
2011: Each year ScienceOnline seems to improve but in 2011 the conference really went up a notch. The Beer and Books evening networking event was totally cool, even if it wasn’t possible to hear every word read by every author. The swag was also amazingly creative: for example lip balm being given out with The Science of Kissing fliers. In 2011 I did my first demo – I presented our free resource search portal to an interested group who asked many questions and offered suggestions. I also met John Ben DeVette, who is now acting as our rep in Asia. I was also introduced to Prezi, and met Mary Canady of Comprendia, among others. #scio11
2012: Time will only tell exactly what OpenHelix will gain from attending ScienceOnline2012, but I’m sure it will be significant! Stay tuned to find out… #scio12@scio12
As many of you know, OpenHelix specializes in helping people access and utilize the gold mine of public bioscience data in order to further research. One of the ways that we do this is by creating materials to train people – researchers, clinicians, librarians, and anyone interested in science - on where to find data they are interested in, and how to access data at particular public databases and data repositories. We’ve got over 100 such tutorials on everything from PubMed to the Functional Glycomics Gateway (more on that later).
In addition creating these tutorials, we also spend a lot of time to keep them accurate and up-to-date. This can be a challenge, especially when lots of databases or resources all have major releases around the same time. Our team continually assesses and updates our materials and in this post I am happy to announce recently released updates to three of our tutorials: UniProt, World Tour, and Overview of Genome Browsers.
Our Introductory UniProt tutorialshows users how to: perform text searches at UniProt for relevant protein information, search with sequences as a starting point, understand the different types of UniProt records, and create multi-sequence alignments from protein records using Clustal.
NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been developed, it has become obvious that new types of information (such as expanded metadata) need to be collected, and new ways of handling data are required.
NCBI has been adapting to such needs throughout the years and recently has been adapting its genome resources. Today’s tip will be based on some of those changes. My video will focus on the “completely redesigned Genome site”, which was recently rolled out and announced in the most recent NCBI newsletter. I haven’t found a publication describing the changes, but the newsletter goes into some detail and the announcement found at the top of the Genome site (& that I point out in the video) has very helpful details about the changes.
As you will see in the announcement, the Genome resource is not the only related resource to have undergone changes recently, including the redesign of the Genome Project resource into the BioProject resource and the creation of the BioSample resource. I won’t have time to go into detail about those two resources but at the end of my post I will link to two recent NCBI publications that came out in Nucleic Acids Research this month – these are good resources to read for more information on BioProject, BioSample, and on the NCBI as a whole. For a historical perspective I also link to the original Genome reference, which is in Bioinformatics and currently free to access.
Some of the changes are very interesting, including that “Single genome records now represent an organism and not a genome for one isolate.” The NCBI newsletter states that “Major improvements include a more natural organization at the level of the organism for prokaryotic, eukaryotic, and viral genomes. Reports include information about the availability of nuclear or prokaryotic primary genomes as well as organelles and plasmids. ” There’s also a note that “Because of the reorganization to a natural classification system, older genome identifiers are no longer valid. Typically these genome identifiers were not exposed in the previous system and were used mainly for programmatic access. ” That makes me wonder what changes this will mandate to other NCBI’s resources, as well as external resources. I haven’t seen any announcements on that yet, so I’ll just have to stay tuned & check around often.
Enjoy the tip & let us, or NCBI, know what you think of their changes!
Historic Entrez Genome reference: Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999). Complete genomes in WWW Entrez: data representation and analysisBioinformatics, 15 (7), 536-543 DOI: 10.1093/bioinformatics/15.7.536
Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K., Resenchuk, S., Tatusova, T., Yaschenko, E., & Ostell, J. (2011). BioProject and BioSample databases at NCBI: facilitating capture and organization of metadataNucleic Acids Research DOI: 10.1093/nar/gkr1163
Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S., Feolo, M., Fingerman, I., Geer, L., Helmberg, W., Kapustin, Y., Krasnov, S., Landsman, D., Lipman, D., Lu, Z., Madden, T., Madej, T., Maglott, D., Marchler-Bauer, A., Miller, V., Karsch-Mizrachi, I., Ostell, J., Panchenko, A., Phan, L., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Wang, Y., Wilbur, W., Yaschenko, E., & Ye, J. (2011). Database resources of the National Center for Biotechnology InformationNucleic Acids Research DOI: 10.1093/nar/gkr1184