dataset: synthetic from PANTHER#71
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ntalluri
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Mar 19, 2026
ntalluri
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Mar 26, 2026
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Can you add two configs specific to the panther pathways and how we are using it for the computational performance and pathway accurary/algo similaity assessments.
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We might want to consider dataset categories. Separate configs for each dataset would kill parallelism.
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| def main(): | ||
| pathways_df = parse_pc_pathways(current_directory / "raw" / "pathways.txt") | ||
| print("Fetching pathways... [This may take some time. On the author's desktop machine, it took 15 minutes.]") |
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| print("Fetching pathways... [This may take some time. On the author's desktop machine, it took 15 minutes.]") | |
| print("Fetching pathways... [This may take some time; around 15 minutes.]") |
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Can you add an overview comment on what is happening in this code.
| human_receptors = human_receptors[["NODE", "uniprot"]] | ||
| human_receptors.to_csv(folder / "sources.txt", sep="\t", index=False) | ||
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| # Finally, scores |
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| # Finally, scores | |
| # Finally, scores and actives |
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| # Finally, scores | ||
| scores = pd.concat([human_tfs, human_receptors]).drop_duplicates() | ||
| scores["prizes"] = 1 |
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| scores["prizes"] = 1 | |
| scores["prizes"] = 1.0 |
| # Then, we need to get the sources and targets, save them, | ||
| # and mark them with 1.0 prizes: | ||
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| # First, for our targets, or transcription factors |
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| # First, for our targets, or transcription factors | |
| # First, for our targets (transcription factors) |
| human_tfs = human_tfs[["NODE", "uniprot"]] | ||
| human_tfs.to_csv(folder / "targets.txt", sep="\t", index=False) | ||
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| # Then, for our receptors. NOTE: we skip the first row since it's empty in the XLSX, so this might break if the surfaceome authors fix this. |
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| # Then, for our receptors. NOTE: we skip the first row since it's empty in the XLSX, so this might break if the surfaceome authors fix this. | |
| # Then, for our receptors (surfaceomes). NOTE: we skip the first row since it's empty in the XLSX, so this might break if the surfaceome authors fix this. |
ntalluri
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Apr 16, 2026
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Why is this trimming to what is in the gold standard? My plan was to trim all data to what is available in the interactome.
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This is a draft since we don't provide any
configslinking to any specific data.