Tag Archives: FLink

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: NCBI’s FLink


Today I’d like to introduce you to FLink, which is a tool that NCBI released earlier this year, and we recently came across  during our ‘regularly scheduled’ update to our NCBI BioSystems tutorial. Although FLink was originally designed as a companion tool to BioSystems it has utility beyond linking a list to BioSystems. FLink, short for Frequency weighted Links and based on a German word for nimble,  links items from one NCBI database to those of another in a weighted and meaningful way.

In the tip movie I do an example of inputting a gene ID list through an Entrez keyword search on “schizophrenia”, and then outputting associated BioSystems items as an example of how you could go from a list of genes – maybe from an array analysis or other – and analyzing for associated BioSystems over-represented in the gene list. I did not use any pauses while recording so the speed that you see is the real tool speed. Being able to do the analysis directly from an Entrez search is VERY convenient, but by no means the only approach that you could take. The documentation for FLink – both the ‘ABOUT‘ and ‘HELP‘ pages – are easy to follow & offer clear descriptions of how to use the tool. I’d suggestion you just try running your favorite list through FLink & seeing what you can learn about your list. If you have any trouble or questions that this quick tip doesn’t answer, check out NCBI’s documentation, or (shameless plug) ask your question some Thursday through our WYP? open thread & we’ll try to answer.

Another cool function that I didn’t get to demonstrate in the movie is that FLink has sort of a history function in that the IDs input during one session remain in FLink for a period of time & can be relinked, or linked to a different database. I find it a bit clunky that I have to enter IDs rather than names – if names were acceptable I could have one list of my favorite genes & theoretically input them as either a gene or protein, but with the Entrez search function this is not too much of a problem. In fact, you could do a normal Entrez gene search, click the ‘Send to:’ option on the results page & select ‘File’ and Format=UI list. Then you could upload that file into FLink as your input. I tried that for the term “schizophrenia” and came up with the same 870 gene records that you’ll see in the tip movie. I could also input to FLink from a past Entrez search.

I’m guessing that like most NCBI tools FLink will continue to grow & improve over time. I can’t wait to see what functions are added – for my part I suggest the ability to accept a variety of identifiers, and increasing the number of databases available for FLink analyses. I can see this being a nice way to accomplish a task that we are often asked how to do – namely if dbSNP were added one could theoretically input a list of dbSNP IDs & output a list of gene likely associated with them, though the weighting might need to be adjusted since only gene is likely to link to any individual SNP ID…

Bottom line, check out this cool new resource from NCBI & let them, or us, know what you think about it.