I really appreciate the work done by the CMD team. We are a research team in cancer vaccine and we are interested in associations of gut microbiome and cancer and/or autoimmune diseases. We really want to use CMD for our research project and want to get some suggestions since we are not savvy in programming, but we would love to ask questions and learn from scratch.

1) We wonder if you could consider adding Zhang et al 2015 Nature Medicine study on RA (https://www.nature.com/articles/nm.3914) for inclusion in the next release? Metagenomic sequencing data for all samples have been deposited in the European Bioinformatic Institute (EBI) database under accession code PRJEB6997 (https://www.ebi.ac.uk/ena/browser/view/PRJEB6997)

2) I noticed the studies listed (https://waldronlab.io/curatedMetagenomicData/articles/available-studies.html) do not include all the recent curated studies as listed in https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/master/inst/curated. I would guess this list CMD curation has is more of a beta version that more checking process are underway, while the CMD studies are more reliable and being used more. I accessed the studies and dataset using R package installed per https://waldronlab.io/curatedMetagenomicData/index.html. Therefore, I did not see those most recent curated studies. Could you advise how could I access the most recent database?

Thanks for your time!

Hello, glad to hear you like curatedMetagenomicData!

1) We would be happy to look into adding this study – I have added a GitHub issue here. If you want to help speed up the process, please read the curation documentation and submit a metadata file to us; otherwise, this may take some time.

2) The curatedMetagenomicData package itself will always lag behind the curation efforts – we curate first and then process and add the studies to the package for Bioconductor releases (April/October). The curatedMetagenomicData package, as it in Bioconductor, contains all the most recent data.

Cheers, Lucas