Giters

BigDataBiology / AMPSphereWebsite

Website for global antimicrobial peptides.

Home Page:https://ampsphere.big-data-biology.org/home

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celiosantosjr opened this issue · comments

commented

User stories

    1. Biochemist trying to figure out if their sequence was already observed and retrieve some info out of AMPSphere:
    • Example peptide: KRVKLLLKGYMRAIEINAALMYGYRPK
    • Search for similar peptides
    • Search for its family
    1. Biochemist trying to produce or characterize one sequence from AMPSphere:
    • Example peptide: AMP10.000_010
    • Text search the access and retrieve the peptide information
    • Check features and peptide secondary structure
    • Check the genes
    1. Ecologist trying to figure out the relationship between a certain bacteria in the microbiota of a given host:
    • Example host: Azolla sp. (a plant) and Nostoc azollae (a bacteria)
    • Browse filtering of the host and the original taxon, retrieve the list of AMPs
    • Entering the AMP access codes and check the location and habitat (guts, mouth, skin...)
    1. Bioinformatician wanting to use AMPSphere as a resource:
    • Download the files
    • Retrieve the peptides and the genes
    • Retrieve families
    1. Now imagine the case where the guy just wants to retrieve quick info
      and maybe export this to somewhere else, like your blog
    • use API
    1. The same bioinformatician wants more info about a family of a certain AMP:
    • Example peptide: AMP10.000_010
    • Find the family, get the number of sequences, distribution in the world, the features, genes, environment, and hosts
    • Retrieve the HMM profile for the family and the logos for the sequence and the model

TODO:

+ implement a column and the filter in the browser tab for the AMP taxon origin (ex. E. coli)
+ implement file format and columns explanation in the download page 
+ add more explanation in the independent and conditional e-values in the HMMer search page (Family search)
commented
  • i is very reasonable: many people will have sequences
  • ii is possible if/once the resource is successful. But how did they even learn about AMP10.000_010?
  • iii seems very forced. Why would AMPSphere be the best solution for this?
  • iv feels under-specified. What does resource mean? Same comments applies tov (also it may not necessarily be a guy)
  • vi: same comment as ii. Hopefully, we'll become successful enough that this is an actual use case

I am missing clicked on the link on twitter/manuscript/... and wants to know what this is all about.

Maybe also person has genome/MAG, wants to find all matches? is a common thing? Many people with genomes out there.