Tag Archives: bioGPS

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • RT @Dr_Bik: Cool visualization w/dragging ability RT @moorejh: Integrative multi-species prediction http://t.co/vZC0QgLU #bioinformatics #genomics [Mary]
  • From NCBI News: “The Netblast client (blastcl3) that has provided batch search access to the NCBI Web BLAST service will be discontinued in the near future. The BLAST+ applications replace and improve upon the functions provided by blastcl3. Blastcl3 users should switch to BLAST+ as soon as possible… ” More information is available here. [Jennifer]
  • Super Science Shoes AWAY!! (can you say weekend project?) RT @DrRubidium featuring @Seelix! -> Make your own superhero heels and walk a mile in Wonder Woman’s shoes http://on.io9.com/JGT2UP via @io9 [Jennifer]
  • RT @GenomeWeb: From CDC’s genomics group: three-tiered list of genomic tests, organized by level of evidence for utility and validity: http://t.co/R9d46Li6 [Mary]
  • More new genome-related tools from NCBI, again announced in their News: “The Genome Remapping Service (Remap) and the Variation Reporter are related tools that find locations on current and past genome builds…The Variation Reporter… takes a set of locations in a human genome assembly and identifies known human variations (NCBI Reference SNPs) at those positions. This service is particularly helpful for identifying experimentally or clinically determined variants. ” [Jennifer]
  • BioGPS is  nice tool. RT @andrewsu: SuLabBlog: BioGPS retrospective – the four year anniversary http://t.co/QasGAbAg [Mary]
  • Fascinating case of genetics, interventions, and law. RT @_Genethics: Reading a grounded and interesting piece on knotty genomic issues @canlawmag Legal lag in medical advances http://t.co/xzrJHu5V [Mary]
  • Very, cool – adding it to our updated tutorial now! :) RT @NCBI: PubMed’s new Filter Sidebar is now available – ex: http://t.co/3LiWNJc6 , Info: http://t.co/p76e0915 & YouTube Video: http://t.co/tH1ViFZc [Jennifer]
  • “an interactive resource for global biodiversity analysis ” RT @AgroBioDiverse: Map of Life goes live http://t.co/x8MSN89A [Mary]

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the Week: New and Improved OMIM®

In the realm of bioinformatics resources, few are more venerable than OMIM®, Online Mendelian Inheritance in Man [well, originally not online, on index cards...]. For those who might be new to OMIM, it is a catalog of genes and their variations, and resulting phenotypes in human, with a more clinical perspective than some resources offer. As I was reviewing the history of OMIM for this post, I began to wonder if there even is any repository in genomics that’s been maintained on a computer framework longer. I know of an older protein analysis program that I wrote about once here–from Margaret Dayhoff and Robert Ledley. But as an ongoing repository or catalog that was stored, Victor McKusick wrote:

Mendelian Inheritance in Man has been maintained on the computer since 1964.

It was stored on a mainframe at Johns Hopkins at that time. The other one that I thought was probably close was RCSB PDB, which is described on their “about” page in this way:

The PDB was established in 1971 at Brookhaven National Laboratory and originally contained 7 structures.

It’s likely that in some form it existed on a computer system earlier than that–and may give MIM a run for the record. Bruno Strasser described 4 resources developed around the same time–1965–as the Cambridge Structural Database, MIM, Index Medicus, and Atlas of Protein Sequence and Structure.

It’s not easy to maintain and develop a resource for this long. Just this past month we learned about the risk of KEGG going away. But in bioinformatics–like biology–a resource needs to evolve or die. (Actually, I can remember in grad school that phrase was used by the chair of our department to describe what biology faculty needs to do as well.) In this week’s tip of the week, I report that OMIM is evolving, and I introduce you to the new interface.

Most people have encountered OMIM at the NCBI. But if you go over to there today, you’ll see this notice on the homepage:

This is because OMIM has a new home. It’s not clear at this time if the NCBI incarnation will be updated going forward. The OMIM team at JHU is requesting that software providers who serve links to OMIM now migrate those links to the new OMIM.org site, which the OMIM team considers to be the official site and will be the up-to-date one.

Let’s talk specifically about the evolved OMIM now: it’s entered a new century! Yay! The incredible deep collection of curated data over the decades still remains, but the new interface is very nice to use and to look at–it no longer looks like 1995 over there. There are also new handy links, and new search options, and new features still to come.

Compare this same record for the APC gene (a contributor to hereditary colon cancer) in both places:

Old OMIM at NCBI: http://www.ncbi.nlm.nih.gov/omim/611731

New OMIM at JHU: http://www.omim.org/entry/611731

I find the new page to be significantly tidier, don’t you? The links you need to other resources are still there, but you can toggle open the menus to find them now. And some of the links are to resources that weren’t available on the old page (for example, BioGPS and PharmGKB which we like very much!).  I’m also told that on appropriate pages there will be links to the DECIPHER resource.

You can still browse around the MIM map by clicking on the Advanced search for Gene Map link: http://www.omim.org/search/advanced/geneMap . I have done this on many days when I have found something intriguing in a chromosomal region and I want to see what was reported in that area and stored at OMIM.

Another feature that I think is very cool is the option to change the language with the Google Translate menu. I know it’s not perfect, but I’m finding increasingly that I want to read blog posts in other languages and I am finding it works pretty well. Making the OMIM data so easily accessible to non-English speakers is a really nice touch.

Although sometimes it is tough to transition to new software, I think this is a good sign. In addition to maintaining the excellent knowledge collection that began so long ago, a new interface means that OMIM is continuing to grow and change to meet the needs of today. And as we move forward to identify more and more genomic variations and alterations that impact human health, well-curated and deep knowledge bases like this are crucial.

Congrats to the OMIM team on the new look and new home.

Quick link to the new OMIM: http://www.omim.org/

(Bonus: did you know there’s also an Online Mendelian Inheritance in Animals OMIA? http://www.ncbi.nlm.nih.gov/omia )

Follow them on Twitter: http://twitter.com/#!/OmimOrg

References:
McKusick, V. (2006). A 60-Year Tale of Spots, Maps, and Genes Annual Review of Genomics and Human Genetics, 7 (1), 1-27 DOI: 10.1146/annurev.genom.7.080505.115749

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

Strasser, B. (2009). Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965 Journal of the History of Biology, 43 (4), 623-660 DOI: 10.1007/s10739-009-9221-0 (PDF available on his faculty web site here.)

Strasser, BJ (2006) “Collecting and Experimenting: The moral economies of biological research, 1960s-1980s.”, Preprints of the Max-Planck Institute for the History of Science, 310, 105-23.

BioGPS is moving…to academia

News appears on my twitter feed this morning:

RT @attilacsordas: BioGPS is moving http://ff.im/-DYv96

I don’t know if y’all had the same experience back in grad school, but we were assured that is was impossible to move back to academia after being in the corporate realm for a long period. Well, it appears that’s not the case! I’ve been seeing that more and more, and I think it’s a good deal. When students are looking for career advice and for networking, the guidance on non-academic careers was a little sparse.

What that means for a database, though, I’m not sure. Now it may have to compete for grants and support in a way that it hadn’t before. And we all know that maintenance support for existing resources is not always so easy to get. This could be true in a corporate setting too–budgets get cut all the time, mergers change priorities, etc. So I’m not saying it’s unique to academic projects. I’m just going to be interested to see how it goes for BioGPS.

They are all very upbeat about it though–excited for the move and the new challenges. Some of the team is going with them. And they promise new features are in the works. That’s great and we’ll keep an eye out for them: we are always looking for good tip-of-the-week ideas! Good luck to the BioGPS team.

If you want to learn a bit about this resource, we did a tip not too long ago.  Tip of the Week: BioGPS for expression data and more

Direct to BioGPS’s announcement:  BioGPS is moving

Visit BioGPS: http://biogps.gnf.org/ New BioGPS: http://BioGPS.org

http://biogps.org/

BioGPS v2.0 now available

Via tweet we learn:

RT @attilacsordas: Introducing BioGPS 2.0 http://ff.im/-C0E0D

Not too long ago I did a tip-of-the-week on BioGPS, or the Gene Portal System. It’s a really nice and customizable tool to search for many different types of data that you might be interested in.

We are always pleased to see tools being updated–that means people are still adding new features and maintaining the tool. So it was great to see the new aspects of BioGPS. It looks like a lot of the front end features we talk about in the tip are still the same, but there are a number of improvements to other features. A really helpful new plug-in search certainly is useful–there are so many things you can plug in to this tool to set it up as you want it, and finding the appropriate plug-ins is quite key there!

The new plug-in ratings may also help you when choosing which ones to use.

Hat tip to Attila–thanks!

BioGPS announcement page: http://biogps.blogspot.com/2011/04/introducing-biogps-20.html

BioGPS tool: http://biogps.gnf.org/ New address: http://BioGPS.org

Tip of the Week: A year in tips III (last half of 2010)

As you may know, we’ve been doing tips-of-the-week for three years now. We have completed around 150 little tidbit introductions to various resources. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

Here are the tips from the first half of the year, and below you will find the tips from the last half of 2010 (you can see past years’ tips here: 2008 I2008 II2009 I2009 II):

July

July 7: Mint for Protein Interactions, an introduction to MINT to study protein-protein interactions
July 14: Introduction to Changes to NCBI’s Protein Database, as it states :D
July 21: 1000 Genome Project Browser, 1000 Genomes project has pilot data out, this is the browser.
July 28: R Genetics at Galaxy, the Galaxy analysis and workflow tool added R genetics analysis tools.

August

August 4: YeastMine, SGD adds an InterMine capability to their database search.
August 11: Gaggle Genome Browser, a tool to allow for the visualization of genomic data, part of the “gaggle components”
August 18: Brenda, comprehensive enzyme information.
August 25: Mouse Genomic Pathology, unlike other tips, this is not a video but rather a detailed introduction to a new website.

September

September 1: Galaxy Pages, and introduction to the new community documentation and sharing capability at Galaxy.
September 8: Varitas. A Plaid Database. A resource that integrates human variation data such as SNPs and CNVs.
September 15: CircuitsDB for TF/miRNA/gene regulation networks.
September 21: Pathcase for pathway data.
September 29: Comparative Toxicogenomics Database (CTD), VennViewer. A new tool to create Venn diagrams to compare associated datasets for genes, diseases or chemicals.

October

October 6: BioExtract Server, a server that allows researcher to store data, analyze data and create workflows of data.
October 13: NCBI Epigenomics, “Beyond the Genome” NCBI’s site for information and data on epigenetics.
October 20: Comparing Microbial Databases including IMG, UCSC Microbial and Archeal browsers, CMR and others.
October 27: iTOL, interactive tree of life

November

November 3: VISTA Enhancer Browser explore possible regulatory elements with comparative genomics
November 10: Getting canonical gene info from the UCSC Browser. Need one gene version to ‘rule them all’?
November 17: ENCODE Data in the UCSC Genome Browser, an entire 35 minute tutorial on the ENCODE project.
November 24: FLink. A tool that links items in one NCBI database to another in a meaningful and weighted manner.

December

December 1: PhylomeDB. A database of gene phylogenies of many species.
December 8: BioGPS for expression data and more.
December 15: RepTar, a database of miRNA target sites.

Tip of the Week: BioGPS for expression data and more

This week’s tip introduces BioGPS, or Gene Portal System. We get a lot of questions about two things that BioGPS can help you to tackle: what do I do with a list of genes to find out what they are? And the next question people have after that is: and where are they expressed? BioGPS can help you with both of those problems. It is a tool that integrates and displays many types of data that researchers would be interested in. It also allows you to customize your display with the types of data that are most relevant to you–using their extensive plug-in collection. And it can do so from your browser, or access the basic portal from your iPhone!

Recently there was a question at BioStar about ways to quickly access some human gene expression data. The top rated answer over there was BioGPS, so we thought we’d provide a look at the kinds of things available to users via BioGPS. This 5-minute movie introduces some of the features.

Basically you can search for a gene or a list of genes, you can search with various types of IDs, you can search by keyword, or you can even search by genomic intervals. Your resulting list will quickly link you to all kinds of information from expression data, to annotation details and wikis, and more.  The results are provided in a handy default view with panels of information which may offer what you are looking for.

But you can go further with BioGPS using their customization and plug-in features. You aren’t tied to the default view. The system offers plug-ins: other tools can pipe their information over to BioGPS so you can use it within that framework. You can  register/create a login and then store views that are suited to your research needs.

At the time they wrote the paper provided below, they already had over 150 plug-ins available. As I write this today there are nearly 400 things you could bring in to supplement the views of the genes you are interested in. And the range of plug-ins is tremendous: interaction data sets, SNPs, phylogenetic data… The Figure 2 in their paper gives a partial list of the plug-ins at that time, and the categories they highlight include: literature searching (such as PubMed, iHop, patents, more), gene portals (such as Entrez Gene, UniProt, Gene Cards, more), genetics (dbSNP, HapMap, HuGE, more), pathway tools (KEGG, Reactome, STRING, more) and even reagent providers. But there are more now, and it looks like more will continue to be developed and added. It really depends on what you need and want to display for your searches. You can browse around or search the plug-in collection to explore what’s available to view.

There are other tools you can use to explore expression data specifically. We like the UCSC Gene Sorter for some types of queries. Of course the large repositories of GEO and ArrayExpress can offer expression data as well. But for some users the BioGPS portal may offer integration and customization features that will suit their research needs. Go over and check it out. Register, set up some views, and you’ll be finding all sorts of useful annotations for your genes or regions of interest.

Just to also quickly mention: you can do searches from your lab bench, or from seminars, with the iPhone version of BioGPS as well. I didn’t have time to cover that in the movie but there’s more information over at their site about the tool. I’ve got mine installed and I’ve found it handy during talks!

Quick links:

BioGPS homepage: http://biogps.gnf.org/ EDIT: has moved: http://biogps.org/

BioGPS iPhone app: http://biogps.gnf.org/iphone/

Reference:
Wu, C., Orozco, C., Boyer, J., Leglise, M., Goodale, J., Batalov, S., Hodge, C., Haase, J., Janes, J., Huss, J., & Su, A. (2009). BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Genome Biology, 10 (11) DOI: 10.1186/gb-2009-10-11-r130