[Bioc-devel] AnnotationHub Integration

[Kern, Lori]

Yes it seems appropriate.

Depending on the type of data maybe ExperimentHub would be preferred over AnnotationHub.  It depends on what information you are providing.

We do have multiple types of data provided in the hubs.  Many data are in database type objects like sqlite and such.  This is absolutely appropriate.

Please reach out if you have any further questions.

Cheers,



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Lihe Liu <lihe.liu using wisc.edu>
Sent: Tuesday, October 10, 2023 6:56 PM
To: hubs using bioconductor.org <hubs using bioconductor.org>; maintainer using bioconductor.org <maintainer using bioconductor.org>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Cc: Francisco Penagaricano <fpenagarican using wisc.edu>
Subject: AnnotationHub Integration


Hi Bioconductor team member,



Hope you are doing well! My name is Lihe Liu, and we are a computational biology team from Animal & Dairy Science Department at UW-Madison.



We have great interests in separate logic and data in our R package development by integrating AnnotationHub.



I went over the CreateAHubPackage vignette and I have two questions:

  1.  Our data is not a typical �annotation�, instead, we have multiple related tabular data items of multiple livestock species. Would this fit in the purpose of AnnotationHub?
  2.  On top of above, we very much prefer to organize the data in to a relational database (read-only), ideally with indexes built and support concurrency. Can we upload a portal database or it has to be built on the fly?



Any other guidance/instructions would be highly appreciated!



Thank you in advance!



Best,

Lihe


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