Tag Archives: MyNCBI

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


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/

MyNCBI and eRA Commons

If you use MyNCBI (which I like) and eRA Commons (got an NIH grant? Then you probably do), MyNCBI now has a handy new feature I just discovered (of course if I looked at the NCBI news last month, I’d have discovered it earlier :D) and thought I’d point out.
The new feature allows you to link your bibliography in MyNCBI (which is absurdly easy to build :) with your eRA commons account. Then, when you view your bibliography, you’ll find a new $ icon. Click that icon and it will give you the following information about all your citations: Whether the citation complies with NIH’s (sort of) new public access policy and if there is NIH funding associated with the citation (which you can link if you have an open grant in your eRA Commons account). Nice feature you might want to check out, and it might be a nice subject for a Tip of the Week in a couple weeks :).

Tip of the Week: Subscribing to journal updates with HubMed

hubmed subscriptionsAs one of the tools (along with Connotea, Faculty1000, MyNCBI, HubMed, etc) to keep abreast of the fire hose of literature that is published, I also use RSS feeds to keep up-to-date on the latest publications from journals of interest. There are a lot of journals out there that publish a lot of data interesting to me, but subscribing to them all IRL of course is cost prohibitive (and environmentally unfriendly). Many will send updates by email of new issues, but the last thing I need is another email in my inbox screaming for my attention. Getting an RSS feed from a journal is a good way to keep up-to-date on new issues (if you haven’t used RSS feeds, read up on them here, find a reader here). Many journals include RSS feeds to new content, others don’t. Another way to get RSS feeds to a specific journal is to use HubMed in a nice feature that allows you to get an RSS news feed for a ‘search.’ I’ll show you how to do that here.

Defrosting the Digital Library

Defrosting the Digital LibraryThat’s the title of a recent paper in PLoS Computational Biology paper I read. This paper is a good read on two levels. It discusses the problems and difficulties (and solutions) with the rising number of digital libraries, published papers and research. Difficulties like identity (identifying papers in a persistent and standard way) and metadata (being able to pull out publication data from a paper in a standard and simple manner, if at all) and solutions like simple and persistent  URIs,  exposing metadata and identifying people and publications.

It was also a good read on another level, here, now and me. The authors discuss several digital libraries and their scope (the graphic here is a representation of some and their overlap) and tools to ‘defrost’ these libraries at a personal level. Many of these tools I use or know about (MyNCBI, CiteULike, Connotea and HubMed) and some I’m not particularly familar with (Zotero, Mendeley and Mekentosj Papers-Mac only! :), but the paper did give me a pretty decent understanding on some better ways for me to start to get a handle on the growing body of literature.

Now I should go do two things… reorganize and reinvigorate my references (back to Connotea! and try out Papers!) and to add the DOI link from CrossRef to this post, you know to standardize!