{ "cells": [ { "cell_type": "markdown", "id": "dbfb1aa7-3761-404c-adc6-880fdb4c6305", "metadata": {}, "source": [ "# Adding annotation from a BioCyc Database" ] }, { "cell_type": "markdown", "id": "38aea7b5-c984-4087-9bc0-c6a9158f637d", "metadata": {}, "source": [ "For details on inputs go to [Description of Inputs](./BasicInputs.ipynb).\n", "\n", "For information about coralME architecture go to [Architecture of coralME](./coralMEArchitecture.ipynb).\n" ] }, { "cell_type": "markdown", "id": "b83faf4c-e7ef-4b4c-b4b9-2c980931a7f4", "metadata": {}, "source": [ "## Download files from BioCyc" ] }, { "cell_type": "markdown", "id": "276384ec-657b-4aa7-aba0-cfda4a2b4655", "metadata": {}, "source": [ "BioCyc files are optional but useful, you should download them after having your gene id consistent M-model and genbank files.\n", "\n", "The quickest way to do this is to copy one of the genes from the genbank file into the BioCyc search bar. Your organism should appear in the list if it is available in BioCyc.\n", "\n", "To download:" ] }, { "cell_type": "markdown", "id": "04801082-579a-46bf-b2af-f359251ae781", "metadata": {}, "source": [ "### Go to Tools>Special SmartTables" ] }, { "cell_type": "markdown", "id": "db3cb707-3aba-4c47-9c66-e8bc117734ec", "metadata": {}, "source": [ "\"Drawing\"" ] }, { "cell_type": "markdown", "id": "34b9d71c-2c99-4269-9003-472f38c1210c", "metadata": {}, "source": [ "From here you can download the 5 optional BioCyc files for your organism." ] }, { "cell_type": "markdown", "id": "14c8b16f-338b-4e99-8c3d-ed8b4e5c2222", "metadata": {}, "source": [ "\"Drawing\"" ] }, { "cell_type": "markdown", "id": "0d5d7dac-b2de-4f78-8c19-60ec45cc8819", "metadata": {}, "source": [ "### Download genes.txt and sequences.fasta" ] }, { "cell_type": "markdown", "id": "dad6ba87-4675-4904-a3c7-cb8cd085e5f0", "metadata": {}, "source": [ "\"Drawing\"" ] }, { "cell_type": "markdown", "id": "0b4693cf-98e3-483a-9047-6a835b1d6e6e", "metadata": {}, "source": [ "### Download proteins.txt, RNAs.txt and TUs.txt" ] }, { "cell_type": "markdown", "id": "3287c091-fd31-4bbe-ae49-18c5f85ee14a", "metadata": {}, "source": [ "The same process of genes.txt applies to proteins.txt, RNAs.txt and TUs.txt.\n", "\n", "Some columns must be added manually using BioCyc's dropdown lists __ADD PROPERTY COLUMN__ and __ADD TRANSFORM COLUMN__ within the SmartTable editing webpage." ] }, { "cell_type": "markdown", "id": "cc0cf2f4-bd4b-46e3-823e-c395e66d6baf", "metadata": {}, "source": [ "\"Drawing\"" ] }, { "cell_type": "markdown", "id": "41a66e56-90cf-4bfe-ab94-d4847307224f", "metadata": {}, "source": [ "#### Download proteins.txt\n", "\n", "The index (Proteins Complexes) is in the SmartTable by default, but you need to add the columns Common-Name, Genes of polypeptide, complex, or RNA, and Locations.\n", "\n", "* Common-Name is available in the dropdown list __ADD PROPERTY COLUMN__\n", "\n", "* Genes of polypeptide, complex, or RNA is available in the dropdown list __ADD TRANSFORM COLUMN__\n", "\n", "* Locations is available in the dropdown list __ADD PROPERTY COLUMN__." ] }, { "cell_type": "markdown", "id": "58e51941-57d9-4aca-ba3e-9f0f0a042a77", "metadata": {}, "source": [ "#### Download RNAs.txt\n", "\n", "The index (All-tRNAs Misc-RNAs rRNAs) is in the SmartTable by default, but you need to add the columns Common-Name, and Gene.\n", "\n", "* Common-Name is available in the dropdown list __ADD PROPERTY COLUMN__\n", "\n", "* Gene is available in the dropdown list __ADD PROPERTY COLUMN__." ] }, { "cell_type": "markdown", "id": "5be5a1f8-947b-4f13-8858-b0d5e8e02869", "metadata": {}, "source": [ "#### Download TUs.txt\n", "\n", "The index Transcription-Units is in the SmartTable by default, but you need to add the columns Genes of transcription unit, and Direction.\n", "\n", "* Genes of transcription unit is available in the dropdown list __ADD TRANSFORM COLUMN__\n", "\n", "* Direction is available in the dropdown list __ADD PROPERTY COLUMN__." ] }, { "cell_type": "markdown", "id": "d22596c4-719a-4845-a138-a73e2a9a363a", "metadata": {}, "source": [ "## Initialize the folder for your organism\n", "Copy your files to create your initial folder" ] }, { "cell_type": "markdown", "id": "82deeea7-d34e-4f41-a887-5c120609c96b", "metadata": {}, "source": [ "\"Drawing\"" ] }, { "cell_type": "markdown", "id": "09abdb74-fb13-424a-b70e-a84b6e5f9834", "metadata": {}, "source": [ "### Define inputs in __input.json__.\n", "\n", "See an example of [input.json](./helper_files/tutorial/input.json)" ] }, { "cell_type": "markdown", "id": "3d577d1c-09e0-46bb-846e-0f4b13131c42", "metadata": {}, "source": [ "### Define parameters in __organism.json__.\n", "\n", "See an example of [organism.json](./helper_files/tutorial/organism.json)" ] }, { "cell_type": "markdown", "id": "a70a4fa7-3e9a-4a48-9c90-df1770808875", "metadata": {}, "source": [ "
\n", "**Note**: You do not need to modify these parameters right away. But once you are at the curation stage you will have to ensure these parameters are applicable to your organism.\n", "
" ] } ], "metadata": { "kernelspec": { "display_name": "coralme-1.1.5", "language": "python", "name": "coralme-1.1.5" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.12" } }, "nbformat": 4, "nbformat_minor": 5 }