I am Francesca Di Cara and pretty new to this community and also to PD research. Since I became a member of the MJFF consortium it has been a very great leraning journey for me and the data shared with the community have been extremely helpful to reinforce our research findings.
I am investigating neuropeptides from the GI as PPMI and I have been browsing the results of all the omics this community has deposited.
As I navigate them and gather information, I was wondering where I could find a single document with all the combined information on the patients recruited in the PPMI? I was going over the proteomics of the plasma done with OLINK, and I found very interesting data relative to my study of intestinal neuropeptide as an early marker of PD, I had to gather many basic informations about the plasma id (e.g. patient or control), sex, other pathology, and age of the individuals from various files. Did I miss one combined file?
And ultimately, if I wanted to follow up to gather information on what happened to some podromal patients? Also, some control had symptoms that could develop into a disease. Where can I gather this information?
My apologies if this question is redundant or naive .
Hi Francesca, welcome! You should be able to see all this information scattered across LONI, just like I’m guessing you found the OLINK data.
For me the easiest way after selecting “Study Data” is to click on “ALL” such that I can just scroll over everything and see what information I’m looking for, though unfortunately sometimes I need to download first to confirm.
One resource you might find useful is the “Curated data cut”, where key information is simplified in a single file, though be aware that obviously it doesn’t contain all information, and sometimes some visits might not be there for the sake of having everything in the same file.
Finally, the symptoms information you are looking for is likely the “Primary Research Diagnosis”, and the main column you want to look for is “PRIMDIAG”. To know what each number is, you just need to get the “Code List - (Annotated)” CSV, and search for “PRIMDIAG” in there.
I second the “curated data cut” as being a good place to start if you’re looking for a combined document. I’d also like to point out that since you’re interested in the prodromal set that there are multiple definitions of prodromal (genetics, hyposmia, RBD, etc.). Not sure which you might be interested in.
For tracking diagnosis over time, I’m going to link to what @jgottesman summarized in another thread - likely you’ll want to track cohort (initial enrollment), primdiag Primary Research Diagnosis, and newclindx Clinical Diagnosis.
For more in depth research, we also have a GitHub repo called PIE-clean that cleans and combines data across modalities, with PIE for more of a machine learning approach to looking at patterns in the data. Lots of work by @cameronreidhamilton and @vcatterson on those two repos if you have any questions.
Thanks, @tiago.azevedo and @ehutchins! @dicara, please let us know if other questions come up and if not we’d love to hear more about your work as it progresses .
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