My name is Ben Busby.
I'm the genomics outreach coordinator for NCBI.
Joining me on the line are Peter Cooper from the NCBI Education Group,
as well as Jeremy from CyVerse, as well as Pat from Mothur.
Today I'm going to tell you about five ways to submit to NCBI's SRA.
This is not an exhaustive list but a list which we are aware of.
If you have another submission platform or offers of this as a service,
we'd love to hear about it.
Please send us an e-mail at webinars@ncbi.
First we'll talk about Basespace.
We'll mention independent consultants.
An example of this, although we certainly don't endorse them is BASE2BIO.
Mothur is a platform for submitting metagenomic analysis
and raw metagenomic data.
then we'll talk about CyVerse, formerly iPlant,
possibly known to many of you as iPlant.
And then finally, we'll talk about the NCBI Direct Submission Portal.
And some updates that we've been doing recently,
some of which have come out today.
So many of you are probably familiar with Basespace.
It's a very large platform, run by Illumina, which is a private company,
and it's trivial to upload data from Illumina sequencing machines to Basespace.
What you may not know is that you can easily import samples to SRA --
or I'm sorry, into Basespace from SRA,
and you can also load samples to NCBI from Basespace using the
SRA Submission App.
Typically, Basespace does not have the metadata required for SRA,
so Basespace provides an input form with submission and sample details,
and then everything is submitted to SRA.
Here's additional information in case you want to talk to Basespace about your
submissions or simply get more information.
As I mentioned earlier, Mothur is a resource with many,
many tools for analyzing 16S time sequences.
It's the most cited tool for analyzing 16S ribosomal RNA gene sequences,
and it's completely open source, operating system independent.
Deposition of 16S is challenging for many users.
That's why many of you are listening to this webinar.
Mothur worked with the SRA staff to make a customized portal.
And so far a lot of data has been submitted.
You can check out all of this on the Mothur Wiki.
All you need to do is provide the necessary MIMARKS,
metadata with the Get MIMARKS package and a PubMed Central,
or an article that's been deposited to PubMed Central about MIMARKS,
there's a link provided here.
You can check out what MIMARKS.
Then, if you give all the necessary metadata to Mothur,
then Mothur will submit that, along with the data to SRA.
Finally, you just need to give it a little bit of information about yourself.
CyVerse, formerly known as iPlant,
is a large NSF-funded mandate to support lots of life science; hence,
why they changed their name from iPlant, in my personal opinion.
And if you have any questions about this,
you can contact Jeremy at this e-mail address.
CyVerse has a discovery environment, which is built on the IRODs platform.
It supports many bioinformatics applications and also has a lot of data.
Via this discovery environment, you can submit to SRA
and Checksums in all that are automatically created by CyVerse.
You can also create or update BioProjects, as well BioSamples.
So here is a pipeline view of the CyVerse-enabled SRA submission,
and there are efficient both command line,
as well as GUI tools for submitting to SRA.
Also, you can put in the BioProject and BioSample
and all the sequencing metadata via templates,
and those templates are simply uploaded from the NCBI templates,
which I'll talk about in a little bit.
Finally, we can use the contact e-mail to transfer ownership over to
your NCBI account.
But the discovery environment will retrieve an error report,
and so you can correct things and resubmit them.
I've been asked to mention that anyone can use CyVerse for free
upon creating an account.
Finally, I'd like to talk a little bit about the NCBI Submission Portal.
This is under continuous development
and if you have comments about the Submission Portal,
please send them to Leila Rassi at this address at NCBI.
I'm going to talk a little bit about BioProject
and a little bit about BioSample,
then I will talk about the new Submission Portal mediated SRA submissions.
The first thing that you would do if you were submitting through NCBI
Submission Portal is to submit a BioProject.
So first we would just need a little bit of personal information to attribute
your submission to,
and also to be able to contact you should we have any questions.
Next, you would give us the name of your organism, or a mix thereof,
and a technical overview of your data generation,
including some specifics about sample prep,
although you'll give other sort of ontology-based submission information in
the SRA part of the submission.
And if this is part of a search project,
your research intent should be stated,
as well as the relevance of your project.
And there are many options.
After submitting a BioProject,
which is sort of like the specific aim for a grant,
a whole bunch of things can go under there, say sequencing data,
biological metadata that's submitted to BioSample,
as well as links to other types of data that you might have the
arise for, for example.
The next thing that you would do when going about one of these submissions --
and you do this with the other submission pipelines we discussed --
is to create a BioSample.
In various ways the other submission platforms have included the
templates that we have for BioSample.
One thing I suggest to all submitters is that if you want to submit to
BioSample, Google for BioSample template,
select the template that's appropriate for you and look at what metadata,
biological metadata, you need to collect before starting your submission.
It's really important to note that, from a user perspective, accurate,
and preferably ontology-mediated metadata, is really crucial for adequate use.
So please submit the most accurate
and complete biological metadata that you can.
After completing a BioProject and a BioSample for each biological entity,
then you would proceed through submission portal to submitting the SRA data.
With the SRA data we need a little bit of technical metadata,
which can be submitted through either a tab delimited file
or an Excel spreadsheet like this one.
Collection of the technical metadata is accomplished in a variety of ways with
the other three platforms that I discussed earlier.
Here we can see the Excel spreadsheet that can be downloaded from
Submission Portal.
And if you mouse over some of the descriptions,
boxes will pop up describing exactly the information that's necessary to
complete the submission.
Finally, if you go to "Submit Data Files," it will bring up a directory
and you can select the appropriate files to submit.
I'd like to thank everybody for listening to this rather short webinar
and thank all these people.
On the line, like I said, I have Pat and Jeremy from Mothur and CyVerse,
respectively, as well as Yuriy Skripchenko from the SRA Submission Group.
We'd be happy to answer any of your questions.
What I'll do now is we'll select some of the questions,
and I will either answer them myself or I will read them to
Pat and/or Jeremy, as appropriate.
It looks like we've answered a bunch of technical questions.
Are there any questions specifically about SRA?
So someone had a question about what types of data are supported on SRA.
So Illumina do account for many of our sequences.
However, we support an enormous amount of next-generation
sequencing platforms, including 454, Pacbio, Ion Torrent,
and many other next-generation sequencing platforms,
pretty much any one you can think of.
And if your sequencing platform isn't supported,
please send us an e-mail at sra@ncbi.
At this point there's a question about CyVerse.
Somebody asked, "Is CyVerse for plant or all types of submission types?"
And I see that Jeremy answered it.
All types of BioSamples are submitted within the CyVerse pipeline now.
Somebody had a question about logins,
and that's something that's under active develop.
We're going to get back to you.
We'll actually post the answers to those questions on our FTP site.
Yes, this PowerPoint will be posted to the NCBI FTP site.
The easiest way to find it is to Google for "NCBI webinars"
and you'll be able to link to it from our webinars page.
There is one more question.
"Do you need to generate a new BioSample for each sample submitted
with the BioProject?
The answer is for each distinct biological entity -- say you're submitting
three type of cell lines for a BioProject -- you would want to generate a
BioSample for each of those.
However, if you have technical replicates within one
particular biological entity, then you would not want to generate a
new BioSample for those.
You do not need to provide an MD5 Checksum for east fastQ.
Checksums need to be generated.
That's in the in the SRA submission documentation.
And as we mentioned, most of the external submission platforms
will generate Checksums for you.
All right, great.
Well thank you everyone for attending,
and I hope everyone has a fantastic week.