Tag Archives: OMIM

Video Tip of the Week: Nowomics, set up alert feeds for new data

Yeah, I know you know. There’s a lot of genomics and proteomics data coming out every day–some of it in the traditional publication route, but some of it isn’t–and it’s only getting harder and harder to wrangle the useful information to access the signal from the noise.  I can remember when merely looking through the (er, paper-based) table of contents of Cell and Nature would get me up to speed for a week. But increasingly, the data I need isn’t even coming through the papers.

Like everyone else, I have a variety of strategies to keep notified of different things I need to see. I use the MyNCBI stored searches to keep me posted on things that come from via the NCBI system. I signed up for the OMIM new “MIM-Match” service as well. But there’s still a lot of room for new ways to collect and filter new data and information. Today’s tip focuses on a service to do that: Nowomics. This is a freely available tool to help you keep track of important new data. Here’s a quick video overview of how to see what’s going on with Nowomics.

The goal of Nowomics is to offer you an actively updated feed of relevant information on genes or topics of interest, using text mining and ontology term harvesting from a range of sources. What makes them different from MyNCBI or OMIM is the range and types of data sources they use. The user sets up some genes or Gene Ontology terms to “follow”, and the software regularly checks for changes in the source sites. You can go in an look at your feed, you can filter it for different types of data, and you can see what’s new (“latest”) or what’s being hotly chattered about (“popular”) using Altmetric strategies. For example, here’s a paper that people seemed to find worth talking about, based on the tweets and the Mendeley occurrences.

example_paper This tool is in early stages of development–if there are features you’d like to see or other sources you’d think are useful, the Nowomics team is eager for feedback. You can find a link to contact them over at their site, or locate them on Facebook and Twitter. You can also learn more from their blog. You can also learn more about the philosophy and foundations of Nowomics from their slide presentation below.

 

Quick links:

Nowomics: http://nowomics.com/

Example gene feed: http://nowomics.com/gene/human/BRCA2

References:

Acland A., T. Barrett, J. Beck, D. A. Benson, C. Bollin, E. Bolton, S. H. Bryant, K. Canese, D. M. Church & K. Clark & (2014). Database resources of the National Center for Biotechnology Information, Nucleic Acids Research, 42 (D1) D7-D17. DOI: http://dx.doi.org/10.1093/nar/gkt1146

Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), July 22 2014. World Wide Web URL: http://omim.org/

Video Tip of the Week: list of genes associated with a disease

I am currently in Puerto Varas, Chile at an EMBO genomics workshop. The workshop is mainly for grad students and the instructors are, for the most part, alumni of the Bork group. I gave a tutorial on genomics databases.

Anyway, the last two days of the workshop is a challenge, in teams of 3-4 advised by an instructor, students are to develop a list of genes associated with epilepsy. Obviously, this could be a trivial task, just go to OMIM or GENECARDS and grab a list. But this challenge requires them to go behind that and use the available data and make predictions. My team attempted, on my suggestion, some brainstorming techniques to ensure a more creative solution than they could come up with individually or just jumping into normal group dynamics. It seemed to work, their solution was quite creative and we will find out today how that worked.

That was my long way of saying, in the process we came across many databases of gene-disease information. above you will find a video of rat gene disease associations from RGD, often used of course to investigate human gene disease associations.

Below you will find a list of some excellent databases and resources to find similar lists:

Gene Association Database  http://geneticassociationdb.nih.gov/

G2D http://g2d2.ogic.ca

OMIM http://www.omim.org

Diseases http://diseases.jensenlab.org/

GeneCards http://genecards.org

DisGeNET http://ibi.imim.es/web/DisGeNET/

Several NCBI resources http://www.ncbi.nlm.nih.gov/guide/howto/find-gen-phen/

UCSC Genome Browser’s tracks for disease and phenotype http://genome.ucsc.edu

There are several others I’m sure, if you have a favorite not on this list, please comment.

Reference for RGD:
Laulederkind S.J.F., Hayman G.T., Wang S.J., Smith J.R., Lowry T.F., Nigam R., Petri V., de Pons J., Dwinell M.R. & Shimoyama M. & (2013). The Rat Genome Database 2013–data, tools and users, Briefings in Bioinformatics, 14 (4) 520-526. DOI:

Video Tips of the Week, Annual Review 2013 (part 1)

As you may know, we’ve been doing these video tips-of-the-week for SiX years now. We have completed or collected around 300 little tidbit introductions to various resources through this past year, 2013. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 II (next week).

Annual Review VI:

January 2013:
January 2: Annual Review V part deux
January 9: The New and Improved OMIM®
January 16: InSilico DB
January 23: ZooBank and species nomenclature
January 30: ScienceGameCenter #edtech

February 2013:
February 6: MotifLab workbench for TFBS analysis
February 13: UCSC Genome Browser restriction enzyme display
February 20: ENCODE Data at UCSC (reminder)
February 27: NetGestalt

March 2013:
March 6: NCBI Genomics Workbench
March 13: FlyBase
March 20: figshare + GenoCAD = outreach
March 27: Enzyme Portal and User-Centered Design

April 2013:
April 3: Phytozome and the Peach Genome
April 10: Introductory Cheminformatics
April 17: Sharing H7N9 data at GISAID.org with EpiFlu™
April 24: Cancer Atlas roadmap

May 2013:
May 1: My Cancer Genome
May 8: Transfac (and HGMD, Proteome, etc)
May 15: Influenza Research Database (IRD)
May 22: Canary Database for sentinels of human health
May 29: QIIME for Quantitative Insights Into Microbial Ecology

June 2013:
June 5: Prezi and other nonlinear presentation methods
June 12: TrioVis for family genome data sets
June 19: ENCODE ChIP-Seq Significance Tool
June 26: InnateDB, Systems Biology of the Innate Immune Response

Video Tip of the Week: Mobile-device enabled tutorial suites

For decade now we’ve been offering our video tutorial suites to help people learn how to use bioinformatics resources. We’ve used a couple of delivery platforms, and we’ve changed the website a few times. But we also know that people like consistency with software, and if there are going to be major changes to the behavior of something, there better be a good reason.

We have a good reason. With the rise of mobile devices and the increasing use of them by students, our subscribers wanted us to make watching the tutorials on iPads and Androids and Surfaces more friendly. So we’re doing it.

This week’s video tip demonstrates the change to our tutorial movies that we’re rolling out. The basics are the same–each video offers details about how to use the software features at some database or tool site. We explain the display features, and the search mechanisms. We offer the video as well as the slides and some exercises to use as well. The only thing we’ve changed is the menu and controller options. The YouTube video here illustrates that.

So soon when you launch a tutorial video, you will have to swipe over the edges to access the menus and the slider. You can still click individual chapters, or move ahead with the controller. But those items move out of the way when you aren’t using them.

Everything else is the same. The landing pages for each tutorial suite will still have the launch buttons for all the items you need to access everything.

For subscribers, all of the suites will have this new functionality. If your site doesn’t have a subscription, you can still try it out on our sponsored training suites, such as: GenoCAD, OMIM, UCSC Genome Browser, or anything else from the “free” tutorials page: http://openhelix.com/free .

To learn more about our philosophy of training materials, you can check out our paper (below). Regular readers may already understand what we do, but if you are accessing these for the first time it might help you to know more about what we offer and how we do it.

Let us know if you have any issue with the new interface and we’ll take a look right away.

Quick link:

Free tutorials to try out: http://openhelix.com/free

Reference:

Williams J.M., Mangan M.E., Perreault-Micale C., Lathe S., Sirohi N. & Lathe W.C. (2010). OpenHelix: bioinformatics education outside of a different box, Briefings in Bioinformatics, 11 (6) 598-609. DOI:

Video Tip of the Week: the new and improved OMIM®

For this week’s Tip of the Week we highlight our new tutorial on OMIM, Online Mendelian Inheritance in Man. If you haven’t looked at OMIM for a while, or if you usually only think about it as a link in some other database you use, look again. There’s more there than you realize.

OMIM is one of the first online tools I became aware of way back in my career. That shared Mac in the back of the lab, with it’s teeny little screen–and accessing the link to OMIM from that NCBI interface–remember that old interface? Even then OMIM was a venerable resource with an unmatched collection of human genes, traits, and phenotype data. There was a great paper about the history of OMIM that Victor McKusik wrote about his own career and his work, and he recounts the beginnings of his human gene information collection and many other aspects of the human genetic knowledge realm. It’s a fascinating look at one guy’s path and influences that lead us to where we are today. But here’s the short history of OMIM as a computational resource:

Mendelian Inheritance in Man has been maintained on the computer since 1964. With the first print edition in 1966, it was a pioneer in computer-based publication. In the 1980s, MIM was prepared for online presentation, with a search engine that enhanced its usefulness. Online access, as OMIM, was provided generally beginning in 1987, first from the Welch Medical Library at Johns Hopkins and since December 1995 from the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (27).

Because of how long OMIM® has been around and its utility and depth, it’s been incorporated into probably almost every bioinformatics resource you use around the world. I love the UCSC Genome Browser track option that you can turn on to supplement your look at genomic regions and quickly find disease-causing genes, for example. But just seeing a link to OMIM doesn’t give you the full scope of understanding of the features it offers. With the move away from the NCBI site, the OMIM team changed their interface quite a bit to offer a lot more features than they were able to before. New links to appropriate resources have been added. New ways to integrate knowledge have been provided.

Have a fresh look at OMIM today, and you can also download slides to use and exercises to perform to help you perform more complex searches and exploration of the wealth of data they have.

The training materials are freely available because they are sponsored by the OMIM team, who worked with us to create them. They are free for a limited time, so check them out soon.

Quick links:

OMIM tutorial: http://openhelix.com/OMIM

OMIM main site: http://www.omim.org (but note there are mirror sites in the US and Europe that may be good options)

References:

McKusick, V. (2006). A 60-Year Tale of Spots, Maps, and Genes Annual Review of Genomics and Human Genetics, 7 (1), 1-27 DOI: 10.1146/annurev.genom.7.080505.115749

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

Friday SNPpets

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…

What’s the Answer? (OMIM API now available)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question was raised in the last month, and there was some discussion–but there’s been a big change in the options since, and I wanted to highlight that so people know:

Question: Is OMIM no longer available as structured data?

One of our project used to query OMIM data as XML through NCBI’s efetch utility, as described here for example:

[?]What is the best way to interact programmatically with OMIM?[?]

However, it seems the service has stopped functioning a few months ago. It now simply returns the following error:

Database: omim – is not supported

I can find no mention of an update to the API on NCBI’s website or anywhere else. At the same time, the pages accessible directly on OMIM’s website offer no link to structured data (XML or otherwise) and the downloadable file, while using some specific format to delimit fields, is still far from the flexibility of the former XML files (for example, it is impossible to retrieve metadata for each reference).

Is there currently any way to regain access to OMIM data in a structured, parsable format (XML…)?

There was a lot of discussion about the changes since OMIM at NCBI moved away from to its new spot at OMIM.org, but just this week I spotted a tweet from OMIM which directly answers the access issue now:

I’ve you’ve been waiting for the OMIM API access, check it out at the Help page.

(one) Video Tip of the Week (to hold them all): Variation and Disease Databases

After again reading Daniel MacArthur’s good rundown about the state of databases of human disease-causing variation from last year (One database to hold them all), I thought it might be nice to do a tip comparing several of them. I couldn’t get it under our self-imposed 5 minute limit for our tips (and technical limit of software I’m using, but that’s about to change). But as I perused our tips and other sites, I found we and others have quite a list of how-to tips to use these databases. So in today’s tip I’ve gathered video tips for 3 of the databases listed in the linked post. Below those tips I’ll link to other how-to videos for additional human variation and disease.

The databases mentioned are OMIM, Human Gene Mutation Database (HGMD), MutaDATABASE and The Human Variome Project . There are video tips for the first three.

OMIM.

Last year OMIM moved to http://www.omim.org and had a entire new interface. Mary was on top of it and did a tip on the new OMIM interface with lots of information on the move and OMIM in the post:

Our full tutorial on the new OMIM is coming soon.

HGMD:
HGMD has a public site and a by-subscription site. The latter includes access to the most current data and some added features. The publicly accessible site is out-of-date by three years. Because of HGMD restrictions, we aren’t able to do a tutorial or a tip on HGMD, but they do have an introduction video to their database:

 

Additionally, there is a good background page for more information.

MutaDATABASE:

Mary did a tip on MutaDatabase last summer:

 

Another excellent resource is Gen2Phen. The Gen2Phen project “aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality.”  In that vein, they have quite an extensive list of Locus-specific databases and additional resources.

There are several other resources available for human disease variation including CGAP, dbGAP, GAD, PhenomicDB and several others. We have tutorials on all those if you wish to check those out.

Of course there’s dbSNP :D of which we have a tutorial and tip about searching human variation.

You can find an extensive list of other resources at Human Genome Variation Society (HGVS).

And an oft-asked question on Biostar is what kind of resources are there for this kind of data. You can find answers here, here and here.

Video Tip of the Week: New Genetic Testing Registry (GTR) Resource


Late last month the National Center for Biotechnology Information, or NCBI, released a new resource containing information on genetic tests. The resource’s name is the Genetic Testing Registry (GTR), and according to its homepage, the GTR:

” 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. 

Quick Links:

The Genetic Testing Registry (GTR) – http://www.ncbi.nlm.nih.gov/gtr/

GTR YouTube Tips from NCBI – http://www.youtube.com/playlist?list=PL1C4A2AFF811F6F0B

GeneTests – http://www.ncbi.nlm.nih.gov/sites/GeneTests/?db=GeneTests

GeneTests Introductory Tutorial by OpenHelix* – http://bit.ly/genetests

Genetic Home Reference (GHR) – http://ghr.nlm.nih.gov/

GHR Introductory Tutorial by OpenHelix* – http://bit.ly/geneticshomeref

Online Mendelian Inheritance in Man (OMIM) – http://www.omim.org/

OMIM Introductory Tutorial by OpenHelix – (coming soon, currently being updated)

Orphanet – http://www.orpha.net/

form.

*OpenHelix tutorials for these resources available for individual purchase or through a subscription

Available References:

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

Video Tip of the Week: OMIA, Online Mendelian Inheritance in Animals

Many people are probably familiar with OMIM, Online Mendelian Inheritance in Man. It’s one of the oldest online collections of human genetic traits around. But many people may not be aware that OMIM inspired OMIA–Online Mendelian Inheritance in Animals.

The team from the University of Sydney that develops and curates OMIA collects information on animal traits with a specific emphasis on non-laboratory animals and comparative biology. The species range is huge. You can see traits from water buffalo and from rainbow trout, and more. The amount of detail may vary–sometimes you will find just links to papers that describe a phenotype. But there are other cases where there are not only links to the papers, but the gene features may be available in that species with information about the molecular details. Further, if there is a human trait that may be related, they will link to the OMIM pages for those.  The sample page that I used to illustrate this in the short video is Aranochomelia, and you can see these types of links and details.

You can access OMIA at the Australian site, but there is also a mirror available via NCBI.  It contains the same information, but since it is integrated with other NCBI tools you can use your mad NCBI skillz to do custom queries of all sorts with limits and structured syntax, or save queries with your MyNCBI account, and more. Visit OMIA at NCBI for that access.

This week’s tip is a 5 minute look at the ways to access OMIA and explores sample records. Check them out. I think they are going to become increasingly important as “big data” projects like 10K Genomes, and numerous other next-gen sequencing projects, bring us access to hoards of new genomes. Many of those genomes are going to have limited information that we can use to annotate the features. OMIA could really help with that.

Quick links:

OMIA (Univ. of Sydney): http://omia.angis.org.au/

OMIA at NCBI: http://www.ncbi.nlm.nih.gov/omia

OMIM: http://www.omim.org/

References:

Nicholas, F. (2003). Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals Nucleic Acids Research, 31 (1), 275-277 DOI: 10.1093/nar/gkg074

Lenffer, J., Nicholas FW., Castle K., Rao A., Gregory S., Poidinger M., Mailman MD., & Ranganathan S. (2006). OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI Nucleic Acids Research, 34 (90001) DOI: 10.1093/nar/gkj152

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 Information Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1184