HI,
I can?t find the clinical data for ROSMAP proteomic data. The IDs are from the ROSMAP clinical coding. Is there a separate clinical file for the proteomic data or a ID mapping file?
Also for BLSA and Banner clinical data, where can we find the coding book for that? We need to determine the exact meaning for the numbers coded for these two datasets.
Thanks a lot for the help!
Jie
Created by Jie Zhang jiezhang For sex, BLSA defines female as 0 and male as 1, and Banner defines female as 2 and male as 1. Outside of the -1 values, the CERAD values look normal; I am not sure what the -1 stands for. I am not sure about the APOE genotypes for either of them. Until we update these studies to the new formats with the standardized dictionary terms, the best way to figure out these terms would be to contact [Duc Duong](https://www.synapse.org/#!Profile:3320325), who uploaded this data. Thanks a lot, Nicole. That solves the ROSMAP ID mapping issue. I had an old version of the ROSMAP clinical.csv which misses the individual ID column, and your link led me to the new file. Thanks!
As for BLSA and Banner study, my question is that their clinical info coding are not clear, for example, in BLSA (syn3606086) clinical data, ApoE status is -1,1,0,2, not clear which is corresponding to which genotype, so are CERAD scores. For Banner study (syn22024835), the gender coding is 1 and 2, not sure which is male, which is female, and what does CERAD score -1 mean?
Thank you again for the help! To get the full ROSMAP proteomics metadata would require joining the [clinical metadata file](https://www.synapse.org/#!Synapse:syn3191087) to the [biospecimen metadata file](https://www.synapse.org/#!Synapse:syn21323366) (by _individualID_) and the [proteomics assay metadata file](https://www.synapse.org/#!Synapse:syn21323404) (by _specimenID_).
BLSA and Banner have not been updated to have separate metadata files for the biospecimens and individuals. Instead, they have a proteomics_pfc_traits file. These have [SanpleName](https://www.synapse.org/#!Synapse:syn7417639) [sic] and [Sample](https://www.synapse.org/#!Synapse:syn9740295) as the identifiers. The raw data has the identifiers in the name of the file. HI, HI,
Thank you very much for the help. I can only find the meta data for ROSMAP general projects, but not for the proteomics data, in which IDs (in both TMT and SRM data) are different from the general ROSMAP clinical data. They are neither Individual IDs, nor project IDs, they are sample IDs in a different naming format. And I can't find any matching info between those IDs in the ROSMAP clinical.csv.
As for the coding book, that only exists for ROSMAP data, but not for BLSA (syn3606086) and Banner study (syn22024835). These two studies' column coding of the clinical data is different from ROSMAP.
If possible, please help me locate the relevant resources , many thanks!
Jie
Thank you very much for the help. I can only find the meta data for ROSMAP general projects, but not for the proteomics data, in which IDs (in both TMT and SRM data) are different from the general ROSMAP clinical data. They are neither Individual IDs, nor project IDs, they are sample IDs in a different naming format. And I can't find any matching info between those IDs in the ROSMAP clinical.csv.
As for the coding book, that only exists for ROSMAP data, but not for BLSA (syn3606086) and Banner study (syn22024835). These two studies' column coding of the clinical data is different from ROSMAP.
Please help me locate the relevant resources , many thanks!
Jie This information should be found within the metadata files of each study. For example, the ROSMAP Clinical Codebook metadata file has a mapping of individualID to projid. There is also a dictionary file for definitions of columns in the ROSMAP codebook.
Metadata for each study can be found in the AD Knowledge Portal study pages. There is a table called Metadata Files.
[ROSMAP Study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn3219045)
[BLSA Study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn3606086)
[Banner Study](https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn7170616)
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