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- May 23, 2012
- 08:49 AM
- 25 views
Video Tip of the Week: the New PubMed Filters Sidebar
In today’s tip I am linking to a YouTube video from NCBI that briefly explains the new Filters Sidebar feature that has been added to PubMed. We first saw a tweet that the change was coming back on May 2nd, just as I was completing a total update to our full PubMed tutorial*. I struggled with [...]... Read more »
Sayers E. W., Barrett T., Benson D. A., Bolton E., Bryant S. H., Canese K., Chetvernin V., Church D. M., DiCuccio M., & Federhen S. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 40(D1). DOI: 10.1093/nar/gkr1184
- April 18, 2012
- 10:00 AM
- 117 views
Video Tip of the Week – The Cell: An Image Library
Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. The Cell Image Library is brought to you by the The American Society for Cell Biology (ASCB), and contains thousands of images, time series and groups of images, videos and animations of cells in a variety of organisms. Images are organized by Cell Process, Cell Component, Cell Type, Organism and Recently added. You can browse images or do a basic search from the homepage, or perform advanced searches. The advanced search form allows users to query with keywords, and for image attributes, specific image licensing categories, biological categories, imaging techniques, or associated anatomy terms.... Read more »
Miller, K. (2010) Finding the key – cell biology and science education. Trends in Cell Biology, 20(12), 691-694. DOI: 10.1016/j.tcb.2010.08.008
- April 18, 2012
- 09:10 AM
- 42 views
Video Tip of the Week – The Cell: An Image Library
Who says social media is a waste of time? Not me – my LinkedIn updates keep including announcements of the “Image of the week” from The Cell: An Image Library. For my tip this week I decided to follow up on that & check out the images available from this resource, & I’m glad I did. [...]... Read more »
Miller, K. (2010) Finding the key – cell biology and science education. Trends in Cell Biology, 20(12), 691-694. DOI: 10.1016/j.tcb.2010.08.008
- March 14, 2012
- 09:40 AM
- 171 views
Video Tip of the Week: New Genetic Testing Registry (GTR) Resource
For more information, see our blog post at http://blog.openhelix.eu/?p=11439. In this movie we compare the new GTR resource from NCBI to other clinical resources that you may already be using, to answer why you may want to use the GTR.... Read more »
Pagon RA. (2006) GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94(3), 343-8. PMID: 16888670
Mitchell JA, Fomous C, & Fun J. (2006) Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94(3), 336-42. PMID: 16888669
Amberger, J., Bocchini, C., & Hamosh, A. (2011) A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Human Mutation, 32(5), 564-567. DOI: 10.1002/humu.21466
Aymé, S., & Schmidtke, J. (2007) Networking for rare diseases: a necessity for Europe. Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz, 50(12), 1477-1483. DOI: 10.1007/s00103-007-0381-9
- February 22, 2012
- 10:09 AM
- 219 views
Video tip of the week: Updated Introductory Tutorial on the RCSB PDB
This post is part of OpenHelix's "Tip of the Week" blog feature. For today’s tip I am offering our full introductory tutorial on the RCSB PDB, which we completely updated to cover their Top Search Bar, PDB 101 education feature, and more. ... Read more »
Berman, H., & et al. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
- January 18, 2012
- 09:00 AM
- 271 views
Video tip of the week: OpenHelix App on SciVerse to Extend Research
In today’s tip I will introduce you to another one of our efforts to “extend research” by showing you a glimpse of an OpenHelix app that we designed for the SciVerse platform from Elsevier. This app scans a ScienceDirect journal article for any database names or URLs that we train on, and then displays a list of such resources in the window of the app.... Read more »
Mortensen, H., & Euling, S. (2011) Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century. Toxicology and Applied Pharmacology. DOI: 10.1016/j.taap.2011.01.015
Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010) OpenHelix: bioinformatics education outside of a different box. Briefings in Bioinformatics, 11(6), 598-609. DOI: 10.1093/bib/bbq026
Bengtson, J. (2011) ScienceDirect Through SciVerse: A New Way To Approach Elsevier. Medical Reference Services Quarterly, 30(1), 42-49. DOI: 10.1080/02763869.2011.541346
- January 11, 2012
- 10:00 AM
- 402 views
Video tip of the week: Functional Glycomics Gateway
by Mary Mangan in OpenHelix
This week’s tip is on our newest tutorial suite on the Functional Glycomics Gateway. It is freely available to everyone because it is sponsored by the Consortium for Functional Glycomics. From the suite landing page, click on the “Launch Online Tutorial” button to view the movie.... Read more »
Raman, R., Raguram, S., Venkataraman, G., Paulson, J., & Sasisekharan, R. (2005) Glycomics: an integrated systems approach to structure-function relationships of glycans. Nature Methods, 2(11), 817-824. DOI: 10.1038/nmeth807
Raman, R., Venkataraman, M., Ramakrishnan, S., Lang, W., Raguram, S., & Sasisekharan, S. (2006) Advancing glycomics: Implementation strategies at the Consortium for Functional Glycomics. Glycobiology, 16(5), 82-90. DOI: 10.1093/glycob/cwj080
Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, & Etzler ME. (2009) Essentials of Glycobiology, 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. PMID: 20301239
- December 14, 2011
- 09:05 AM
- 1,341 views
Video Tip of the Week: Big Changes to NCBI’s Genome Resources
NCBI was created in 1988 and has maintained the GenBank database for years. They also provide many computational resources and data retrieval systems for many types of biological data. As such they know all too well how quickly the data that biologists collect has changed and expanded. As uses for various data types have been [...]... Read more »
Tatusova, T., Karsch-Mizrachi, I., & Ostell, J. (1999) Complete genomes in WWW Entrez: data representation and analysis. Bioinformatics, 15(7), 536-543. DOI: 10.1093/bioinformatics/15.7.536
Barrett, T., Clark, K., Gevorgyan, R., Gorelenkov, V., Gribov, E., Karsch-Mizrachi, I., Kimelman, M., Pruitt, K., Resenchuk, S., Tatusova, T.... (2011) BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. Nucleic Acids Research. DOI: 10.1093/nar/gkr1163
Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S.... (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. DOI: 10.1093/nar/gkr1184
- November 9, 2011
- 09:06 AM
- 570 views
Video Tip of the Week: The New Database of Genomic Variants – DGV2
In today’s tip I will briefly introduce you to the beta version of the updated DGV resource. The Database of Genomic Variants, or DGV, was created in 2004 at a time early in the understanding of human structural variation, or SV, which is defined by DGV as genomic variation larger than 50bp. DGV has historically [...]... Read more »
Church, D., Lappalainen, I., Sneddon, T., Hinton, J., Maguire, M., Lopez, J., Garner, J., Paschall, J., DiCuccio, M., Yaschenko, E.... (2010) Public data archives for genomic structural variation. Nature Genetics, 42(10), 813-814. DOI: 10.1038/ng1010-813
- October 31, 2011
- 06:17 PM
- 384 views
On a Mission for Protein Information
It’s probably just the human brain’s ability to connect dots & find patterns, but it can be interesting how many “unrelated” events and information bits accumulate in my head & eventually get mulled into an idea or theory. Take, for example, a recent biotech mixer, bits from an education leadership series & a past Nature [...]... Read more »
Sierpinski P, Garrett J, Ma J, Apel P, Klorig D, Smith T, Koman LA, Atala A, & Van Dyke M. (2008) The use of keratin biomaterials derived from human hair for the promotion of rapid regeneration of peripheral nerves. Biomaterials, 29(1), 118-28. PMID: 17919720
Edwards, A., Isserlin, R., Bader, G., Frye, S., Willson, T., & Yu, F. (2011) Too many roads not taken. Nature, 470(7333), 163-165. DOI: 10.1038/470163a
- October 26, 2011
- 09:03 AM
- 462 views
Video Tip of the Week: Variation Data from Ensembl
Trey introduced me to this “decent collection of video tutorials ” from Ensembl, but he and Mary are currently in Morocco teaching a 3-day bioinformatics workshop & then attending the conference (yes, I am envious!). I am therefore creating this week’s tip based on the tutorials that Trey pointed me to. In today’s tip I am [...]... Read more »
Flicek, P., Aken, B., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S.... (2009) Ensembl's 10th year. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp972
- October 5, 2011
- 08:34 AM
- 522 views
Tip of the Week: VnD Resource for Genetic Variation and Drug Information (with video)
In today’s tip I am going to feature a resource that I found recently. I’ve been updating our dbSNP tutorial, which Mary & Trey will be presenting at workshops in Morocco, and also our free PDB tutorial, which is sponsored by the RCSB PDB team. I have therefore been thinking about protein structures and small [...]... Read more »
Yang, J., Oh, S., Ko, G., Park, S., Kim, W., Lee, B., & Lee, S. (2010) VnD: a structure-centric database of disease-related SNPs and drugs. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq957
- August 31, 2011
- 09:02 AM
- 780 views
Tip of the Week: From UniProt to the PSI SBKB and Back Again
It is often beneficial to visit multiple biomedical databases or resources, even if they seem to provide overlapping information because no two resources focus on the exact same information, or present it in exactly the same way. Instead of duplicating each others’ curation efforts, database often link out to related information at other resources. You [...]... Read more »
The UniProt Consortium. (2009) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp846
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L.... (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn790
- July 27, 2011
- 09:18 AM
- 835 views
Tip of the Week: the New SIB Bioinformatics Resource Portal
A few years ago I did a tip on the proteomic tools list available from the ExPASy site. You can still get to that list, but it is no longer being updated. Instead the entire ExPASy site has been updated and reorganized and is now the new Swiss Institute of Bioinformatics (SIB) Bioinformatics Resource Portal. [...]... Read more »
Gasteiger, E. (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784-3788. DOI: 10.1093/nar/gkg563
- May 18, 2011
- 08:47 AM
- 866 views
Tip of the Week: Allen Institute’s Brain Explorer
Not that long ago Mary posted on updates that occurred recently at the Allen Institute for Brain Science & hinted that there might be a tip coming about their cool 3D Brain Explorer tool – well, today’s the day! As Mary mentions in her post, the Allen Institute has created some phenomenal tools and detailed datasets for brain
From the Brain Explorer documentation, the Explorer allows users to:
# View a fully interactive version of the Allen Human Brain Atlas in 3D for two donors.
*View gene expression data in 3D: partially-inflated white matter surfaces are colored by gene expression values of nearby samples.... Read more »
Lau, C., Ng, L., Thompson, C., Pathak, S., Kuan, L., Jones, A., & Hawrylycz, M. (2008) Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain. BMC Bioinformatics, 9(1), 153. DOI: 10.1186/1471-2105-9-153
- April 27, 2011
- 12:43 PM
- 936 views
Sage Bioinformatics Advice, But…
Bioinformatics analysis is a powerful technique applicable to a wide variety of fields, and the subject of many a blog post here at OpenHelix. I’ve had two particular bioinformatics articles on my desk for a couple of months now, waiting for me to be able to articulate my thoughts on them. They both offer great [...]... Read more »
Cline, M., & Karchin, R. (2010) Using bioinformatics to predict the functional impact of SNVs. Bioinformatics, 27(4), 441-448. DOI: 10.1093/bioinformatics/btq695
Vincent Shen. (2011) Mistaken identities in proteomics. BioTechniques. info:other/http://www.biotechniques.com/news/biotechniquesNews/biotechniques-312015.html
- April 13, 2011
- 09:16 AM
- 590 views
Tip of the week: VirusMINT
In this week’s tip I’d like to introduce you to VirusMINT. We found VirusMINT during our ‘regularly scheduled’ update of our Introductory tutorial on MINT, or the Molecular INTeraction database. We really like MINT for all the great interaction information they provide on a wide variety of species. When we saw they had a ‘virally focused’ database, we had to check it out.
It turns out that VirusMINT is really unique in that it shows interactions BETWEEN human and viral proteins, all on the same interaction map. PLUS, from the VirusMINT homepage description:
VirusMINT uses the PSI-MI standard and is fully integrated with the MINT database.
You can either search for any viral or human protein by entering either common names or database identifiers in the form in the left frame or display a complete viral interactome by pressing the corresponding button in the frame below.
I only had time to show you the most basic VirusMINT features in this short movie. After you watch it, be sure to head over to MINT & check out all their great features, which currently includes 4 sister databases: MINT, HomoMINT (an inferred human network), Domino (a domain peptide interactions database) and VirusMINT. These four databases are a really nice protein interaction resource because each offers a clean set of information on important areas of protein interactions and are all integrated with one another. The MINT databases use PSI_MI standard formatting to capture curated protein interaction information from literature & direct user submissions. Not only is data integrated across each of the four databases, each database provides interactive viewers for visually displaying the data. Outputting and downloading the data is also possible.
For more details of their full functionality: consider checking out our full MINT tutorial – available through a subscription to our full database of training materials (currently on sale); purchasing an individual access to the tutorial; or checking out the references listed below.
References:
Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M., Cusick, M., & Cesareni, G. (2009). VirusMINT: a viral protein interaction database Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn739
Chatr-aryamontri, A., Ceol, A., Palazzi, L., Nardelli, G., Schneider, M., Castagnoli, L., & Cesareni, G. (2007). MINT: the Molecular INTeraction database Nucleic Acids Research, 35 (Database) DOI: 10.1093/nar/gkl950
Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L., & Cesareni, G. (2009). MINT, the molecular interaction database: 2009 update Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp983
... Read more »
Chatr-aryamontri, A., Ceol, A., Peluso, D., Nardozza, A., Panni, S., Sacco, F., Tinti, M., Smolyar, A., Castagnoli, L., Vidal, M.... (2009) VirusMINT: a viral protein interaction database. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn739
Chatr-aryamontri, A., Ceol, A., Palazzi, L., Nardelli, G., Schneider, M., Castagnoli, L., & Cesareni, G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Research, 35(Database). DOI: 10.1093/nar/gkl950
Ceol, A., Chatr Aryamontri, A., Licata, L., Peluso, D., Briganti, L., Perfetto, L., Castagnoli, L., & Cesareni, G. (2009) MINT, the molecular interaction database: 2009 update. Nucleic Acids Research, 38(Database). DOI: 10.1093/nar/gkp983
- March 28, 2011
- 09:15 AM
- 988 views
Protein Structure Analysis – How Far We’ve Come!
The team here at OpenHelix has recently updated our sponsored tutorials on two excellent structural biology resources, the RCSB Protein Data Bank (PBD) and the PSI-Nature Structural Biology Knowledgebase (PSI SBKB). Because the tutorials are sponsored by these resources they are free for anyone to view and download in full. You can access our training materials for the resources at our RCSB PDB landing page, or our PSI SBKB landing page. I’m very happy with both tutorial suites, so please check them out.
As my personal celebration for these releases I have been reading a variety of articles showing the scope of how far our abilities to analyze protein structures have come. The first article is one that Mary pointed me to a while back, which discusses the infancy of bioinformatics, entitled “The Roots of Bioinformatics in Protein Evolution” by RF Doolittle (cited below, as are all articles mentioned). In this wonderful perspective Dr. Doolittle describes a time when DNA sequencing was unimaginable and protein sequencing was laborious, slow, and yet so new that each day was full of excitement as one more amino acid was identified. It is a revealing glimpse at a research era gone by – to quote Doolittle, “Science as an endeavor thrives on obsolescence.” – and mentions the contributions of Margaret Dayhoff, who Mary has blogged about.
The next historical article that I read was entitled “The Early Years of Retroviral Protease Crystal Structures” by M Miller (freely available on PMC). As you can tell from the title, this covers a time more recent than the Doolittle article, when protein crystallization studies were possible. Dr. Miller traces the X-ray crystal studies of retroviral proteases at the NCI-Fredrick in the late 1980′s and early 1990′s, and she describes how chemical synthesis of HIV1-PR was critical to obtaining enough protein for crystallization and how the crystal structure of it (deposited into the PDB archive and therefore freely available for all researchers to study) was invaluable for the design of inhibitors of HIV1-PR as anti-AIDS drugs.
I’ve also be perusing more recent papers that highlight how protein structures can aid biological investigations. These include: “Structure of mammalian AMPK and its regulation by ADP“, “Bioinformatics analysis of disordered proteins in prokaryotes“, “Crystal structure of inhibitor of κB kinase β” and others. It would also be fun to attend “The 25th Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and Their Application to Targeted Drug Design” to learn more, but alas I will not be in the area at the time of the meeting. As I’ve posted before, I am a geneticist by education. To me seeing the development of protein studies (through the historical reviews) and the studies currently occurring in the field of structural biology, combined with the amazing offerings available freely through both the RCSB PDB and the PSI SBKB really does feel like an appropriate, and enjoyable, celebration for the completion of our tutorial updates. Let me know what you think about them, when you get a chance!
References:
Berman, H. (2000). The Protein Data Bank Nucleic Acids Research, 28 (1), 235-242 DOI: 10.1093/nar/28.1.235
Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L., Kopp, J., Podvinec, M., Adams, P., Carter, L., Minor, W., Nair, R., & Baer, J. (2009). The protein structure initiative structural genomics knowledgebase Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn790
Doolittle, R. (2010). The Roots of Bioinformatics in Protein Evolution PLoS Computational Biology, 6 (7) DOI: 10.1371/journal.pcbi.1000875
Miller, M. (2010). The early years of retroviral protease crystal structures Biopolymers, 94 (4), 521-529 DOI: 10.1002/bip.21387
... Read more »
Berman, H. (2000) The Protein Data Bank. Nucleic Acids Research, 28(1), 235-242. DOI: 10.1093/nar/28.1.235
Berman, H., Westbrook, J., Gabanyi, M., Tao, W., Shah, R., Kouranov, A., Schwede, T., Arnold, K., Kiefer, F., Bordoli, L.... (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37(Database). DOI: 10.1093/nar/gkn790
Doolittle, R. (2010) The Roots of Bioinformatics in Protein Evolution. PLoS Computational Biology, 6(7). DOI: 10.1371/journal.pcbi.1000875
Miller, M. (2010) The early years of retroviral protease crystal structures. Biopolymers, 94(4), 521-529. DOI: 10.1002/bip.21387
- March 9, 2011
- 09:15 AM
- 672 views
Tip of the Week: World Tour of Genomics Resources
Most weeks our tip is a five-minute movie that quickly introduces you to a new resource, or a cool new function at an established resource. Occasionally we feature one of our full resource tutorial that is being made freely available through resource sponsorship of our training suite. In this week’s tip we provide access to one of our tutorials that is especially near and dear to our heart. It is a World Tour of Genomics Resources in which we explore a variety of publicly-available biomedical, bioinformatics and bioscience databases and other resources.
This tutorial is quite different from our usual ones. Generally we focus on a specific software resource and describe step-by-step how to use its functions such as how to do basic and advanced searches, how to understand and modify displays, where to find specific types of data such as FASTA sequences, etc. and even provide tips on ‘hidden features’ that power users even find useful and informative. This type of software training is absolutely critical.
But many people need an even earlier step: just the *awareness* that resources are available that might serve their needs. This tutorial fills that niche. We present a sampling of resources, all free to use, from each of 9 categories including: Analysis & Algorithms, Expression, Genome Browsers (for Eukaryotes and for Prokaryotes and Viruses), Genome Variation, Literature, Nucleotides, Pathways and Proteins. After the World Tour, which is the majority of the tutorial, we then describe how to use OpenHelix’s free search and learn portal to find bioscience resources most appropriate for your research needs. From this the tour transitions into a brief discussion of the format of our training materials and how to use them, and then ends with information about other learning resources that we provide.
This tutorial has been wildly popular whenever we’ve done it as a live seminar. At the NIH they actually had to lock the doors because we’d hit the capacity of the room, and people were turned away. In fact, it has been so popular that we decided to produce it as a full tutorial suite and release it as one of our free trainings so that anyone and everyone could learn about the breadth of great public software options available for free use.
In addition to this free tutorial, we also have published a paper entitled “OpenHelix: bioinformatics education outside of a different box” in a special issue of Briefings in Bioinformatics entitled “Special Issue: Education in Bioinformatics“. This paper describes a plethora of sources where researchers can access informal educational sources of learning on publicly available bioinformatics resources. The sources of information include a wide variety of formats including lists of resources, journals that regularly feature tool descriptions, and eLearning resources sources such as the MIT OpenCourseWare effort. If you know of other such resources that aren’t covered in our tour or paper, comment & let us know about them – we love to learn as much as we love to teach!
Quick link to World Tour of Genomics Resources tutorial here.
Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010). OpenHelix: bioinformatics education outside of a different box Briefings in Bioinformatics, 11 (6), 598-609 DOI: 10.1093/bib/bbq026
... Read more »
Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010) OpenHelix: bioinformatics education outside of a different box. Briefings in Bioinformatics, 11(6), 598-609. DOI: 10.1093/bib/bbq026
- February 2, 2011
- 09:05 AM
- 725 views
Tip of the Week: RCSB PDB Data Distribution Summaries
In today’s tip I will feature the data distribution summaries and their drill down features which you can see from many RCSB PDB searches. We are in the process of updating our full tutorial sponsored by the RCSB PDB team, and as part of that effort I’ve gotten to know and appreciate this new data presentation format. Over the last five years the RCSB PDB has really been working hard at redesigning their resource to be more easily accessed by a wide variety of users. Below you will find a recent citation from the group explaining all of their updates and the logic behind them. The paper is a good read because I won’t have time to do anything except scratch the surface of the redesign & you’ll get the details there, but also because the intro also gives a great glimpse into what resources are dealing with in the way of ‘data deluge’. The increase in users AND data that the RCSB PDB has experienced over the last few years is mind boggling!
OK, back to the data distributions. To me these are really elegant ways of helping any user – PDB is by no means just for structural biologists – come to the RCSB PDB & quickly and easily access whole categories of interesting information and then drill down in detailed ways to access the specific structure or data that they are most interested in. For example, I could begin with a keyword search for something as general as ‘kinase’. This search retrieves over 4 thousand hits, which could be quite daunting, but at the top of the report results are displayed under categories such as Organism, Taxonomy, Experimental Method, SCOP classification and more. Subcategories under each of these categories lets me know how many hits are, for example are a mixed Polymer type, are human hits, or are alpha and beta proteins. I can mouse over any subcategory title to find out the percent of hits in this category compared to all hits, or click on the title to further drill-down the data distribution on just that subcategory of results. The distribution summaries are updated to then focus specifically on the distribution of THOSE data. Using these summaries is much more intuitive than any text description description that I can muster.
My advice? Check out the tip, then check out the data distribution summaries, drill down utility, and all the other great features of the RCSB PDB & see how easy it is to find information on your favorite gene. Oh yea, and be watching for us to release our full, free & newly updated tutorial on the RCSB PDB resource soon!
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J., Young, J., Yukich, B., Zardecki, C., Berman, H., & Bourne, P. (2010). The RCSB Protein Data Bank: redesigned web site and web services Nucleic Acids Research, 39 (Database) DOI: 10.1093/nar/gkq1021
... Read more »
Rose, P., Beran, B., Bi, C., Bluhm, W., Dimitropoulos, D., Goodsell, D., Prlic, A., Quesada, M., Quinn, G., Westbrook, J.... (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 39(Database). DOI: 10.1093/nar/gkq1021
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