dataset: DISEASES #39
Conversation
|
One quick general thing I noticed is that the macOS |
| text_mining.columns = ["geneID", "geneName", "diseaseID", "diseaseName", "zScore", "confidenceScore", "sourceUrl"] | ||
| knowledge.columns = ["geneID", "geneName", "diseaseID", "diseaseName", "sourceDB", "evidenceType", "confidenceScore"] | ||
|
|
||
| # The DISEASES data is in the ENSP namespace, but we want to work in ENSG. |
| # GS_group = GS_ids.groupby('diseaseName') | ||
| # GS_dict = {k:v for k,v in GS_group} | ||
| # GS_count = {x:len(GS_dict[x]) for x in GS_dict.keys()} | ||
| # print('count quantiles: ',stats.quantiles(GS_count.values())) | ||
| # print('score quantiles: ',stats.quantiles(GS_ids['confidenceScore'])) |
There was a problem hiding this comment.
Do we need this for anything? This is a leftover of the jupyter notebook, and we can just leave it in git history instead.
|
Is there any information on how to use the scripts and the data? Something similar to Grace's Cell line ReadMe would be helpful. |
|
There isn't. I don't believe this even has a Snakefile attached, either. I wasn't able to go through the same documentation process as in #42 with this PR, so this is something to ask @AMINOexe for. Also, my above review is stale: while I didn't ask about general code workings, there is a stable |
There was a problem hiding this comment.
Is there a way to have these downloaded locally instead of relying on requesting it from the site directly? (I'm not sure how stable the requesting is / if this is the only way to do this).
There was a problem hiding this comment.
@agitter mentioned this earlier. I forgot to talk to Justin about using OSDF for this, since I'm worried that this repository's clone size is becoming too big.
There was a problem hiding this comment.
I mentioned an idea to @tristan-f-r that we may want to experiment with having a local cache of these datasets somewhere (e.g. Google drive?) while we work on a the full plan of how to use OSDF. That would keep the large files out of GitHub and under our control. Before migrating to OSDF, we'll need to establish 1) what storage to use and 2) how to organize that storage (paths, versioning, etc.).
added DISEASE db benchmarking