Thank you so much for CMD! It's such a wonderful resource.
I have been searching for metaphlan3 taxonomic profiles for the full HMP1 healthy human subjects cohort (includes shotgun metagenomic sequencing data for phase 1 and phase 2 study subjects). Looking through CMD I see that there is the HMP_2012 data which includes the HMP1-Phase1 subjects but can't seem to find the extended HMP1-Phase 2 subjects reported in Lloyd-Price 2017.
Is this data available under another study name or would anyone be able to guide me to finding the taxonomic profiles for both phases of HMP1's healthy human subjects?
Hi Pauline, thank you for the kind words and apologies for the late reply! We unfortunately haven't added the HMP1 - phase 2 data to cMD, I guess because with the data being in hmpdacc.org instead of SRA there have been other lower-hanging fruit for adding more participants. I've created an issue including a file manifest, metadata, and summary of how many subjects are and aren't in cMD3, at https://github.com/waldronlab/curatedMetagenomicDataCuration/issues/71, but can't say when it'll be ingested. The only thing I can offer in the meantime is that there are thousands of control participants from other studies in cMD3 which we've used effectively in various analyses, although they are stool-focused and don't have the variety of body sites that HMP does.