[Bioc-devel] EXTERNAL: SQLForge Question about creating a new species package for Chlamydomonas reinhardtii

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Fri Aug 3 21:05:50 CEST 2018

Is there a reason one of the existing annotations provided in AnnotationHub cannot be used?

> library(AnnotationHub)

> ah = AnnotationHub()
qusnapshotDate(): 2018-08-01

> query(ah, "Chlamydomonas_reinhardtii")
AnnotationHub with 2 records
# snapshotDate(): 2018-08-01
# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Chlamydomonas reinhardtii
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH10477"]]'

  AH10477 | hom.Chlamydomonas_reinhardtii.inp8.sqlite
  AH62519 | org.Chlamydomonas_reinhardtii.eg.sqlite

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 using r-project.org> on behalf of Bijie Ren <b3ren using ucsd.edu>
Sent: Wednesday, August 1, 2018 1:50:10 PM
To: bioc-devel using r-project.org
Subject: EXTERNAL: [Bioc-devel] SQLForge Question about creating a new species package for Chlamydomonas reinhardtii

Dear all,

I wanna create a new annotation package for Chlamydomonas reinhardtii.
However, sequencing data in NCBI for this species is not updated while
there's a updated version of genome information and annotation in
Phytozyome. I'm wondering can I use phytozome ID as an input to create such
annotation package in R for WGCNA? If so will SQLForge use them to compare
with intermediate?

Best Regards,

Bijie Ren

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