Tag Archives: MMDB

Many Protein Resources Have Recently Announced Updates

PDB structure 3rg9

 

 

 

 

In our ongoing pursuit of up-to-date tutorials, I’ve been tracking changes that are occurring at resources and planning our updates accordingly. Protein resources are especially going to keep me out of trouble this summer, because their developers and curators have been busy! I’ve compiled a short synopsis below, and would appreciate comments on any other resources you know about, or want to brag about! :)

  • I featured the ExPASy list of proteomic tools in a past tip. As of  Tuesday this list is no longer being kept up-to-date, but the ExPASy resource has been expanded beyond being “just” a proteomics resource and is now the new SIB Bioinformatics Resource Portal. According to its developers, the portal:

    “provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. … On this portal you find resources from many different SIB groups as well as external institutions.”

    And never fear, there is still an up-to-date list of proteomics tools found here.

  • I mentioned in my tip last week that NCBI’s MMDB has undergone an update & I’ll be updating our tutorial on it soon.
  • NCI/Nature Pathway Interaction Database, or PID, had an update June 14th that includes new and updated pathway information.
  • PROSITE had an update June 21st, which is Release 20.73, and now includes 1618 documentation entries, 1308 patterns, 936 profiles and 925 ProRules.
  • The RCSB PDB resource has announced updates to their Browse Database function, enhanced sequence displays from structure summary pages and the PDB-101 educational resource available from blackboard logos on PDB pages. For more details on using PDB, please see our free PDB Introductory tutorial sponsored by the RCSB.
  • STRING’s 9.0 release is now available, and we’ll be looking into anything we need to update in our tutorial as a result.
  • UniProt released an update June 28th that included a major update on many bacterial and archaeal Type II Toxin-Antitoxin modules, as is described here.

Enjoy all the new information – I know I will! :)

(re)Funding Databases II

ResearchBlogging.orgSo, I wrote about defunding resources and briefly mentioned a paper in Database about funding (or ‘re’funding) databases and resources. I’d like to discuss this a bit further. The paper, by Chandras et. al, discusses how databases and, to use their term, Biological Resource Centers (BRCs) are to maintain financial viability.

Let me state first, I completely agree with their premise, that databases and resources have become imperative. The earlier model of “publication of experimental results and sharing of the reated research materials” needs to be extended. As they state:

It is however no longer adequate to share data through traditional modes of publication, and, particularly with high throughput (‘-omics) technologies, sharing of datasets requires submission to public databases as has long been the case with nucleic acid and protein sequence data.

The authors state, factually, that the financial model for most biological databases (we are talking the thousands that exist), has often been a 3-5 year development funding, that once runs out, the infrastructure needs to be supported by another source. In fact, this has lead to the defunding of databases such as TAIR and VBRC (and many others), excellent resources with irreplaceable data and tools, that then must struggle to find funding to maintain the considerable costs of funding infrastructure and continued development.

The demands of scientific research, open, shared data, require a funding model that maintains the publicly available nature of these databases. And thus the problem as they state:

If, for financial reasons, BRCs are unable to perform their tasks under conditions that meet the requirements of sceintfic research and the deamnds of industry, scientists will either see valuable information lost or being transferred into strictly commercial environment with at east two consequences: (i) blockade of access to this information and/or high costs and (ii) loss of data and potentioal for technology transfer for the foreseeable future. In either case the effect on both the scientific and broader community will be detrimental.

Again, I agree.

They discuss several possible solutions to maintaining the viability of publicly available databases including a private-public dual tier system where for-profits paid an annual fee and academic researchers have free access. They mention Uniprot, which underwent a funding crisis over a decade ago, as an example. Uniprot (then Swissprot) went back to complete public funding in 2002. There are still several other databases that are attempting to fund themselves by such a model. BioBase is one where several databases have been folded. TransFac is one. There is a free, reduced functionality, version that is available to academics through gene-regulation.com and the fuller version for a subscription at BioBase. This former version allows some data to be shared, as one could see at VISTA or UCSC. I am not privy to the financials of BioBase and other similar models, and I assume that will work for some, but I agree with the authors that many useful databases and resources would be hard-pressed to be maintained this way.

Other possibilities include fully  including databases under a single public institution funding mechanism. The many databases of NCBI and EBI fit this model. In fact, there is even a recent case of a resource being folded into this model at NCBI. Again, this works for some, but not all useful resources.

Most will have to find variable methods for funding their databases. Considering the importance of doing so, it is imperative that viable models are found. The authors reject, out of hand, advertising. As they mention, most advertisers will not be drawn to website advertising without a visibility of at least 10,000 visitors per month. There might be some truth to this (and I need to read the reference they cite that use to back that up).

But the next model they suggest seems to me to have the same drawback. In this model, the database or resource would have a ‘partnership of core competencies.’ An example they cite is MMdb (not to be confused with MMDB). This virtual mutant mouse repository provides direct trial links to Invitrogen from it’s gene information to the product page. They mention that though 6 companies were approached, only one responded. It would seem that this model has the same issues as directly selling advertising.

They also mention that, at least for their research community of mouse functional genomics, “Institutional Funding” seems the best solution for long-term viability and open access. Unfortunately, until institutions like NIH and EMBL are willing or able to fund these databases, I’m not sure that’s thats a solution.

As they mention in the paper, the rate of growth of the amounts and types of data that is being generated is exponential. I am not sure that government or institutional funding can financially keep up with housing the infrastructure needed to maintain and further develop these databases so that all the data generated can remain publicly and freely accessible.

Information is should be free, but unfortunately it is not without cost. It will be interesting to see how funding of databases and resources evolves in this fast growing genomics world (and imperative we figure out solutions).

PS: On a personal note, the authors use their resource, EMMA (European Mouse Mutant Archive), as an example in the paper. I like the name since it’s the name of my daughter, but it just goes to prove that names come in waves. We named our daughter thinking few would name their daughter the same. When even databases name the same name, you know that’s not the case.

Chandras, C., Weaver, T., Zouberakis, M., Smedley, D., Schughart, K., Rosenthal, N., Hancock, J., Kollias, G., Schofield, P., & Aidinis, V. (2009). Models for financial sustainability of biological databases and resources Database, 2009 DOI: 10.1093/database/bap017

New and Updated Online Tutorials for ASTD, Entrez Protein and MMDB

Comprehensive tutorials on the ASTD, Entrez Protein, and MMDB databases enable researchers to quickly and effectively use these invaluable variation resources.

Seattle, WA September 24, 2008 — OpenHelix today announced the availability of new tutorial suites on the Alternative Splicing and Transcript Diversity (ASTD) database, Entrez Protein and the Molecular Modeling Database (MMDB). ASTD is an European Bioinformatics Institute (EBI) resource for alternative splice events and transcripts for the human, mouse, and rat systems. Entrez protein is a comprehensive database of protein information brought to you by the National Center for Biotechnology Information (NCBI). MMDB is another NCBI resource which contains an extensive collection of three-dimensional protein structures with detailed annotation that can be used to learn about the structure and function of many proteins. Together these three tutorials give the researcher an excellent set of resources to carry their research from transcript to 3d protein structure.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

ASTD

  • to perform Quick and Advanced searches
  • to navigate gene and transcript report pages
  • to predict intron/exon boundaries and likely regulatory protein binding site
  • to search manually curated data regarding alternate splicing

Entrez Protein

  • to perform basic and advanced searches utilizing the many available tools and options
  • to understand the protein records and exploit the many internal and external links you are provided with
  • to explore some of the resources provided by the NCBI network of databases, such as “My NCBI”

MMDB

  • to search MMDB using both basic and advanced query techniques
  • to understand the detailed results you obtain
  • to visualize and manipulate structures using NCBI’s Cn3D structural viewer
  • to locate and view structurally aligned homologs

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

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix currently provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.