Tag Archives: NCBI

Video Tip of the Week: 1000 Genomes Dataset Browser from NCBI


A recent NCBI Newsletter announced the release of a new resource named the 1000 Genomes Dataset Browser, and that is the resource that I will be featuring in this tip. It is one of the tools available through the new NCBI Variation resources page, which also features resources such as dbSNP, dbVar, dbGaP and ClinVar (many of which OpenHelix has tutorials for) as well as other variation tools – Variation Reporter (pre-release version), Clinical Remap (beta version) and the Phenotype-Genotype Integrator.

Before I discuss NCBI’s 1000 Genomes Dataset Browser, I’d like to spend a bit of time on the 1000 Genomes project, in order to distinguish what is from NCBI and what is from the project itself. From the 1000 Genomes Pilot paper:

“The aim of the 1000 Genomes Project is to discover, genotype and provide accurate haplotype information on all forms of human DNA polymorphism in multiple human populations. Specifically, the goal is to characterize over 95% of variants that are in genomic regions accessible to current high-throughput sequencing technologies and that have allele frequency of 1% or higher (the classical definition of polymorphism) in each of five major population groups (populations in or with ancestry from Europe, East Asia, South Asia, West Africa and the Americas).”

You can access the full paper from the link below. The project has now moved past the pilot phase and is releasing new data all the time. You can see announcements and project details, or access that data, through the official 1000 Genomes project site, or through the official 1000 Genomes version of the Ensembl Browser. As you might imagine for a “big data” project such as this, data has been added to a variety of NCBI databases, including dbSNP, the Sequence Read Archive (SRA) and BioSample. Although you could search for this data through the universal Entrez search system, previously to view the data you would have to view individual results at each separate database. The 1000 Genomes Browser at NCBI has been created as a powerful interface for comprehensively searching for, and viewing, 1000 Genomes data contained in NCBI resources on a single page.

In the video tip I will familiarize you to the various areas of the page - the browser is created with series of widgets, each with its own function. I will not be able to cover all of the features, or demonstrate how users can upload their own variation data to the browser – I’ll leave you the fun of exploring those on your own. Because the tool is so young, bugs and suggestions/comments are still being actively requested – if you find something, check out the FAQs (which discuss bugs at various stages of being fixed) and then email the team.

Quick Links:
NCBI Newsletter announcement July 20, 2012: http://1.usa.gov/RQu5dR

NCBI Variation page: http://www.ncbi.nlm.nih.gov/variation/

NCBI 1000 Genomes Browser page:
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/

1000 Genomes Project site: http://www.1000genomes.org/home

The 1000 genomes project specific version of the Ensembl Browser:
http://browser.1000genomes.org

Reference:
The 1000 Genomes Project Consortium (2010). A map of human genome variation from population-scale sequencing Nature, 467, 1061-1073 DOI: 10.1038/nature09534

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…

Video Tip of the Week: the New PubMed Filters Sidebar

In today’s tip I am linking to a YouTube video from NCBI that briefly explains the new Filters Sidebar feature that has been added to PubMed. We first saw a tweet that the change was coming back on May 2nd, just as I was completing a total update to our full PubMed tutorial*.

I struggled with whether to hold our production team for the new sidebar, or to produce our tutorial with the plan to update in the near future – it is always a struggle to know which is the best option because resource changes can occur at the speed of light, or according to geological time scales (ok, that’s an exaggeration but it feels that way when you want to release a wonderful, up-to-date project & something holds you up and causes delayed publication of our tutorial materials). With PubMed I was lucky – I saw a tweet that the sidebar feature would be added “in the next week”. I asked our voice professional to put the script on hold & I paced around PubMed waiting to see what (& when) things would occur.

True to their word, the sidebar feature showed up on PubMed results on May 10th, exactly one week since I had seen the “in the next week” announcement – my THANKS to the NCBI & PubMed Teams! :) Not only did they push out their updates in a timely manner, they made a YouTube video explaining the changes & discussing where future changes are slated to go. The video is clear, and quick, so I am using it as my tip this week. I’m not sure the feature is 100% stable, as I show in the image below, and describe later in the post, but I think the change might accomplish NCBI’s goal – for more people to notice & utilize filters for their searches.

In the video the narrator states that the filters area is gone & the two default filters are permanently selected, as indicated by the check marks that can’t be “unclicked”. I”m not seeing those check marks on either “Free full text available” link (shown) or the “Review” link, which is not in view in my image. I also see a difference as to whether I get the right filtered subsets depending on whether I am logged into My NCBI (the upper window shown in the back of the image), or not (the lower, front window). In my hands IE 9.0 & Firefox 12.0 both function similarly in these aspects.

The NCBI video doesn’t really show how results look after filters are added, but in playing with it to me it looks like all of your filters are applied to your search & you only get one set of results, not links to various subsets. Although it is now easier to add filters to searches, if that’s how filters are going to work going forward, I think I will miss the old filters – I kind of like being able to switch between various subcategories of results without having to change my filters or rerun searches. Be sure to share your thoughts & preferences with NCBI so that they can create the best resource for their users needs!

* OpenHelix tutorial for this resource available for individual purchase or through a subscription.

Quick links:

OpenHelix Introductory Tutorial on using PubMed (soon to be updated): http://www.openhelix.com/cgi/tutorialInfo.cgi?id=70

PubMed Resource: http://www.pubmed.gov/

PubMed Reference:
Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Federhen, S. & (2011). Database resources of the National Center for Biotechnology Information, Nucleic Acids Research, 40 (D1) D25. DOI: 10.1093/nar/gkr1184

Video Tip of Week: Bioproject, it’s where to start finding data (hint, not the papers so much anymore))


A few months ago, Jennifer did a nice tip on on NCBI’s Genome Resources and the changes there. There she briefly mentioned Genome Project resource moving to a new home, BioProject, just about a year ago. Today, I’d like to give you a quick overview of BioProject. It was described in this year’s issue of NAR’s database issue: “BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata.From the abstract:

As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata. Although metadata has been collected for some archival databases, previously, there was no centralized approach at NCBI for collecting this information and using it across databases. The BioProject database was recently established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases.

This is just one step in the process the biological science community will have to do to get a handle of the data deluge. If scientists are to get a handle of the projects and data that is spewing at breakneck speeds, a key is knowing what data is being generated, organizing the projects.

As Mary (and we here at OpenHelix) keep not-so-gently reminding you, the data isn’t in the papers any more. Huge projects like 1000 Genomes, ENCODE and others and reduced sequencing costs produce enough data that finding it is difficult.

BioProject grew out of a need to better organize these large projects’ datasets and metadata and replaces NCBI’s Genome Project resource. These projects produce data which is then deposited in several repositories. BioProject “provides an organizational framework to access metadata about research projects and the data from those projects which is deposited, or planned for deposition, into archival databases.”

Quick Links:

BioProject
BioProject Help
BioSample (descriptions of biological source materials used in experimental assays)
ENCODE (sponsored tutorial)
1000 Genomes 

Reference:

 
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 metadata Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1163

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: Big Changes to NCBI’s Genome Resources


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! :)

Quick Links:

NCBI Homepage: http://www.ncbi.nlm.nih.gov/

Entrez Genome Resource Homepage: http://www.ncbi.nlm.nih.gov/genome

BioProject Resource Homepage: http://www.ncbi.nlm.nih.gov/bioproject/

References:

Historic Entrez Genome reference: Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999). Complete genomes in WWW Entrez: data representation and analysis Bioinformatics, 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 metadata Nucleic 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 Information Nucleic Acids Research DOI: 10.1093/nar/gkr1184

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…

  • And we’ll monitor this so we can update our tutorial on WormBase when the new interface is out of beta and stable. RT @wormbase: Public beta period of the new WormBase website now open! http://bit.ly/qsLqCw and http://beta.wormbase.org/ #softlaunch #celegans [Mary]
  • RT @GenePattern: Announcing GParc: the GenePattern Archive. Share your modules and grow the GP community. http://bit.ly/fwlYqY #bioinformatics #genomics [Mary]
  • A predicted 9.3 billion people alive by 2050 – that’s hard for me to wrap my brain around. Special issue of Science (29 July 2011) deals with Population and Development, a lot of the content is open. [Jennifer]
  • RT @bffo: New COSMIC update includes update of Cancer Census Gene http://bit.ly/qXcI5L  #bioinformatics #cancer #genomics [Mary]
  • Medicinal plant genomes–very cool. PhytoMetaSyn: RT @mikesgene: Canadian scientists open gene database to public to help create new opportunities for biotechnology industry  http://bit.ly/nqPH6Q  #genome [Mary]
  • Man, I wanna play! Cool classroom resource for K-undergrad, per this Science article – “Beckman Institute’s Bugscope, http://bugscope.beckman.illinois.edu, a free educational technology outreach project, which enables kindergarten to 12th grade (K-12) and undergraduate students and teachers to remotely access and control the microscope in real time from their classroom computers.” [Jennifer]
  • Yay BioStar! RT @bioinformer: OpenSource bioinformatics tools are often so poorly documented, but @BioStarQuestion once again pulls through with what I needed. [Mary]
  • I just saw this press release” EDU-SCIENCE PREMIERS SCIENTIFIC AMERICAN
    BRANDED LINE OF SCIENCE TOYS AT FALL TOY PREVIEW IN DALLAS
    ” – but will they be available for Christmas? [Jennifer]
  • RT @eurogene: viewer looks interesting, now i need my genome MT @pathogenomenick: Tablet  – lots of plans for this excellent viewer http://bit.ly/mSEMkJ [Mary]
  • This is a nice little tool–custom genome diagrams: RT @NCBI: Upload your genome annotations, see them displayed on an ideogram and download an svg or eps file. http://1.usa.gov/mTGIze #genomics [Mary]

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…

Tip of the Week: Update to NCBI’s Cn3D Viewer


As I say in the tip movie, I like to visit NCBI’s homepage & just roam around over there to get an idea of what’s new. They develop so many bioscience tools, algorithms & other resources that there’s always SOMETHING new. Today I found out that they have updated their Cn3D interactive 3D viewer software from version 4.1 to 4.3 – version 4.2 was a preview version released only in a bundle with CDTree software. The 4.3 version is a stand alone version that can communicate with CDTree, and that allows users some advanced features compared to the 4.1 version of the Cn3D software. It may be important to note for some of you that 4.3 is only offered for Windows & Mac. Users wanting to use a Unix version will have to continue using version 4.1, as explained here.

Before using the Cn3D software you must download it to your computer. Previously downloading the 4.1 version of Cn3D does not affect your ability download and use the 4.3 version. In fact you can use them side-by-side, if you wish. As I said, the Cn3D software is a 3D interactive viewer so once you download the software you will probably visit another database that provides protein structure views in a Cn3D format. In the tip I use the myosin VI structure summary page from NCBI’s Molecular Modeling Database (MMDB) as my example. I didn’t have time to show you how to access the page in the tip movie, but it is the exact page we use in our full MMDB tutorial so you can find all the details there. (NOTE: I’ll be updating the MMDB tutorial soon, so watch for that announcement later.)

Opening the myosin vi file in the Cn3D viewer allows you rotate the molecule, label it as you desire, or view it in stereo. The controls are pretty intuitive & you can click around & see how it affects your image. For example, under the “Style>Rendering Shortcuts” menu you can render the molecule as worms, tubes, wire, ball & stick or space filled using the . You can also go under the “Style>Coloring Shortcuts” and select to color the image by domains, residues, charge, and many other options. If you want more details, check out the Cn3D “Help” menu or the Cn3D citation (below), or work through their tutorial.

I know MMDB and GoMiner use the Cn3D viewer – are there other resources where you use the Cn3D software?

References:

Baxevanis AD. (2008) Searching NCBI databases using Entrez. Curr Protoc Bioinformatics. 2008 Dec;Chapter 1:Unit 1.3. DOI: 10.1002/0471250953.bi0103s24

Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH. (2000) Cn3D: sequence and structure views for Entrez. Trends Biochem Sci. 2000 Jun;25(6):300-2. DOI: 10.1016/S0968-0004(00)01561-9 (subscription required)

Tip of the Week: New and Improved OMIM®

In the realm of bioinformatics resources, few are more venerable than OMIM®, Online Mendelian Inheritance in Man [well, originally not online, on index cards...]. For those who might be new to OMIM, it is a catalog of genes and their variations, and resulting phenotypes in human, with a more clinical perspective than some resources offer. As I was reviewing the history of OMIM for this post, I began to wonder if there even is any repository in genomics that’s been maintained on a computer framework longer. I know of an older protein analysis program that I wrote about once here–from Margaret Dayhoff and Robert Ledley. But as an ongoing repository or catalog that was stored, Victor McKusick wrote:

Mendelian Inheritance in Man has been maintained on the computer since 1964.

It was stored on a mainframe at Johns Hopkins at that time. The other one that I thought was probably close was RCSB PDB, which is described on their “about” page in this way:

The PDB was established in 1971 at Brookhaven National Laboratory and originally contained 7 structures.

It’s likely that in some form it existed on a computer system earlier than that–and may give MIM a run for the record. Bruno Strasser described 4 resources developed around the same time–1965–as the Cambridge Structural Database, MIM, Index Medicus, and Atlas of Protein Sequence and Structure.

It’s not easy to maintain and develop a resource for this long. Just this past month we learned about the risk of KEGG going away. But in bioinformatics–like biology–a resource needs to evolve or die. (Actually, I can remember in grad school that phrase was used by the chair of our department to describe what biology faculty needs to do as well.) In this week’s tip of the week, I report that OMIM is evolving, and I introduce you to the new interface.

Most people have encountered OMIM at the NCBI. But if you go over to there today, you’ll see this notice on the homepage:

This is because OMIM has a new home. It’s not clear at this time if the NCBI incarnation will be updated going forward. The OMIM team at JHU is requesting that software providers who serve links to OMIM now migrate those links to the new OMIM.org site, which the OMIM team considers to be the official site and will be the up-to-date one.

Let’s talk specifically about the evolved OMIM now: it’s entered a new century! Yay! The incredible deep collection of curated data over the decades still remains, but the new interface is very nice to use and to look at–it no longer looks like 1995 over there. There are also new handy links, and new search options, and new features still to come.

Compare this same record for the APC gene (a contributor to hereditary colon cancer) in both places:

Old OMIM at NCBI: http://www.ncbi.nlm.nih.gov/omim/611731

New OMIM at JHU: http://www.omim.org/entry/611731

I find the new page to be significantly tidier, don’t you? The links you need to other resources are still there, but you can toggle open the menus to find them now. And some of the links are to resources that weren’t available on the old page (for example, BioGPS and PharmGKB which we like very much!).  I’m also told that on appropriate pages there will be links to the DECIPHER resource.

You can still browse around the MIM map by clicking on the Advanced search for Gene Map link: http://www.omim.org/search/advanced/geneMap . I have done this on many days when I have found something intriguing in a chromosomal region and I want to see what was reported in that area and stored at OMIM.

Another feature that I think is very cool is the option to change the language with the Google Translate menu. I know it’s not perfect, but I’m finding increasingly that I want to read blog posts in other languages and I am finding it works pretty well. Making the OMIM data so easily accessible to non-English speakers is a really nice touch.

Although sometimes it is tough to transition to new software, I think this is a good sign. In addition to maintaining the excellent knowledge collection that began so long ago, a new interface means that OMIM is continuing to grow and change to meet the needs of today. And as we move forward to identify more and more genomic variations and alterations that impact human health, well-curated and deep knowledge bases like this are crucial.

Congrats to the OMIM team on the new look and new home.

Quick link to the new OMIM: http://www.omim.org/

(Bonus: did you know there’s also an Online Mendelian Inheritance in Animals OMIA? http://www.ncbi.nlm.nih.gov/omia )

Follow them on Twitter: http://twitter.com/#!/OmimOrg

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

Strasser, B. (2009). Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965 Journal of the History of Biology, 43 (4), 623-660 DOI: 10.1007/s10739-009-9221-0 (PDF available on his faculty web site here.)

Strasser, BJ (2006) “Collecting and Experimenting: The moral economies of biological research, 1960s-1980s.”, Preprints of the Max-Planck Institute for the History of Science, 310, 105-23.