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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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Question about KEGG and BiGG_reaction annotations #386

Open silvtal opened 2 years ago

silvtal commented 2 years ago

Thank you for developing eggnog-mapper, I've been including it in my pipelines to generate CarveMe metabolic models for a couple of years now.

The current eggnog-mapper outputs a .tsv file that includes, among others, KEGG_ko, KEGG_Reaction and BiGG_Reaction annotators. The column that CarveMe uses to make its models is the BiGG_Reaction one.

Recently, I've been trying out a different genome annotator, MicrobeAnnotator, which outputs KEGG_kos. I would love to be able to generate CarveMe models from this output as well, but for that I need BiGG identifiers.

I do know how to easily obtain KEGG_Reaction identifiers from them, but I have no clue how to associate them to BiGG_Reactions. How does eggnog-mapper draw this connection between identifiers? This is from old code, but I did notice that there seems to be a direct database link between identifiers.

Could you give me some insight on this, and maybe some guidelines as for how I can use the eggnog database to get BiGG_reaction annotations from KOs?

Thank you so much in advance

NanYang90 commented 2 years ago

Thank you for developing eggnog-mapper, I've been including it in my pipelines to generate CarveMe metabolic models for a couple of years now.

The current eggnog-mapper outputs a .tsv file that includes, among others, KEGG_ko, KEGG_Reaction and BiGG_Reaction annotators. The column that CarveMe uses to make its models is the BiGG_Reaction one.

Recently, I've been trying out a different genome annotator, MicrobeAnnotator, which outputs KEGG_kos. I would love to be able to generate CarveMe models from this output as well, but for that I need BiGG identifiers.

I do know how to easily obtain KEGG_Reaction identifiers from them, but I have no clue how to associate them to BiGG_Reactions. How does eggnog-mapper draw this connection between identifiers? This is from old code, but I did notice that there seems to be a direct database link between identifiers.

Could you give me some insight on this, and maybe some guidelines as for how I can use the eggnog database to get BiGG_reaction annotations from KOs?

Thank you so much in advance

Hi, I am trying to use eggnog-mapper outputs .tsv (generated by eggnog online annotation) as CarveMe metabolic models input file, with script like this: carve --egg eggnog_output.tsv But I got an error: "The input genome did not match sufficient genes/reactions in the database." Do you have an idea how to fix this problem?

Thank you so much in advance!

silvtal commented 2 years ago

"The input genome did not match sufficient genes/reactions in the database."

You should check the file, maybe it failed somehow and it's blank. But assuming the annotation went well, it's probably because CarveMe is not reading the file correctly. Check the highlighted lines of your eggnog.py script, they should be the same columns that you have in your .tsv. If they are not, I would simply edit them so they are. It's possible that the web service returns different columns than the command line service

NanYang90 commented 2 years ago

I would simply edit them so they are. It's possible that the web service returns different columns than the command line service

Thank you so much! I will modify the tsv manually with your suggestions. Should I remove the first row of columnname?

Thanks

silvtal commented 2 years ago

You don't need to remove the lines starting with # nor the row with the column names

NanYang90 commented 2 years ago

You don't need to remove the lines starting with # nor the row with the column names

I modified it to 17 columns corresponding to updated script, but I still got the error. Could I ask you help me to check my .tsv file? If is possible I can send it to you?

silvtal commented 2 years ago

I think you should check the script itself, you might have the old version

I don't mind if you write me via email. But I think you should also open a different issue, it's actually better because this issue is supposed to be about other thing đŸ˜…

Cantalapiedra commented 2 years ago

Hi @silvtal ,

Sorry for the delay answering. The link that you provided is where the data is retrieved from eggnog-mapper's database. So, in that sense, the link was established previously, during the annotation of eggNOG proteins. To be honest, I was not involved in the annotation of eggnog proteins, maybe @jhcepas could be of more help here.

I found this very old thread https://www.biostars.org/p/9047/ or things like https://bikegg.github.io/, https://pubs.rsc.org/en/content/articlelanding/2016/mb/c6mb00532b

Also here http://bigg.ucsd.edu/data_access there are some examples of database_links. I am not sure if that is what you are looking for.

I hope that you could get some clue from any of those.

Best, Carlos