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clb21565 / mobileOG-db

code repo for mobileOG-db
GNU General Public License v3.0
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When will the database be updated next? or will it be updated ? #18

Open balaram26 opened 4 months ago

balaram26 commented 4 months ago

Hey hii, i like the the mobileOG db and the small script you have given for quick analysis. do u have idea to update this database? will this be maintained going forward?

clb21565 commented 4 months ago

Hi there! Thanks for using mobileOG-db and for your question. We are working on a medium-size update to mobileOG-db that should be out in a few weeks, and then a more major upgrade within a few months. The larger update will include a new deep learning pipeline and database with enhanced class (e.g., phage, plasmid) labelling.

In the mean time, if you have any requests and/or suggestions for additions, please do let us know!

balaram26 commented 4 months ago

Thats great to know. I think one of things I came across your database is, it has also somehow included some ARGs in them, as when I looking at amr results and urs, some regions had same amr hits, and ur gene names were also same as the ARG. So this aspect could be improved I think.

clb21565 commented 4 months ago

which ARG database were you using?

there are rare cases where the annotation is genuinely ambiguous-- for example-- transcriptional regulators that promote resistance and conjugation. We've debated removing those

clb21565 commented 3 months ago

Hi there!

Just wanted to check in on this - we are hoping to release an updated version in the next few months, and I recalled you mentioned we had some overlap with ARGs. Do you know which database of ARGs you were using? Thanks so much!

balaram26 commented 3 months ago

Hi sure,it was the MEGARes database from AMRplusplus pipeline, here is the github link: https://meglab.org/megares/ their AMR and your mobileOGdb MGE protein both had same gene name hits on my sample data on the same regions as wel.

balaram26 commented 1 week ago

Hi, how is it going? looking forward for the update you mentioned. @clb21565 .

clb21565 commented 1 week ago

Almost there - but - I can offer a V. 1.7 if that's of interest with updated element labels. the final (2.0) version will be substantially larger.