The OpenHelix Blog

For another project I’m on, I had to research some of the sources of information around phenotyping experimental animal models.  And just as I needed it, the RGD team produced a very nice screencast of access to the phenotyping data and resources that they offer about rat phenotyping.  If you are interested in that type of data, go have a look at their video and explore the resources that they introduce:  RGD Phenotyping Portal screencast.

If that is data you are interested in, you might also explore some of the other things I’ve been looking at.  The MGI team Jackson Laboratory has a division that focuses on mouse phenotype data as well.  Called Mouse Phenome Database (MPD), you can access quite a range of data that already exists. They also have protocols for phenotyping that may be useful to folks who are characterizing animal models.

I also came across a project based in the EU that offers data and standardized protocols for phenotyping.  EUMORPHIA offers the Empress SOPs that they are developing, as well as access to the Europhenome database that contains the results.

As much as I still love to look at genomes, I’m ready to move down the path and look at the phenomes too

Today’s tip is on a new genotype/phenotype resource from the Swiss Institute of Bioinformatics, or SIB. I was already a fan of many SIB tools and resources, and was using one (ENZYME) when I found a notice about SwissVar. SwissVar is described as ‘a portal to Swiss-Prot diseases and variants.’ It includes information about genotype-phenotype relationships for each specific variant, manually annotated from literature. Manual annotation adds a level of quality and believability to this data. The SwissVar portal also contains various pre-computed information that may aid in determining the effect of the variant. Genotype-phenotype searches can begin with either Medical Subject Headings, or MeSH terms (Disease), gene or protein names (General characteristics) or variants (Functional/structural features). There are multiple ways to modify your searches, and results are clean tables of data including gene/protein accessions, names, links to MeSH definitions and links to variation reports.

If your research could benefit from high quality, manually curated genotype/phenotype information, I suggest you watch this tip, and then explore SwissVar according to your own interests.

SwissVar – a Portal to Swiss-Prot Diseases and Variants: http://www.expasy.ch/swissvar/

From the MGI mailing list the other day came notice of 2 new SNP sets that have been added to the Mouse Phenome Database SNP collection (MPD).

From their note:

- Center for Genome Dynamics (CGD) – SNP data from Mouse Diversity Genotyping Array (CGD2). 582,000+ locations and 72 strains.

- Palmer A – SNP data, 8200+ locations, 58 strains (Chicago1)

I like the mouse SNP tools at MGI.  I covered them in my full tutorial that you can watch for free here.  But there’s a separate access point for mouse SNPs from the MPD interface as well.  Phenotype might be an interesting way to be thinking about your genes and topics of interest if you haven’t considered that before.  A lot of people start with their genes of interest and look under the flashlight, but maybe look around at phenotypes as a starting point for some new ideas and directions.

Today’s tip is on a new resource brought to you by the National Human Genome Research Institute, or NHGRI. The resource is PhenX Toolkit version 2.1, which was released on May 22 2009. The PhenX Toolkit provides protocols for taking standardized measurements of research subjects’ physical characteristics and their environmental exposures. You can browse for protocols by domain or measurement type, or search for protocols. If you register, you are also able to collect sets of reports. These can be save for each of your projects, or for later modification. I’ll introduce you (briefly) to all of this and more in this tip.

I learned about this new resource from a GenomeWeb Daily News article in which they published NHGRI’s press release.

One of the things I’ve been thinking about lately are connections between genotype and phenotype – it is a topic in the news & I have been working on tutorials for the genotype-to-phenotype resources PhenomicDB & NCI’s dbGaP. Recently a friend notified of an article in Science featuring the PhysioNet – a resource intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals. The article was interesting & so I checked out this nice resource. In this short video I introduce you to a few of the features and data types available from the PhysioNet. You can read more about the PhysioNet, or see their mission statment by following the ‘continue reading’ link.

that was fun writing that title. A recent correspondence in Nature Genetics outlined some changes in the HuGE Navigator. This database has been available in some form since 2001. The basic purpose of the database is to…

navigate and mine the growing scientific literature on human gene-disease associations and related data in human genome epidemiology. As an interconnected system of applications that users can enter by using genes, diseases, or risk factors as the starting point, HuGE Navigator provides a potential bridge between epidemiologic and genetic research domains.

The bloggers here at OpenHelix and some of our family and friends decided to do the taste tests. You know the ones. You probably did them in your genetics class. I used them in my introductory biology class at CCSF years ago and had hundreds of the test strips left. So, we thought we’d distribute them to the bloggers and families here and see what the results were. The test strips are for sodium benzoate, PTC and thiourea. There is also a control strip of no taste (but paper). I numbered the strips and sent them to the bloggers and families (so they wouldn’t know what they were tasting, control or otherwise). And here are the results (and some database links to more about the genetics of taste):