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salvadorlab / Bovis-PangenomeOfReservoirs

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Extract Data #1

Closed noahaus closed 4 years ago

noahaus commented 4 years ago

I will take all sequence data that was used in 3 papers that have reservoir data:

1) Disease management at the wildlife-livestock interface: Using whole-genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan, USA. - https://www.ncbi.nlm.nih.gov/pubmed/30807679 2) Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3569-x 3) Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system - https://elifesciences.org/articles/45833

noahaus commented 4 years ago

May 7th

A description of the new data that I have. Number of Species, colored by reservoir status. Should Bovine be labelled a target species?

image

noahaus commented 4 years ago

May 8th A number of things to think on: 1) Crispell et al., 2017 doesn't make a distinction between the CERVINE group in New Zealand, but there are many types of deer in NZ (at least six). 2) in that same paper, the research just states that 'wildlife and cattle are transmitting to each other', but how do I label that relationship? 3) This is the data that we have for sequence data involving animal reservoirs. UK only contains reservoir data (badger, cattle), USA has many deer and a few cattle, NZ seems to just include a maintenance community. If we only included USA & UK, then the data would not be reflective of my question. If we keep NZ, then the relationship between the species need to be better understood, which isn't impossible but could be a ton of work within itself (each of these papers are dedicated to answering these questions).

What should I do!!!!!