How to download the KO (KEGG Orthology) Database, or list all pathways and their KEGG Orthology for 100 species.
I known keggREST. However, bad request error appeared many times. Do you have a code example?
Merry K P
Access the KEGG Orthology database: You can access the KEGG Orthology database through the KEGG website (https://www.genome.jp/kegg/ko.html). Search for the KO ID: Use the search bar to find the KO ID for the gene or protein of interest. You can also search for the KO ID by keyword or sequence. Retrieve the pathway information: Once you have identified the KO ID, click on the "Pathway" button to retrieve the information about the pathways associated with the gene or protein. This will show you the KEGG pathway maps that include the gene or protein. Explore the pathways: Click on the pathway maps to explore the pathways associated with the gene or protein. You can also access detailed information about each pathway by clicking on the "Description" button. Extract the pathway data: You can extract the pathway data by manually copying and pasting the information or by using automated scripts to extract the data. Analyze the pathway data: Once you have extracted the pathway data, you can analyze it using various tools and software to identify the significant pathways and their roles in different biological processes.
The KEGG Orthology (KO) database provides a comprehensive collection of pathways and functional annotations for genes and proteins. Here are the steps to extract pathways from the KEGG Orthology database:
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Rafael Piergiorge
You could try using:
https://www.bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html
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