Annotation, Sharing, and Publishing

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En provenance du cours de Johns Hopkins University

Genomic Data Science with Galaxy

430 notes

Johns Hopkins University

Genomic Data Science with Galaxy

430 notes

Cours 2 sur 8 dans Specialization Genomic Data Science

Learn to use the tools that are available from the Galaxy Project. This is the second course in the Genomic Big Data Science Specialization.

À partir de la leçon

Galaxy 101

In this module and the following modules we will start to use Galaxy to perform different types of analysis.

Galaxy 101: Genomic Intervals16:08

Galaxy 101: Workflows12:29

Annotation, Sharing, and Publishing13:45

Rencontrer les enseignants

James Taylor, PhD
Associate Professor of Biology and Computer Science

In this lecture we're going to talk about some of Galaxy's features for

annotating your data, sharing with other, others, and

publishing it with the community.

First I want to talk about tagging annotation.

Tagging annotation gives you a way that you can add extra information to

an entities in Galaxy, so data sets, histories, workflows, other entities

in Galaxy that we haven't talked about yet, can all be tagged and annotated.

Tags are short pieces of structured metadata that you apply to an object.

While an annotation is more of a free form description that you

can use to say anything you want about that particular object.

So if we go again, back to our web browser and

if you haven't already log in and pull up the history that we

used in the last lecture, which I had called Exons and CpG Islands.

We, see we have, all our data sets here.

And above the data sets, there's a few icons that we haven't talked about yet.

So, there's this icon that looks like a set of tags, and

this icon that looks like a speech bubble.

The tag icon will allow us to actually add text to our history.

So, I can say Exons, I can say CpG.

And so, now these are tags that are stored with my history.

I can also click on this edit annotation.

This just gives me a free form text box and

I can say whatever I want about this history.

This is a history where I scored exons for overlap.

With CpG islands.

All right.

So, this basically gives you a way that you can store any information you want,

both for yourself about this history and information that will be available to

others if you share this history with them.

We can do exactly the same thing for data sets.

So, e, each individual data set you'll see it has a similar tag and annotation icon.

And so, I can, for example, annotate this data set.

And say, Exons joined

against CpG Islands.

So now I, I've saved an annotation for

an individual data set, I've saved annotation for the entire history.

One reason tags are useful, so if you see the Saved Histories list here,

next to each history I have whether it has tags and in this case it says two tags,

and I can click to see them.

And these tags can actually be used in searching.

So, search for exons and

it's going to search based on both the history name and that tag.

I can also just click on a tag directly, and so now I've got a search that's

just for history that have been tagged with the tag Exons.

So this is a very, very useful way to organize your data and Galaxy and

to be able to easily find history as you start to have a large number of them.

Click analyze data again, that will take us back to the home interface.

So that's tagging annotation, now I want to talk a little bit about sharing and

publishing.

So these are, two different concepts in Galaxy.

So when we talk about sharing.

We're usually referring to making a entity like a data set or history, or

a workflow available to particular users.

Where when we publish something, it becomes available to everyone.

And it's actually listed in, the published Section.

And so, for histories, again I'm going to go to the cog, which is history options.

And you'll see share or publish.

And so, I have a couple of options here.

The first is I can share with a specific user.

I click there, I'm actually asked to put in an email address

of a user who I want to share this.

So I can put in there their email address.

And if they're a Galaxy user, they have an account under that email address.

Then they will not be able to access this particular history.

I can also make a history accessible via link.

So if I say make accessible via link, now immediately Galaxy has given me this link.

Link.

Now, earlier I talked about your public name, this is why you want to set one,

because you're going to have a URL to your history which is /u/your

public name/ h and then the name that you gave your history.

You can of course edit this, particularly if you have not given your history

a useful name you can edit the URL.

And now I can take this link.

And I can give this to anyone, I can share it by an e-mail, I can post it on

an another website, and anyone who has the link can get access to the history.

However, it's not published until I actually say, Publish History.

So right now, this history will not be in the published history's list.

If I click Publish History now it's going to be available.

So, to see all the published histories, you can go up to Shared Data here.

And, toward the bottom here, we have Published Histories,

Published Workflows, Published Visualizations and Published Pages.

And so, if I click on Published Histories, I'm going to get a list of

all of the histories that Galaxy users have chosen to publish.

And you'll see why is was useful that I provide the annotation.

The annotation is, is shown here in this list.

It tells you who the owner is.

It tells you the tags associated with that history.

But you can see there's many other histories that

various users in Galaxy have shared.

We can do things like sort them by ratings, so

you can actually rate the quality of shared objects and so.

We can see some

of the more popular histories that have been shared through Galaxy in this way.

So I'm going to go ahead since this history is actually just a demo.

I'm going to go ahead and unshare it and

I would suggest you do the same if you're following along.

So we're just going to say Unpublish History.

And Disable Access to History Link.

You can do this at anytime.

If you have something that you shared in Galaxy and

you no longer want it to be accessible.

So in addition to sharing and publishing, we have

another way that we can try and communicate analysis through Galaxy.

And this is called the Galaxy Page.

Galaxy Page is actually a text document

describing complex analysis where we can embed Galaxy objects,

like data sets, workflows, and histories, right in the page.

So pages, in particular, are another way in which Galaxy is

trying to push forward both reproducibility and transparency analysis.

Because in a galaxy page, a user can read about analysis but then they can also,

they're directly connected to the the specific details of that analysis.

They can drill down and actually see all of the parameters associated with each

step of every part of analysis that's included in that page.

We find this particularly useful for

things like supplemental data so here's a paper of ours where we've provided, a,

link to a Galaxy page and on that Galaxy page you can actually see

all of the, histories that are described, that are associated with the publication.

You can see the work flows that were used.

So let's go ahead and create our own Galaxy page.

So, back from the analyzed data interface

where your create pages is actually under user.

And so, here, this is, the things that are associated with your Galaxy

account are often under the user tab.

And so, here, we, this is another way to get to saved histories.

You can also get to all of your data sets.

And we can get to save pages.

You click on save pages, you'll see a number of different

pages in my case, but you probably won't have any yet.

We can click Add New Page.

We'll give it a title, which is going to be Demonstration Page, and

then we can Edit the content of the page by clicking Edit content.

And now we're taken into a, web based editor.

And so, I can just go ahead and start typing and

so I'm going to say, this is a page for

course in progress and we can say for

example that this a heading, right.

So this is a formatted, formatted, editor.

We can paste things in from other word processors.

Serious people like Google Docs or like Microsoft Word.

But the interesting thing here is that i can embed objects, and so I can say for

example here is the first demo history, exons and repeats.

And I'm just going to make my life easier.

I'm going to copy, here is demo workflow.

And second

demo history.

And I can go ahead and use this insert, or embed Galaxy object,

to actually inline the history that I've described.

So I can say embed Galaxy object.

I select Exons repeats, click Embed.

Now, in the editor I'm not going to see it,

I'm just going to see this placeholder.

I can go ahead and also embed the workflow.

Click Embed.

And the same thing for our Second history.

We also have the option here of just inserting links rather than embedding.

That will allow the user to click on the link and see

the the Galaxy entity in question.

So if I go ahead and say Save, and Close, now I can view this page.

And in the, and, and, so now, when reviewing a page,

we can actually see the embedded objects directly.

Over here, there's information about the page, it tells you, again,

the author is James, that's my public name, you can see all published pages or

pages just published by me.

But the important thing over here, is in the page, we have our histories,

we have our workflows, and we can click to expand, and

actually see all of the steps of the history directly inside the page.

And, I believe for the second one, I actually included annotations, and so now,

your annotations are also available here.

Right? So this is

how you can actually communicate, why you did this step.

What this step of your analysis actually means, by, by modifying this annotation.

And I can look at the actual data set, itself.

Similarly for a workflow.

If I click here, I see the steps of the workflow and

if I had associated annotation with them, I would see the annotation.

So again you can describe exactly why you've done each step of this workflow.

And then over to the right here, we have a couple of very important links.

We have the view history, view workflow, or go-to workflow links, but also import.

So, suppose I want to actually rerun some steps of this.

I'm a, I'm a viewer now of Galaxy.

You've published this page and you're making it available to me.

I can click import.

And now I have an exact copy of the history you used in your analysis and

described in your page and

I can go ahead and use the rerun button we've talked about previously to

actually see the exact parameters that were used in your analysis.

I can import your workflows and rerun them.

And so this allows you to describe your analysis, communicate it with context, and

allows the reader to actually see every detail and to pull out your analysis

workflows and reuse them.

Finally, I just want to mention two other ways that data shared in Galaxy.

One, is data libraries.

So under, up here under shared data is data libraries.

This is a slightly different way of sharing data.

And so the data library is basically a public or

potentially access controlled group of data.

Hierarchically organized and so for example, here is data set from

this [INAUDIBLE] paper that was published in Nature in 2010 and

all of the data associated with it is available through Data Library.

And then finally, the Galaxy Tool Shed which actually allows

sharing of tools and data types and we'll talk about that more in a later lecture.

So in summary, everything you do in Galaxy can be shared and published for

others to access.

Tagging and annotations allow you to provide more information about the steps

of your analysis.

Workflow and actually put it in context.

And Galaxy pages give you a way to describe multiple entities that make

up an entire analysis in a way that readers can easily access all the details.

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