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SuLab / WikiGenomesBase

A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.
https://chlambase.org/
MIT License
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Mutants with missing locus tags #144

Closed djow2019 closed 6 years ago

djow2019 commented 6 years ago

Some mutants are stored in the database without locus tags. They will never be displayed, so we need to determine if there was an error in importing the data from here:

https://www.sciencedirect.com/science/article/pii/S1931312815001316?via%3Dihub

An abbreviated print out of an entry (Did not update from today's meeting): {         "id" : "CTL2M402(pmpB_null)--400809",         "ref_base" : "C",         "locusTag" : "",         "snv_type" : "SO:0000183",         "name" : "CTL2M402 (pmpB null)",         "variant_base" : "T",         "date" : ISODate("2018-07-11T21:19:28.861Z"),         "doi" : null,         "coordinate" : {                 "start" : "400809",                 "end" : "400809"         },         "pub" : "25920978",         "aa_effect" : "",         "mutant_type" : 0 }

djow2019 commented 6 years ago

The data is actually correct. These are the mutants that are produced between genes, so naturally they won't have locus tags. However, we don't have a way of annotating these in chlambase since it is gene based.