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forensicgenomics / mitoTree-viewer

mitoTree is an interactive tool for visualizing and exploring mitochondrial DNA (mtDNA) lineages and their evolutionary relationships, helping users explore genetic diversity and maternal ancestry.
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Issues regarding Representative Genomes and Metadata #10

Open niki0211 opened 3 weeks ago

niki0211 commented 3 weeks ago

Add available information about existing Publications.

niki0211 commented 3 weeks ago

We could add another column with DOIs, or PubMed IDs.

minimops commented 3 weeks ago

Carried over from other issues:

For some sample, we don't have representative genomes from Genbank but only from empop-db. E.G. "B2a1c" has no representative in GenBank dataset but in our internal empop-db: "AZMH045, AZMH044".

In such cases we can show: EMP00847;USA

Todo: update "mitoTree_61302_representatives.txt"

the country for OR182493.1 is listed as NA, but I seen in its Genbank entry: "/note="ethnicity:Ashkenazi; origin_locality:Hungary:Tiszaszentimre". This is due to the fact that we are retrieving the country information from the NCBI FEATURE '/origin'. (see documentation).

Adapt the logic to retrieve origin information also from NCBI FEATURE "/note" "origin_locality"

minimops commented 3 weeks ago

Additionally, add hyperlinks

minimops commented 3 weeks ago

Update documentation to include all of these.

minimops commented 3 weeks ago

All of the above will be included in the new data pipeline.

niki0211 commented 2 weeks ago

From Feedback: Add variants info and add download functionality as in:

https://www.mitomap.org/cgi-bin/haplo_group?data=1&hg=H1a1a1

Keep in mind and try if this can be realized. Maybe this would need another card with "Representative Mitogenome Sequences".

niki0211 commented 1 week ago

added a file with updated representatives. See commit 67ea0b7.

The file contains header lines marked with "#" for now. Should be deleted when the issue is closed.

Need to add the new profiles to profiles.csv as well.

niki0211 commented 1 week ago

added file for 1000genomes with commit 45a65f3 as well.

empop files were sent to @minimops. Maybe you can add them here as well?

Not sure if we should keep them seperated or put them alltogether.