dib-lab / 2022-sra-gather

Classify all the metagenomes. ALL THE METAGENOMES. (Eventually.)
Other
0 stars 1 forks source link

ScientificNames that made sense for me to include in a random forests analysis #3

Open taylorreiter opened 2 years ago

taylorreiter commented 2 years ago

Edit: woops -- i did this on the gather results, which meant that each genome obvs was counted as a biome obvs. Fixed below.

Set of 71 ScientificNames. Excludes anything that was named as a species name (eukaryotic, viral, bacterial, or archaeal). Excludes amorphous names like "environmental samples" or "mixed sample". Excludes any set that didn't have at least 10 observations.

'human gut metagenome', 'gut metagenome', 'metagenome', 'human metagenome', 'soil metagenome', 
'mouse gut metagenome', 'human skin metagenome', 'marine metagenome', 'human oral metagenome', 
'freshwater metagenome', 'indoor metagenome', 'sediment metagenome', 'pig gut metagenome', 
'rhizosphere metagenome', 'viral metagenome', 'oral metagenome', 'feces metagenome', 'food metagenome',
'sponge metagenome', 'aquatic metagenome', 'wastewater metagenome', 'bovine gut metagenome',
'seawater metagenome', 'human nasopharyngeal metagenome', 'biofilm metagenome', 'plant metagenome',
'human blood metagenome', 'mouse metagenome', 'bird metagenome', 'fish gut metagenome', 
'human lung metagenome', 'human vaginal metagenome', 'bioreactor metagenome', 'groundwater metagenome', 
'bat metagenome', 'hot springs metagenome', 'mosquito metagenome', 'terrestrial metagenome',
'milk metagenome', 'algae metagenome', 'chicken gut metagenome', 'peat metagenome',
'marine sediment metagenome', 'air metagenome', 'food fermentation metagenome', 'insect metagenome', 
'insect gut metagenome', 'unidentified', 'fish metagenome', 'synthetic metagenome', 'dust metagenome', 
'rat gut metagenome', 'wetland metagenome', 'activated sludge metagenome', 'estuary metagenome', 
'microbial mat metagenome', 'blood metagenome', 'bovine metagenome', 'human saliva metagenome', 
'lake water metagenome', 'hydrothermal vent metagenome', 'anaerobic digester metagenome', 
'pig metagenome', 'fossil metagenome', 'sludge metagenome', 'food production metagenome', 
'drinking water metagenome', 'marine plankton metagenome', 'mollusc metagenome', 'root metagenome',
'Severe acute respiratory syndrome coronavirus 2'