Good morning.
My name is Ben Busby, and I'm the Genomics Outreach Coordinator for NCBI.
Thank you for coming to our short, informal webinar series, The NCBI Minute.
Our NCBI Minute installment this week is going to be on BioProject, a fast way to get genomic data from NCBI.
A video recording of this webinar will be available on our YouTube channel very soon,
and please remember to subscribe to our YouTube channel.
Also, all of the questions that you guys ask will be available in this document after the webinar.
I'd like to tell you, in three minutes or less, how to get the genomic data you want from an NCBI.
If you were to search for a term like "mouse" or "tuberculosis" in the traditional Entrez search,
you would get somewhere on the order of eight million hits for mouse, anyway.
The advantage of using the BioProject database is that there is a faceted search bar on the left.
For example, if I wanted RNA-seq data, I could facet by Transcriptome and SRA.
SRA is the Sequence Read Archive where we keep our next generation sequencing data.
And then that would specifically give me RNA-seq datasets for mouse.
Similarly, if I wanted epigenomics data, I could facet by Epigenomics.
If I click on one example of this -- I believe it's the fourth or fifth link down -- I get one particular project.
So here, I get an umbrella project of 224 SRA experiments linked to a PubMed abstract and also GEO DataSets,
which are pre-analyzed data analyzed by the investigators that submitted this data.
Some of the features of this are being able to look at the abstract that they've submitted to BioProject.
Now, what you'll notice is this is a much more data-centered abstract than the corresponding PubMed abstract,
which really talks about the entire study and the paper that they have published.
If we go back to BioProject, we can also click on the link for SRA experiments.
Note that this is an active link.
We can go there; and then once we get to SRA,
we can send those to something called the Run Selector from the Send To button.
And then we're able to filter farther via this SOLAR-based filtering here on the left.
For example, if I wanted to filter by assembly name, I could select Assembly Name here and select GRCh37.
Also, if I go to the SRA data and go to the Send To button, I can select some of these studies
and send them to my standard BLAST interface.
In that way, I can BLAST any particular gene or nucleotide sequence that I'm interested in into these SRA runs.
And, as we can see here, I get a standard BLAST output.
Soon, we will also have this output available in SAM format.
Finally, I'd like to talk about reporting.
As many of you know, the NIH genomic data sharing standards will be in effect as of September 2015.
PIs will have to document sharing of data with public repositories, such as NCBI.
BioProject accession numbers make it very easy for PIs to document their genomic data sharing projects
in the NIH grant project review system.
Once again, thank you very much for attending our NCBI Minute.
My name is Ben Busby.
Please subscribe to our YouTube channel. And have a great day.