Every ENA sample object should have a taxonomic classification. The INSDC maintains a database of all unique taxonomy classifications known to us and you should apply one from this database when you create your samples. Each classification has a unique id and this is expanded to show the scientific name and common name of the organism when the sample is viewed.
The interactive submission service has a look up table which you can use before you download the spreadsheet template so that you already know what taxonomy identifications to apply when you are creating your samples offline (step 8 in module 1). There is also a look up here, in the taxon domain of the ENA advanced search.
Submitters using REST API will apply the taxonomic information to the sample object using the sample_name block
<SAMPLE_NAME>
<TAXON_ID>450267</TAXON_ID>
<SCIENTIFIC_NAME>Chlamyphorus truncatus</SCIENTIFIC_NAME>
<COMMON_NAME>Pink fairy armadillo</COMMON_NAME>
</SAMPLE_NAME>Submitters using the REST API to programmatically submit samples in XML format can use the taxonomy database look up to find what tax id they need to apply to their sample using these REST endpoints:
If you know the scientific name of the organism you can find the taxonomy id with this endpoint www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/scientific-name/. Simply append the scientific name to the URL. You can use a browser or use cURL at the command line (the "see URL" program available on Linux and Mac). Note the use of %20 to represent a space character. This is URL encoding and you may find the commands do not work unless you replace space characters with %20
> curl "http://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/scientific-name/Leptonycteris%20nivalis"
[
{
"taxId": "59456",
"scientificName": "Leptonycteris nivalis",
"commonName": "Mexican long-nosed bat",
"formalName": "true",
"rank": "species",
"division": "MAM",
"lineage": "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Chiroptera; Microchiroptera; Phyllostomidae; Glossophaginae; Leptonycteris; ",
"geneticCode": "1",
"mitochondrialGeneticCode": "2",
"submittable": "true"
}
]You can do the same with the common name. Use endpoint http://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/any-name/ and append the name
> curl "http://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/any-name/golden%20arrow%20poison%20frog"
[
{
"taxId": "377316",
"scientificName": "Atelopus zeteki",
"commonName": "golden arrow poison frog",
"formalName": "true",
"rank": "species",
"division": "VRT",
"lineage": "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Neobatrachia; Hyloidea; Bufonidae; Atelopus; ",
"geneticCode": "1",
"mitochondrialGeneticCode": "2",
"submittable": "true"
}
]If you do not know the scientific name or the common name but you have an idea, you can use this suggest endpoint http://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/suggest-for-submission/
> curl "http://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/suggest-for-submission/curry"
[
{
"taxId": "159030",
"scientificName": "Murraya koenigii",
"displayName": "curry leaf"
},
{
"taxId": "261786",
"scientificName": "Helichrysum italicum",
"displayName": "curry plant"
}
]In each case above a JSON document is outputted and you will be looking for the taxId field. Outputting JSON format will help you to automate the call if appropriate.
Every sample object in the ENA must have a taxonomic classification assigned to it. Of course environmental samples typically collected for metagenomic studies can not have a single organism identifier because they represent an environment with an unknown variety and number of organisms. For this purpose we have entries in the taxonomic database to apply exclusively to environmental samples. You can search for these terms using the methods described above - they tend to have "metagenome" as part of the scientific name.
curl "www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/suggest-for-submission/marsupial%20meta"
[
{
"taxId": "1477400",
"scientificName": "marsupial metagenome",
"displayName": "marsupial metagenome"
}To have an idea of what environmental sample names are available, below is a list.
metagenome
synthetic metagenome
ecological metagenomes
organismal metagenomes
Specific
ecological metagenomes sub nodes
activated carbon metagenome
activated sludge metagenome
aerosol metagenome
air metagenome
alkali sediment metagenome
anaerobic digester metagenome
anchialine metagenome
ant fungus garden metagenome
aquatic metagenome
aquifer metagenome
ballast water metagenome
beach sand metagenome
bioanode metagenome
biocathode metagenome
biofilm metagenome
biofilter metagenome
biofloc metagenome
biogas fermenter metagenome
bioreactor metagenome
bioreactor sludge metagenome
biosolids metagenome
cave metagenome
clinical metagenome
cloud metagenome
coal metagenome
cold seep metagenome
compost metagenome
concrete metagenome
coral reef metagenome
cow dung metagenome
crude oil metagenome
decomposition metagenome
dietary supplements metagenome
dust metagenome
electrolysis cell metagenome
estuary metagenome
fermentation metagenome
fertilizer metagenome
floral nectar metagenome
flotsam metagenome
food contamination metagenome
food fermentation metagenome
food metagenome
food production metagenome
freshwater metagenome
freshwater sediment metagenome
fuel tank metagenome
gas well metagenome
glacier lake metagenome
glacier metagenome
groundwater metagenome
halite metagenome
herbal medicine metagenome
honey metagenome
hospital metagenome
hot springs metagenome
HVAC metagenome
hydrocarbon metagenome
hydrothermal vent metagenome
hypersaline lake metagenome
hyphosphere metagenome
hypolithon metagenome
ice metagenome
indoor metagenome
industrial waste metagenome
interstitial water metagenome
lagoon metagenome
lake water metagenome
landfill metagenome
leaf litter metagenome
lichen crust metagenome
lobster shelll metagenome
mangrove metagenome
manure metagenome
marine metagenome
marine plankton metagenome
marine sediment metagenome
metal metagenome
microbial fuel cell metagenome
microbial mat metagenome
milk metagenome
mine drainage metagenome
mine tailings metagenome
mixed culture metagenome
money metagenome
moonmilk metagenome
mud volcano metagenome
museum specimen metagenome
musk metagenome
neuston metagenome
oasis metagenome
oil field metagenome
oil metagenome
oil production facility metagenome
oil sands metagenome
outdoor metagenome
paper pulp metagenome
parchment metagenome
peat metagenome
periphyton metagenome
permafrost metagenome
phytotelma metagenome
pitcher plant inquiline metagenome
plastisphere metagenome
pond metagenome
poultry litter metagenome
power plant metagenome
probiotic metagenome
retting metagenome
rhizoplane metagenome
rhizosphere metagenome
rice paddy metagenome
riverine metagenome
rock metagenome
rock porewater metagenome
root associated fungus metagenome
saline spring metagenome
salt lake metagenome
salt marsh metagenome
salt mine metagenome
saltern metagenome
sand metagenome
seawater metagenome
sediment metagenome
shale gas metegenome
silage metagenome
sludge metagenome
snow metagenome
snowblower vent metagenome
soda lake metagenome
soil crust metagenome
soil metagenome
solid waste metagenome
steel metagenome
stromatolite metagenome
subsurface metagenome
surface metagenome
tar pit metagenome
termitarium metagenome
termite fungus garden metagenome
terrestrial metagenome
tidal flat metagenome
tin mine metagenome
tobacco metagenome
tomb wall metagenome
urban metagenome
wastewater metagenome
wetland metagenome
whale fall metagenome
wine metagenome
wood decay metagenome
organismal metagenomes sub nodes
algae metagenome
annelid metagenome
ant metagenome
aquatic viral metagenome
bat metagenome
bear gut metagenome
beetle metagenome
bird metagenome
blood metagenome
bovine gut metagenome
bovine metagenome
cetacean metagenome
chicken gut metagenome
ciliate metagenome
coral metagenome
crab metagenome
crustacean metagenome
ctenophore metagenome
dinoflagellate metagenome
ear metagenome
echinoderm metagenome
endophyte metagenome
epibiont metagenome
eye metagenome
feces metagenome
feline metagenome
fish gut metagenome
fish metagenome
flower metagenome
fossil metagenome
frog metagenome
fungus metagenome
gill metagenome
gonad metagenome
grain metagenome
grasshopper gut metagenome
gut metagenome
honeybee metagenome
human bile metagenome
human blood metagenome
human brain metagenome
human eye metagenome
human gut metagenome
human gut metagenome gcode 4
human lung metagenome
human metagenome
human milk metagenome
human nasopharyngeal metagenome
human oral metagenome
human reproductive system metagenome
human saliva metagenome
human semen metagenome
human skeleton metagenome
human skin metagenome
human tracheal metagenome
human vaginal metagenome
hydrozoan metagenome
insect gut metagenome
insect metagenome
invertebrate gut metagenome
invertebrate metagenome
jellyfish metagenome
koala metagenome
leaf metagenome
lichen metagenome
liver metagenome
lung metagenome
marsupial metagenome
mite metagenome
mollusc metagenome
mosquito metagenome
moss metagenome
mouse gut metagenome
mouse metagenome
mouse skin metagenome
nematode metagenome
oral metagenome
oral-nasopharyngeal metagenome
ovine metagenome
oyster metagenome
parasite metagenome
phage metagenome
phyllosphere metagenome
pig gut metagenome
pig metagenome
placenta metagenome
plant metagenome
pollen metagenome
primate metagenome
psyllid metagenome
rat gut metagenome
rat metagenome
reproductive system metagenome
respiratory tract metagenome
rodent metagenome
root metagenome
scorpion gut metagenome
sea anemone metagenome
sea squirt metagenome
sea urchin metagenome
seagrass metagenome
seed metagenome
sheep gut metagenome
sheep metagenome
shoot metagenome
shrimp gut metagenome
skin metagenome
snake metagenome
spider metagenome
sponge metagenome
stomach metagenome
symbiont metagenome
termite gut metagenome
termite metagenome
tick metagenome
upper respiratory tract metagenome
urine metagenome
urogenital metagenome
vaginal metagenome
viral metagenome
wallaby gut metagenome
wasp metagenome
zebrafish metagenome
This list is not updated so you should check the ENA tax portal for the most recent additions. Click on the Tax tree tab and click the '+' icons to expand the categories:
These environmental terms go in the scientific name field of the sample object. To find the tax id use the method outlined above (scientific-name endpoint). For example you can paste the following into your browser to find the tax id for termite fungus garden metagenome: http://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/scientific-name/termite fungus garden metagenome.