Hi,
I recently reviewed the PD Microbiome metadata and I am curious if metadata exists for the Control group as well? If so, could you point me in the right direction? The FoxInsight.csv file I accessed seems to feature only participant data.
Thanks,
Brittani
Hi @bmbrown317, you may want to glance at the publication data from Stagaman et al. (2024) located in Fox Den > Resources > Recent Publications > Stagaman Survey data (2024)
This has a linkage between case/control status and IDs. I hope this helps!
Matt
Thanks @bmbrown317 and @mattk ! I was actually planning on posting about this resource tomorrow, so going to instead add onto this thread a bit.
Happy to report that thanks to work from @keatons and @mattk, we’ve been able to make additional metadata, data, and documentation available for the Fox Insight PD Microbiome (PDMB) cohort. This includes the following:
All of these are hosted on Fox DEN, a research tool which investigators can use to explore, download and apply statistical models on aggregated data collected for the Fox Insight online clinical study.
The PD Microbiome resources can specifically be found here in the resources section of the platform (login required): link.
Please feel free to reach out with any questions and @bmbrown317 keep us posted about your work – I’m sure others on here would like to learn more as it progresses!
Thanks so much for the information @mattk
Thanks so much, @jgottesman for the updates. I already retrieved the KEGG Ortho annotations and OTUs. I just needed to obtain additional survey data. Looking forward to sharing my work-- perhaps a publication even–later this year.
Best regards,
Brittani
Hi @mattk @bmbrown317 thank you for your awnser. I checked the resource of the paper from keatons, together with the metadata IDs provided at the Fox Insight PD Microbiome (PDMB) cohort, but I couldn’t locate the information of 32 control IDs. These are the following:
17
23
31
50
55
67
80
92
93
96
105
111
151
154
162
183
188
189
190
212
220
229
233
235
250
257
258
261
270
277
280
287
Any idea of where could I find this information? Thank you!!
Hi Albert,
Thank you for your question. When searching these IDs against Stagaman Survey data (2024) indeed 22 of these IDs have missing values for the survey data and 10 IDs are not present in the survey data. Is this consistent with what you are receiving on your end?
Best,
Matt
Hi Albert and Matt,
I am also missing the exact entries. I presume the data for these controls are just unavailable. However, if we can find the missing data then that’d be amazing. The way I incorporate the demographic data eliminates some samples so I had not noticed until now. Here’s hoping for updated demographic data. Cheers until we geek again.
Best,
Brittani
Hi @bmbrown317 and @Albert ,
Thank you for bringing this to my attention. I’ll look into these missing data and get back to the group.
Best,
Matt
Hi All, upon further inspection of the demographic data, it looks like there’s quite a bit of information mislabeled, missing, and duplicate entries. When I convert the data into a table and filter for PD case, I found numerical values instead of the usual FOX_###### ID used for PD Cases: (this is copy/paste from Excel so forgive the formatting)
FoxDEN_ID parkinsons
001 PD case
001 PD case
009 PD case
009 PD case
019 PD case
019 PD case
027 PD case
027 PD case
032 PD case
032 PD case
039 PD case
039 PD case
046 PD case
046 PD case
051 PD case
051 PD case
054 PD case
054 PD case
076 PD case
076 PD case
081 PD case
081 PD case
082 PD case
082 PD case
083 PD case
083 PD case
095 PD case
095 PD case
098 PD case
098 PD case
102 PD case
102 PD case
116 PD case
116 PD case
120 PD case
120 PD case
131 PD case
131 PD case
132 PD case
132 PD case
135 PD case
135 PD case
145 PD case
145 PD case
167 PD case
167 PD case
170 PD case
170 PD case
171 PD case
171 PD case
179 PD case
179 PD case
198 PD case
198 PD case
199 PD case
199 PD case
203 PD case
203 PD case
208 PD case
208 PD case
215 PD case
215 PD case
216 PD case
216 PD case
217 PD case
217 PD case
223 PD case
223 PD case
225 PD case
225 PD case
231 PD case
231 PD case
251 PD case
251 PD case
252 PD case
252 PD case
253 PD case
253 PD case
259 PD case
259 PD case
260 PD case
260 PD case
264 PD case
264 PD case
276 PD case
276 PD case
279 PD case
279 PD case
282 PD case
282 PD case
285 PD case
285 PD case
289 PD case
289 PD case
295 PD case
295 PD case
I have not checked to determine if any of the FOX_###### IDs are missing, but the likelyhood is high.
When I filter for Controls, several entries are missing (some overlap with the unusual PD Case labels–perhaps they were misclassified as PD and should be Controls?):
001
009
017
019
023
027
031
032
039
046
050
051
054
055
067
076
080
081
082
083
092
093
094
095
096
098
102
105
111
116
120
131
132
135
145
151
154
162
167
170
171
179
183
188
189
190
198
199
203
208
212
215
216
217
220
222
223
225
229
231
235
250
251
252
253
257
258
259
260
261
264
270
276
277
279
280
282
285
287
289
295
Duplicative entries within the controls (I can’t attach the image because apparently I’m still classified as a new user?)
And some PD Cases with no identifier at all:
I think this survey data definitely needs to be audited. There’s the possibility than some entries are mislabeled and some entries are missing entirely.
Looking forward to a resolution.
Thanks,
Brittani
Thank you for the note @bmbrown317. I’m currently auditing the data and will get back to you on this. I do know that when Keaton analyzed the data, he noted that several participants that were labeled as “controls” when downloading the microbiome data were indeed PD cases according to the surveys. I am not sure whether this information has been updated yet in Fox DEN (when downloading the microbiome data), but I’ll confirm this during my audit.
If any other issues come up, please don’t hesitate to post.
Best,
Matt
Hi Matt,
Any update on this issue? Looking forward to hearing from you.
Thanks!
Hi @bmbrown317 , thank you for your patience on this. I’m just returning from the MDS conference and am catching up on messages.
I’ve been making progress on diagnosing some of the discrepancies and will write a report I can share with the community soon. If this is blocking your progress, please feel free to message me to set up a call and I can share my findings so far prior to a more shareable document.
Best,
Matt
Hi Matthew,
Yes, the demographic data is a crucial component to my research. When do you believe you’ll be able to share the full report?
Thanks,
Brittani
Hi @bmbrown317, I’m aiming to finalize the report in about two weeks. I appreciate your patience on this one!
Thanks,
Matt
Hi Matthew,
I hope you’re doing well. Have you finalized the report? If so, could you provide me with a direct link to the updated metadata? I have a committee meeting in December and I’d like to be able to present the data with demographics. Looking forward to hearing from you.
Thanks,
Brittani
Hi Brittani,
Thanks for checking in! The report is coming along nicely and I will post an update as soon as I’m able.
Best regards,
Matt
Hi Matthew,
I just wanted to kindly check in to see if there’s any update on the audit regarding the missing demographic data and the control/PD labeling issue. If the report is ready or if you have any preliminary findings, it would be great to share them with the group so we can move forward.
Thank you so much for your efforts on this!
Thanks,
Albert
Hi Albert,
Thank you for checking in. My report is complete and currently in the final approval process. I’m monitoring progress closely and will share an update with you and the community as soon as it’s cleared for posting.
Best,
Matt
