search

OpenTreeOfLife / reference-taxonomy

Open Tree Reference Taxonomy (OTT) tools
BSD 2-Clause "Simplified" License
11 stars 12 forks source link

dealing with contaminants from SILVA #201

Open mtholder opened 8 years ago

mtholder commented 8 years ago

I don't know what we want to do, but https://tree.opentreeoflife.org/taxonomy/browse?id=5252840 seems suboptimal:

  1. "Not Caenorhabditis elegans" is an odd name
  2. "Caenorhabditis elegans" is listed as a synonym
  3. ncbi link is to C. elegans, but SILVA link is to the unidentified taxon in Burkholderia
jar398 commented 8 years ago

I don't know either. Just delete them maybe? Or use the SILVA cluster reference sequence id as (or in) the name.

jar398 commented 8 years ago
  1. Will change the name to 'cluster JN975069'
  2. This was a bug, has been fixed (for 2.10)
  3. There will be no NCBI link for this taxon in 2.10, I believe

Other cases like this that I know about:

'Trichoderma harzianum',
'Sclerotinia homoeocarpa',
'Puccinia triticina',
'Daphnia pulex',
'Nematostella vectensis',
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/104
'Caenorhabditis elegans',
# https://github.com/OpenTreeOfLife/reference-taxonomy/issues/100
'Solanum lycopersicum',