Open
Conversation
not needed just yet
This was referenced Mar 18, 2026
Open
Open
tristan-f-r
changed the title
ntalluri
reviewed
Mar 18, 2026
ntalluri
reviewed
Mar 18, 2026
Collaborator
ntalluri
left a comment
ntalluri
left a comment
There was a problem hiding this comment.
I did a light review of the PR; did not look to hard at the code itself yet. I mostly was gathering ideas on what was happening from the READMEs.
Co-authored-by: Neha Talluri <78840540+ntalluri@users.noreply.github.com>
ntalluri
reviewed
Mar 19, 2026
ntalluri
reviewed
Mar 19, 2026
Open
ntalluri
reviewed
Mar 25, 2026
|
|
||
| The score data (`egfr-prizes.txt`), gold standard nodes `eight-egfr-reference-all.txt`, and the (now-deprecated) manually edited `iRefIndex`-based interactome are all from [_Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data_](https://doi.org/10.1016/j.celrep.2018.08.085). | ||
|
|
||
| We also use the StringDB human interactome and UniProt mapping files. See `cache/directory.py` for more info on these. |
Collaborator
There was a problem hiding this comment.
Suggested change
| We also use the StringDB human interactome and UniProt mapping files. See `cache/directory.py` for more info on these. | |
| We also use the StringDB v12 human interactome and UniProt mapping files. See `cache/directory.py` for more info on these. |
what is the date of the UniProt mapping file (when was it downloaded)? Please add that date to this as well.
Collaborator
There was a problem hiding this comment.
Can you also add that identifiers we are mapping from and mapping to for each of the data.
Collaborator
There was a problem hiding this comment.
That for the iRefIndex/PhosphoSite we use Uniprot IDs for all the data and for String we use ENSP.
| ``` | ||
|
|
||
| `spras` is the cloned submodule of [SPRAS](https://github.com/reed-compbio/spras), | ||
| `configs` is the YAML file used to talk to SPRAS, and `datasets` contains the raw data. `cache` is utility for `datasets` which provides a convenient |
Collaborator
There was a problem hiding this comment.
Suggested change
| `configs` is the YAML file used to talk to SPRAS, and `datasets` contains the raw data. `cache` is utility for `datasets` which provides a convenient | |
| `configs` is the YAML file used to set up workflows in SPRAS, and `datasets` contains the raw and processed data. `cache` is utility for `datasets` which provides a convenient |
ntalluri
reviewed
Mar 25, 2026
Collaborator
There was a problem hiding this comment.
are we doing the trimming in this PR?
Co-authored-by: Neha Talluri <78840540+ntalluri@users.noreply.github.com>
to move to web
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
We bundle EGFR along with the rest of the caching infrastructure. Notes:
cache/README.md.pra.yamlfor now, as the only PRAs are the synthetic data and the ResponseNet data, and soon the DepMap data.CONTRIBUTING.mdfile is not finalized, and is simply there to not break Changes to CONTRIBUTING guide #57. I may split all contributing material into Changes to CONTRIBUTING guide #57 later.directory.pycontains unnecessary files from other datasets that were deemed universal.webfolder even though I'm aware no one is currently in a position to review it.