{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Growth media for the CARVEME database\n", "\n", "CARVEME is a database targeting all complete genomes inRefseq. To yield a growth medium for the human gut we will start from the western diet used for the AGORA database and complete it so that all taxa in the database can grow.\n", "\n", "For that we had to map all metabolites from AGORA to CARVEME. The ones that had a clear mapping can be found in the basic `carveme_skeleton.csv`.\n", "\n", "We can take a look by reading it using micom." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | reaction | \n", "metabolite | \n", "global_id | \n", "flux | \n", "dilution | \n", "keggId | \n", "casRegistry | \n", "
---|---|---|---|---|---|---|---|
1 | \n", "EX_26dap__M_m | \n", "26dap__M_m | \n", "EX_26dap__M_e | \n", "0.10000 | \n", "0.1 | \n", "C00680 | \n", "NaN | \n", "
3 | \n", "EX_ac_m | \n", "ac_m | \n", "EX_ac_e | \n", "0.10000 | \n", "0.1 | \n", "C00033 | \n", "64-19-7 | \n", "
4 | \n", "EX_acgam_m | \n", "acgam_m | \n", "EX_acgam_e | \n", "0.10000 | \n", "0.1 | \n", "C00140 | \n", "7512-17-6 | \n", "
5 | \n", "EX_ala__L_m | \n", "ala__L_m | \n", "EX_ala__L_e | \n", "0.10000 | \n", "0.1 | \n", "C00041 | \n", "56-41-7 | \n", "
6 | \n", "EX_amp_m | \n", "amp_m | \n", "EX_amp_e | \n", "0.10000 | \n", "0.1 | \n", "C00020 | \n", "61-19-8 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
139 | \n", "EX_amylose300_m | \n", "amylose300_m | \n", "EX_amylose300_e | \n", "0.00010 | \n", "1.0 | \n", "NaN | \n", "NaN | \n", "
148 | \n", "EX_lmn30_m | \n", "lmn30_m | \n", "EX_lmn30_e | \n", "0.00047 | \n", "1.0 | \n", "NaN | \n", "NaN | \n", "
152 | \n", "EX_acmana_m | \n", "acmana_m | \n", "EX_acmana_e | \n", "0.10000 | \n", "0.1 | \n", "C00645 | \n", "3615-17-6 | \n", "
153 | \n", "EX_starch1200_m | \n", "starch1200_m | \n", "EX_starch1200_e | \n", "0.00010 | \n", "1.0 | \n", "NaN | \n", "NaN | \n", "
158 | \n", "EX_fald_m | \n", "fald_m | \n", "EX_fald_e | \n", "0.10000 | \n", "0.1 | \n", "C00067 | \n", "50-00-0 | \n", "
123 rows × 7 columns
\n", "