[Bioc-devel] AnnotationHub (2)

[Shepherd, Lori]

It is still a work in progress.  For now the old-style is still active and encouraged to use.  We would recommend making an Annotation Package that utilizes AnnotaitonHub


https://bioconductor.org/packages/release/bioc/vignettes/AnnotationHub/inst/doc/CreateAnAnnotationPackage.html


We will keep in mind the request to add annotation specific metadata as we continue to develop the next generation hub.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Sent: Tuesday, March 27, 2018 5:16:34 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] AnnotationHub (2)

What is the current state for AnnotationHub (2)? I have recently figured
out (read: pestered the people who knows the arcane incantations for this
resource; I have been taught the sacred rituals) the interface to the
encode data portal and we should make an AnnotationHub interface to this.
But should this be old-style or new?

Also, this has uncovered a table of structured metadata for the resource,
essentially a spreadsheet with organized columns.  It seems very relevant
for users to get access to the data in this spreadsheet, which would
essentially be a resource dependent data.frame. I don't think this is
supported by the classic AnnotationHub, but I very much think this should
be supported in the future.  One could also envision resource and
dataset-dependent information such as the phenotypes in GEO for a fixed
experiment.

Best,
Kasper

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