Tag Archives: BioSystems

Tip of the Week: PathCase for pathway data

We spend a lot of time exploring genomic data, variations, and annotations. But of course a linear perspective on the genes and sequences is not the only way to examine the data. Understanding the pathways in which genes and molecular entities interact is crucial to understanding systems biology.

There are a number of tools which can help you to visualize and explore this kind of data. KEGG is one of the most venerable tools in bioinformatics, BioCyc is well known and used, Reactome is one of our favorites. Recently NCBI BioSystems has come along, and the BioModels tool at EBI provides more data of this type as well. Pathway Interaction Database is another place to try. What you’ll find is that each one has different emphasis, species focus or data sets available, and different tools to use to graphically display the databases. The ways to customize or interact with the data will vary as well. So you may need to try several to find the one you want for your purposes.

But for today’s tip of the week I will highlight PathCase, a Pathways Database System from Case Western Reserve University. This is a  tool I’ve  had my eye on for a number of years, and they continue to add new features and data sets to their visualization and search interface which are very nicely done.

PathCase offers you several ways to browse and search for pathways, processes, organisms, and also molecular entities (such as ATP, ions, etc) as well as genes and proteins. It’s all integrated into the system, so when you find an item of interest you can move to the other related pieces.  For example, from the Pathways you can find genes and learn more about the genes. From genes you can load the pathways in which they participate.

When you have the pathway graphics loaded, you can interact with that pathway by clicking, dragging, re-organizing and more. Right-clicking offers more details about the items and ways to visualize the data. One option I didn’t have time to show in the movie is that you can use the H20/CO2 box to load up pathways that are linked to the one you are looking at and load those up, going even further along any route that you might be interested in. Here’s just a quick sample of that: from the NARS2 gene page I loaded the alanine pathway, and then added the fatty acid metabolism pathway. Now I can explore both of them with all the standard PathCase tools and understand many of their relationships. Once you start exploring these pathways you be amazed at how complex visualizations are possible.

So if you are interested in biological pathways, exploring them and representing them, check out PathCase.

PathCase site: http://nashua.cwru.edu/pathwaysweb/

Reference:
Elliott, B., Kirac, M., Cakmak, A., Yavas, G., Mayes, S., Cheng, E., Wang, Y., Gupta, C., Ozsoyoglu, G., & Meral Ozsoyoglu, Z. (2008). PathCase: pathways database system Bioinformatics, 24 (21), 2526-2533 DOI: 10.1093/bioinformatics/btn459

New Online Tutorials for NCBI resources BioSystems and DCODE

Comprehensive tutorials on the publicly available NCBI resources BioSystems and DCODE enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA (PRWEB) February 23, 2010 — OpenHelix today announced the availability of new tutorials on BioSystems and DCODE.

The NCBI BioSystems database provides easy access to information about all the molecules that interact in a biological system, including genes and proteins, small molecules in a pathway, as well as the genes biomarkers and drugs associated with diseases. DCODE is a public NCBI suite of tools for genomic alignments, multiple and pairwise sequence alignments, identifying gene regulatory elements and conserved transcription binding sites and more. These two tutorials, in conjunction with OpenHelix tutorials on OMIM, PubMed, Entrez Gene, BLAST, GEO and several others, give you a set of training resources that help you become efficient and effective using NCBI resources.

These two tutorials, in conjunction with OpenHelix tutorials on OMIM, PubMed, Entrez Gene, BLAST, GEO and several others, give you a set of training resources that help you become efficient and effective using NCBI resources.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.

These tutorials will teach users:

BioSystems

*to perform basic searches and to understand your results
*to link out to a variety of related information in many different fields
*about Entrez tools that you can use to customize your searches and results*
*how to access and customize full-size pathway images
*some advanced searching techniques, including Boolean queries and batch searching

DCODE

*how to conduct whole genome alignments and identify ECRs
*how to create interactive conservation profiles and phylogenetic trees
*how to identify proximal and distant regulatory elements in desired sequences
*how to identify conserved transcription factor binding sites

To find out more about these and over 85 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Tip of the Week: NCBI's New BioSystems Resource

tip_NCBI_BioSystems At the Biocuration meeting that I attended back in April, Jim Ostell of NCBI announced that they would soon be releasing a new resource on biological networks. A few weeks ago a friend  alerted me that NCBI had released their new BioSystems resource (thanks for the heads-up, Cyndy!) BioSystems is a cool resource that take nice advantage of the interconnectedness of all of NCBI’s Entrez resources to give great pathway information – either species-specific pathways or general pathways with extensive links to other NCBI databases as well as outside resources. NCBI describes their new resource (in part) like this:

A number of databases, such as KEGG and BioCyc, provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. The NCBI BioSystems Database was developed as a collaborative and complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data.

There is NO WAY I can cover all that BioSystems has to offer in this 5 minute tip, but fear not – not only is NCBI’s documentation on BioSystems quite nice, we here at OpenHelix are already at work on a full BioSystems tutorial! We’ll keep you posted on that project, but for now – enjoy the tip & check out the resource for yourself when you’ve got some time.