A popular new resource, JoVE or the Journal of Visualized Experiments, recently got a new look. JoVE is an indexed academic journal publishing in video format rather than in print, and is particularly well known from the protocol videos. JoVE content available through the Levy Library includes Neuroscience, Immunology & Infection, Clinical and Translational Medicine, and Bioengineering.
The Levy Library is pleased to announce access to two new resources from BMJ: BMJ Learning and BMJ Case Reports.
BMJ Learning offers CME/CPD modules through text, video and audio modules. This database will provide recommendations based on your information provided at registration and remember which modules have been completed.
BMJ Case Reports Case Reports is a journal that contains thousands of peer-reviewed cases in many disciplines for reference. The Mount Sinai subscription also covers fees for submitting cases o be published in this journal.
These resources are both available by going to the Levy Library databases page and searching for BMJ.
Need a good resource to find information on environmental factors in health? What about biology or general science topics? Try our new search option, ProQuest Biology, Science and Environment. This search is a facet of ProQuest focusing specifically on scientific and biological resources. Searching this resource searches four databases simultaneously:
Where did Ben Franklin publish information about his kite flying experiments with electricity? In the Philosophical Transactions of the Royal Society, of course. Yesterday the Society announced that all issues from 1665-1945 - including Ben's letter - are now available free online. (You can get access to the newer issues from the Library's E-Journals page.) The Royal Society is committed to open access and providing information to a broad audience and this is part of their strategy. The Transactions is the oldest scientific journal in the world and was the first peer-reviewed journal. In 1886, science had evolved to such an extent that it became necessary to divide the journal in two. Philosophical Transactions A covers the physical sciences and Transactions B deals with the life sciences. Some of the familiar names you can find here are Sir Isaac Newton, Charles Darwin, and William Osler. With a nod to Halloween in a few days, a search of the word 'Monster' returns 55 articles. Enjoy!
OMIM.org is the new, official home of OMIM®, Online Mendelian Inheritance in Man®. For those unfamiliar with OMIM, it provides full-text, referenced overviews on all known mendelian disorders and over 12,000 genes. The database is updated daily and is freely available on the Web.
Health care providers value the ability to search OMIM by symptoms as well as by gene or disease names. It can offer them insight into a gene function or the clinical presentation of a disease, and can assist in making or excluding a diagnosis. And, although OMIM has a more clinical focus than many genetics databases, researchers also use the database, especially for its Gene Map and its copious links to other genetics resources.
Victor A. McKusick of Johns Hopkins University began MIM-Mandelian Inheritance in Man in the early 1960s. At first a print catalog of mendelian traits and disorders, MIM became OMIM when it went online. OMIM is still biocurated at Johns Hopkins in the McKusick-Nathans Institute of Genetic Medicine, and Johns Hopkins owns the copyright to its contents.
Most of those now familiar with OMIM know it as a database available from the National Center for Biotechnology Information (NCBI). NCBI developed OMIM for the Web and hosted it from 1995 until early this year. This year OMIM migrated to a new home, http://omim.org, hosted at the University of California Santa Cruz (UCSC) Genome Bioinformatics. What does this change mean for those who use OMIM?
Search Features
If you prefer, you can continue to search OMIM in much the same way you always have. NCBI still provides a search interface for OMIM (at http://www.ncbi.nlm.nih.gov/omim), so you don't need to change to the new search platform. But now when you click on a search result, NCBI will 'bounce' you to OMIM.org to view the entry.
You may be tempted to stick with searching on NCBI, but I think that most users will want to move to OMIM.org. The new interface is missing a few things are available on NCBI, for example, the Preview/Index and the Clipboard. But OMIM.org offers some attractive enhancements, in particular an uncluttered home page with a simple, Google-like search box. The basic search will probably suffice for most queries, but if it doesn't, there are three Advanced Search options listed on the home page: OMIM, Clinical Synopses, and OMIM Gene Map.
OMIM is where you'll find the helpful search filters still available under Limits at the NCBI site. This, for example, is where you can narrow your search results to genes on specific chromosomes.
Clinicians will like the new Clinical Synopsis filters, which allow you to limit results to affected organ systems.
The OMIM Gene Map isn't new, but researchers will appreciate the added search options, especially the ability to specify genomic coordinates as well as genomic location.
And, for any expert searchers (librarians) in the audience, OMIM.org offers an expansive range of search operators, e.g., proximity operators and term weight boosters. See their Search Help section for details.
Search Results
I like the OMIM's new search interface, but I really like the enhancements to the search results on OMIM.org. OMIM has three types of records, corresponding to the three types of advanced searches. I think the most useful improvements are in the OMIM entries, but we'll look briefly at the Clinical Synopsis and OMIM Gene Map pages as well.
OMIM Records
OMIM records, like the OMIM home page, appear less cluttered and easier to use. More important, though, are the enhancements to the records. The website developers have said that that the new website "emphasizes the relationship between diseases and genes", and the changes start with the record's title.
OMIM search results and records still lead with the MIM number, a unique 6 digit identifier, that is usually preceded by one of four symbols, e.g., an asterisk. The symbol indicates the type of record; in theory, this allows users to quickly distinguish between gene and phenotype records. The MIM number itself reflects the mode of inheritance; for example, records with the MIM numbers from 300,000 to 399,999 represent x-linked genes or phenotypes.
Simple things for simple people: on the new interface, when you mouse over the MIM number, a javascript note tells you what the record covers! Imagine, future generations of OMIM users will not have to remember whether a MIM number that is preceded with an asterisk indicates a gene record (it does), or which number sequences code for sex linked inheritance.
Also highlighting the relationship between genotype and phenotype, a new "Phenotype Gene Relationships" table appears just below the gene or disease names and synonyms. The table makes it easy to switch back and forth between gene records and related phenotype records.
Within the gene records, just above the Relationships Table, you'll see a link labeled Cytogenetic location, which takes you to the OMIM Gene Map. Next to the Cytogenitic location link is another new feature: a link labeled Genomic coordinates. This takes you to a map showing the gene location on the UCSC Genome Browser. As you may recall, UCSC Genome Bioinformatics now hosts OMIM.
OMIM records can be lengthy; it all depends on how much is know about a disease or a gene. For example, the record for Fabry Disease, MIM number #301500, is 38 pages, while that for Fanconi Anemia (type C), MIM number #227645, is only 5 pages. A table of contents (TOC) is essential for navigating a lengthy record, and one was available in NCBI. On the new platform, the TOC floats right so you can use it as you scroll through the text. It can also be toggled opened and closed. The default is closed, minimizing visual clutter. Open it for a quick overview of the entry and to link to selected sections.
OMIM's external links make it an information portal as well as an information source for clinicians and translational researchers. Next to the TOC you'll see new links to ICD9, ICD10 or SNOMED CT codes. Just below the TOC is the extensive collection of external links to organizations such as Gene Tests, Gene Reviews, PharmGKB and Coriell Cell Repositories. External links are now grouped in categories that can be toggled open and closed. And, the links have been expanded to include new resources such as Clinicaltrials.gov, OrphaNet and Ensembl, with more resources reportedly on the way.
All OMIM records are fully referenced. Most of the citations link to PubMed, and the new site also provides links to full-text from publishers' Web sites and Pubget. The publisher links will probably work best on-campus, where many content providers recognize Levy Library's licenses. From off-campus, try Pubget. If an article is not freely available online through Pubget, select your affiliation with Mount Sinai and then authenticate as usual to bring up our FIND IT full-text service.Of course, you can also access articles through Levy Library's E-Journals database. Just plug in the PMID and authenticate when prompted.
Clinical Synopsis
The new Clinical Synopsis result page is a simple table with phenotypic characteristics of a genetic disorder, organized by organ system. In many cases, this will be enough information to enable clinicians to rule in or out a diagnosis. To see the full OMIM record, click the MIM number at the top of the page.
OMIM Gene Map
The OMIM Gene Map is a chromosome-by-chromosome list, provided in a table format, of the genes identified in OMIM and the disorders associated with them. It can be browsed to identify traits and disorders associated with genes located near a known mutation, and that could be affected by an associated insertion or deletion process. The Gene Map provides links to genetic and phenotype MIM records, and now, on OMIM.org, it links to the UCSC Gene browser.
Want to Learn More?
OpenHelix, a provider (licensed by the Levy Library) of online training on bioinformatics and genomics resources, posted a five minute video introducing the new OMIM Web site on the OpenHelix Blog and on SciVee TV. The video is below; for more details, view the complete OpenHelix blog post at: http://blog.openhelix.eu/?p=8539. Or, check out the new OMIM webisite yourself at http://omim.org.
OpenHelix. Tip of the Week: New and Improved OMIM®. 31 May 2011. Available at: http://www.scivee.tv/node/30799 [Accessed 24 July 2011].
A question we answer frequently at the library is whether we have any mouse or rat brain atlases. And we sure do! One of our favorites is the online BrainNavigator, which takes information and images from print brain atlases and, thanks to technology from the Allen Institute for Brain Science, generates interactive 3D brain models for rat, mouse, human and rhesus. Not only can you turn the brain model around on the screen to look at it from different angles, you can also set markers, slice the model at various angles, and even simulate injections into the brain.
BrainNavigator is hosting on online seminar at 11 am on June 2 that will show you how to go beyond even those capabilities listed above and generate custom atlases to meet your needs. You can learn more about the webinar and register for it here.
Do you use ENCODE (Encyclopedia of DNA Elements) data? If so, please participate in this survey to help make it more usable! Our friends at OpenHelix let us know about the survey, and have more information on their blog:
If you don't use ENCODE data right now, but the idea of a project to identify all the functional elements of the human genome sounds good to you, take a look at the ENCODE tutorial from OpenHelix, or the new article about it in PLoS Biology.
Does the image above look more like a bunch of lines and boxes than an information-rich representation of genomic data? Have you been looking for an effective way to find and interpret information from genome sequencing projects and other research? Or, are you already an experienced user of the UCSC Genome Browser, looking to take your queries to the next level with Galaxy? The Library is happy to announce a day-long series of workshops to help get you the skills and information you need. These workshops are sponsored by the UCSC Genome Bioinformatics group and the Galaxy team at Penn State, and presented by trainers from OpenHelix (whose suite of fantastic bioinformatics tutorials we recently started subscribing to). The workshops will be on Monday, January 10, 2011, and the schedule is:
Also consider attending the 1:00 - 1:30 presentation, A Wordl Tour of Genome Resources, which will give you an overview of the many other resources out there for genomic information, and how to find the best one for your needs.
We are very pleased to report the addition of Embase to our growing collection of resources supporting Mount Sinai's initiatives in translational research and evidence-based medicine. Embase, the online version of the print index Excerpta Medica, is an international biomedical and pharmacological database that covers the journal and conference literature. It has significant strengths in the areas of pharmaceutics, pharmacy and toxicology; occupational health; environmental health; alternative medicine; biotechnology; and occupational and environmental health. Embase covers over 7,000 journals, over 25% of which are not in MEDLINE.
Embase is known for its timely, in-depth indexing using Emtree, a hierarchically ordered controlled thesaurus. Emtree, like the MeSH vocabulary used to index MEDLINE, provides a consistent description of biomedical terminology. Emtree is noted for its rich vocabulary for drugs and chemicals, facilitating discovery of reports on drug combinations, adverse drug reactions, medical devices and trade names, drug trade names across the globe, and clinical studies and trials.
Because Embase covers journals not in MEDLINE, and because the Emtree indexing language offers additional avenues to identify reports on biomedical topics, Ebmase is usually needed for comprehensive literature searches, systematic reviews and meta-analyses. In particular, The Cochrane Handbook for Systematic Reviews of Interventions recommends that Cochrane review teams search MEDLINE, Embase and the Cochrane Central Register of Controlled Trials (CENTRAL) to ensure that as many relevant studies as possible are identified.
Our version of Embase is delivered on the OvidSP platform. To access EMBASE, connect both on- and off-campus from the link on Levy Library's Databases page, and select it from the list of Frequently Used Databases at the top. Or, link directly to Embase here.
We're planning workshops on using Embase early next year, so stay tuned to our postings of upcoming classes. In the meantime, OvidSP offers detailed information about searching EMBASE on their platform here. And as always, we encourage you to Ask a Librarian.
Ever tried to find your way around dbSNP, UniProt, or KEGG? Gotten lost in miRBase or the Gene Ontology? Found that the developers of a tool you need didn't quite get around to developing a useful "Help" link? The Library is here for you! We're happy to announce our new subscription to OpenHelix's bioinformatics tutorials. Each one inculdes a narrated tutorial video, downloadable PowerPoint slides and exercises you can complete for practice. And best of all, they keep the tutorials updated to relect changes in the resources. Right now, there are nearly 100 tutorials ranging from genome databases to pathway resources to algorithms and analysis tools, and there are more to come!
You can access the OpenHelix tutorials, both on campus and off, from the Library's Databases page: http://librarycf.mssm.edu/levy/databases/, in the Bioinformatics section.
