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Access to Public Data with no Cytobank

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CRStevens

Contributor

Posts: 28

Joined: Thu Jul 17, 2014 5:07 pm

Post Wed Jan 20, 2021 10:16 pm

Access to Public Data with no Cytobank

Hi all,

I was wondering if anyone could help me out. We decided to opt out of using Cytobank, but have had a request for the below public dataset:

Raw mass cytometry data from: Mitsialis et. al. Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease. Gastroenterology. 2020

I have a collaborator that would be interested in playing with that data and didn't know if anyone on here would have a way to share it somehow that doesn't include Cytobank?
Thanks for any help anyone can give with this.
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sgranjeaud

Master

Posts: 94

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Thu Jan 21, 2021 9:13 am

Re: Access to Public Data with no Cytobank

Hi,

That's a good question, in the sense that I am interested in data access and I don't have the answer.

I tried to figure out from a naive point of view how to access the data. I thought there were available through the community portal, but there are not there. There are available exclusively on the premium portal, that requires a license or a free trial.

At the end of the portals information page, it is clearly stated that those 3 portals (Community, Premium, and Enterprise) are hosted on separate clouds. To be noticed, the community portal is still holding data but is no more present from the product comparison sheet of Cytobank nor as an option when login. The [url=support.cytobank.org/hc/en-us/articles/205271138]procedure to share data across different portals[/url] offers solutions for exporting the experiment as a ACS file or to licensed user. No real solution for an open access IMHO.

Interestingly, Cytobank has a clear procedure for referring deposited data, but I am not sure whether recent articles release their data in that way. There are only 6 users that released experiments on the community portal in 2020. This is very questionable in respect to data retention. If I understand correctly, data deposited using an Enterprise account will be accessible forever. But data deposited as Premium account will be deleted 90 days:
However, if you are registered on Premium Cytobank, your data will be deleted 90 days after your subscription ends. You will receive multiple warning emails, reminding you to renew your subscription if you desire to keep your data and/or continue analysis on Cytobank.

I don't feel this as a good news. BUT, hopefully:
Any data that are public either on Community or Premium Cytobank will be protected and not deleted regardless of the account status. This is a great way to protect publication-associated datasets while sharing them with the scientific community.

I hope Cytobank's users know how to set their data public.

I didn't get more information from this journey in Cytobank's pages, but it helped to have a clearer view.

I ended up with asking directly to the support:
Dear support,
My question is about the free access (no login) to data deposited in Cytobank by researchers that use Cytobank as repository for shared science
The question is related to
viewtopic.php?f=1&t=2280
Those data are on the Premium portal. Is it possible to move those data to a portal to ensure open access? Is the community portal dedicated for such a goal?
Best regards,
Samuel


I will update when I get an answer.
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Thu Jan 21, 2021 1:23 pm

Re: Access to Public Data with no Cytobank

This is not a new situation. "Publicly available" Cytobank experiments have not be truly publicly available in a while.
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CRStevens

Contributor

Posts: 28

Joined: Thu Jul 17, 2014 5:07 pm

Post Thu Jan 21, 2021 3:46 pm

Re: Access to Public Data with no Cytobank

Through some of my own digging if I get on the "community" portal there is data in there, but it is data from people who are just placing data in there in public view, but are not necessarily linked to a paper or the such.

I had a premium subscription and forgot about it, so was able to log in to my premium account and there you see all these huge "public" datasets from publications that people are looking for. So I can see how if you wanted to put a dataset up in the community server and share it with people it would be useful and a truly "open" data forum, but it looks like many researchers are putting their published data in the premium server (I'm guessing this is probably Cytobank wanting this).

Thanks for the help!

-Chad
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mleipold

Guru

Posts: 2640

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Jan 21, 2021 3:58 pm

Re: Access to Public Data with no Cytobank

Hi all,

In my experience, both Community and Premium require an account to be created (you can use many of the same login credentials, but the accounts are formally separate).

And at least in my hands, both Community and Premium datasets are accessible with no charge, but both require logins to access the datasets. I'm not paying anything to Cytobank, but once I log into each account, I can access the datasets.


For example: following this link https://community.cytobank.org/cytobank ... ents/44185 requires me to log in to Community.


While yes, I would prefer not having to create an account in order to access a dataset that's publicly available, Cytobank isn't the only one that requires that. For example, in my experience, Immport allows you to search a dataset, but in order to *download* the files, you have to log in.


Mike
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Thu Jan 21, 2021 4:02 pm

Re: Access to Public Data with no Cytobank

Mike, naive question, how are you logging to premium Cytobank without a paid account? I cannot go on that server with my community credentials. It requires a separate, paid license.
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mleipold

Guru

Posts: 2640

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Jan 21, 2021 4:12 pm

Re: Access to Public Data with no Cytobank

Hi El-ad,

In my case, maybe my institution (Stanford) has an institutional license that covers me somehow? Regardless, Premium and Community require separate account creation: my username is the same, but I have to access Premium through "premium.cytobank.org" and Community through "community.cytobank.org".


Another possibility: the 30-day "free" license for Premium allows you to create a Premium account, but after 30 days, you lose the ability to create or alter experiments if you don't pay. However, your account is still active, so you can download files.

For example: I have a Premium account, but do not have a subscription (see attached screenshot). However, once I logged in, I was able to search for CyTOF, and download some files from "Fisher 2019 Leukemia signaling CyTOF on MF15 and normal BM control used in Fig 6d".


Mike
Attachments
Screen Shot 2021-01-21 at 8.05.23 AM.png
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DanielFisher

Participant

Posts: 1

Joined: Tue Mar 05, 2019 9:28 pm

Post Thu Jan 21, 2021 4:52 pm

Re: Access to Public Data with no Cytobank

Hi,

I'm Fisher from Fisher et al., 2019 Leukemia. I'm happy to hear someone's downloading our data. When we made the data public on Cytobank, I thought it would be accessible through the Community server. Is that not correct? Is it only accessible through Premium? If so, that's very problematic. Recently a colleague asked me if I recommended their data soon to be published to be made public on Cytobank or Flow Repository, and I said Flow Repository would be better because not everyone has Cytobank. We have an institutional Wustl Cytobank server, but every time it comes up for yearly renewal, I hear about how expensive each account is. I worry that Cytobank might be pricing themselves out of being a common data source, despite being (in my view) a great analysis platform for multi-dimensional CyTOF data. Please inform me what is the current status of accessibility of our data, so I know what to do for future published datasets -- and so I know whether I need to put the data in Flow Repository as well. Thanks!
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sgranjeaud

Master

Posts: 94

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Thu Jan 21, 2021 7:17 pm

Re: Access to Public Data with no Cytobank

I thank the support of Cytobank, and I publish here the answer. I don't reveal anything new after the previous messages.

Users can make experiments public in any of the Cytobank server sites. Like that, data will be not deleted. To access public experiment, an account is needed (in both the community and premium servers). It is possible to create free accounts in both servers that could be use for that purpose.

Regarding your second question, "is it possible to move data between servers?" The answer is yes. However, only the owner of the data could do it. If you would like to transfer your experiment from one server to another one, go into the desire experiment, click on the Actions menu, then Export and Export experiment to ACS... This will generate an ACS file that can be uploaded on the second server. Here you have more information on how to export experiments: https://support.cytobank.org/hc/en-us/a ... n-ACS-file


@El-ad maybe have you been blacklisted :lol:
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sgranjeaud

Master

Posts: 94

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Fri Jan 22, 2021 6:31 pm

Re: Access to Public Data with no Cytobank

Dear Daniel,
Your data are available on community.cytobank.org.
One just has to search for Fisher in order to locate all your submissions.
IMHO flowrepository is a better option as a repository only.
Best.

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