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KechrisLab / multiMiR

Development repository for the multiMiR database's R API
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database update status #31

Closed DanielMedic closed 4 years ago

DanielMedic commented 5 years ago

Here's the current status of all databases, from the listing at http://multimir.ucdenver.edu. Most of them need updating, obviously. Once I'm added to the project as a contributor, I'll self-assign this issue, and get access from @kechrisk or @smahaffey to update the databases on the server.

Databases that appear to be up to date:

Databases that need updating:

Databases with uncertain status:

Databases with broken links:

The first two categories are easy enough to deal with. The third ("uncertain status") may take some more work. And I'm honestly not sure what to say about the fourth ("broken links"). Do we want to leave them as they are? If so, should we warn the user, and maybe provide an option not to use anything that isn't known to be up to date? Something to discuss.

umitozorhan commented 5 years ago

Dear Daniel,

Thank you for informing us about the issue. As far as I know, Diana microT CDS 5 now located in "diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index". For reaching miRecords, I found this website "http://c1.accurascience.com/miRecords/" however this looks like a v4.0 also they give some information about that page in this link "https://www.lcsciences.com/discovery/mirecords-a-new-integrated-resource-for-microrna-target-interactions/".

Thus implementing miRbase v22.1 could be a good idea. But I do not know, it could be possible or not. (For example, an unknown miRNA written in the search, the system could simply say this miRNA does not exist yet. miRbase v22.1 "http://www.mirbase.org"

Thusi it is worth noting to implement new databases to improve coverage such as TarPmiR "http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/", SM2miR "http://210.46.85.180:8080/sm2mir/index.jsp", PhenomiR 2.0 "http://mips.helmholtz-muenchen.de/phenomir/", EpimiR "http://www.jianglab.cn/EpimiR/", TSmiR "http://lcbb.swjtu.edu.cn/TSmiR/", Imota "https://ccb-web.cs.uni-saarland.de/imota/sources/", Exocarta for exosomal miRNA "http://exocarta.org/". Also, HMDD v3.0 "http://www.cuilab.cn/hmdd", miR2disease(i don't know if it still exists), starbase v3.0 "http://starbase.sysu.edu.cn", Exo-miRExplorer (Only chinese access might be talking with database owners could be useful) could be good for increasing the coverage further.

Kind Regards,

Ümit Özorhan

DanielMedic commented 5 years ago

Okay, thanks. Including the new databases sounds like a good idea, although I'd like to concentrate on getting everything we currently have as up to date as possible. But after that, yes, I think we should try adding them one at a time, with thorough testing on each.

DanielMedic commented 4 years ago

Tarbase has actually been updated to version 8, but that requires agreement with their license terms http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Fdownloaddataform. Our current version is v.6, and v.7 is available for download without agreeing to the terms. Do we want to go to v.8, or just stick with v.7? We can't really guarantee that people will only use multiMiR "for scientific non-profit and non-commercial use only." For now I'm going to use v.7 and we can think about going to v.8 later.

smahaffey commented 4 years ago

Tarbase is the one we tried repeatedly to contact them about a license and we couldn't ever get a response. I think for now v7 works. It's the version we kept contacting them to use.

On Jul 6, 2019 12:53 PM, DanielMedic notifications@github.com wrote:

Tarbase has actually been updated to version 8, but that requires agreement with their license terms http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Fdownloaddataform. Our current version is v.6, and v.7 is available for download without agreeing to the terms. Do we want to go to v.8, or just stick with v.7? We can't really guarantee that people will only use multiMiR "for scientific non-profit and non-commercial use only." For now I'm going to use v.7 and we can think about going to v.8 later.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/KechrisLab/multiMiR/issues/31?email_source=notifications&email_token=AAR5LBCXAJ535W3YU5GWGJDP6DS3TA5CNFSM4HH5NX52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZK6TEA#issuecomment-508946832, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AAR5LBCDHAW3SO5TMZYJPALP6DS3TANCNFSM4HH5NX5Q.

DanielMedic commented 4 years ago

Okay, sounds reasonable. I'll stick with version 7.

smahaffey commented 4 years ago

v2.3 is ready. I'm going to close this issue, but ongoing updates are needed we should try to release 1-2 times/year including any database updates possible and as much additional ID cleanup as possible.