From 77968d604c148c1eb9158e06efae83e4e73c224b Mon Sep 17 00:00:00 2001 From: Sara Taheri Date: Wed, 17 Jan 2024 11:38:17 +0330 Subject: [PATCH] add docs for ecoli example --- src/eliater/examples/ecoli.py | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/src/eliater/examples/ecoli.py b/src/eliater/examples/ecoli.py index 43fc48e..26cb955 100644 --- a/src/eliater/examples/ecoli.py +++ b/src/eliater/examples/ecoli.py @@ -1,4 +1,14 @@ -"""Examples for transcriptional Escherichia coli K-12 regulatory network.""" +"""Examples for transcriptional Escherichia coli K-12 regulatory network. + +The E. Coli regulatory network was extracted manually (by hand) from the EcoCyc +database [Keseler2021]_ . The nodes represent genes, and the edges represent +regulatory relationships. + +.. [Keseler2021] Keseler, I. M., Gama-Castro, S., Mackie, A., Billington, R., +Bonavides-Mart ́ınez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P. E., +Mu ̃niz-Rascado, L., et al. (2021). 'The EcoCyc database in 2021'. Frontiers in +Microbiology, page 2098. +""" # FIXME add the following documentation. DO NOT remove this fixme without review and confirmation. # 1. Where did this network come from? What physical experimentation was used to create it? @@ -118,9 +128,12 @@ " ... & Vitek, O. (2023). Optimal adjustment sets for causal query estimation in partially" " observed biomolecular networks. Bioinformatics, 39(Supplement_1), i494-i503.", graph=graph, - description="This is the transcriptional E. Coli regulatory network" - " obtained from EcoCyc database ", + description="This is the transcriptional E. Coli regulatory network obtained from EcoCyc database. " + "The experimental data were 260 RNA-seq normalized expression profiles of E. coli K-12" + " MG1655 and BW25113 across 154 unique experimental conditions, extracted from the PRECISE" + " database by (Sastry et al., 2019) from this paper: 'The Escherichia coli transcriptome mostly" + " consists of independently regulated modules' ", example_queries=[Query.from_str(treatments="fur", outcomes="dpiA")], ) -ecoli_transcription_example.__doc__ = ecoli_transcription_example.description +ecoli_transcription_example.__doc__ = ecoli_transcription_example.description \ No newline at end of file