[Request An Update]: add organisms & schemes to mlst dbs

[kapsakcj]

What container needs an update?

It would be nice to add 2 mlst schemes (Providencia spp. & Serratia spp.) to the mlst docker image. Perhaps there are other's that are not included by default with mlst (please note them in a comment below)?

This may be a request that is outside of the scope of this project, as it would be implementing changes to a tool, helper scripts (like those used to download schemes from pubMLST) & mlst's database, but I still wanted to note the request here so we can track any development on it.

• https://pubmlst.org/organisms/providencia-spp
• https://pubmlst.org/organisms/serratia-spp

@erinyoung 's Serratia request on the mlst repo: tseemann/mlst#136

One potential issue is that Torsten's scripts for downloading data from pubMLST may not work properly for certain schemes, depending on when they were added to pubMLST and/or BIGSdb. So this would make it a more difficult to properly download (and update over time!) the schemes from their source. @Kincekara Please correct me or add any info you think is relevant.

[Kincekara]

@kapsakcj You're right. Authentication is required to access data submitted on or before 2024-12-31. I believe PubMLST can provide an API key, but it should be implemented in Torsten's scripts if it doesn't already exist.
You can find the relevant links as json for Serratia and Providencia below.

https://rest.pubmlst.org/db/pubmlst_serratia_seqdef/schemes/1
https://rest.pubmlst.org/db/pubmlst_providencia_seqdef/schemes/1

[kapsakcj]

This is the list of schemes included in pubMLST's XML file that is no longer maintained. Notably, the Providencia spp. and Serratia spp. schemes are not included, so I assume the restAPI will have to be used for those 2 https://pubmlst.org/data/