VGP_specimen_naming_scheme.md

VGP specimen naming scheme

Individual specimens to be seqeunced as part of the Vertebrate Genomes Project (VGP) will be assigned a VGP ID according to the following scheme. The ID will take the form:

[abfmrs]AbcXyz{#}

where

• The one letter prefix [abfmrs] corresponds to one of:

  prefix	class
  a	amphibians
  b	birds
  f	fishes
  m	mammal
  r	reptiles
  s	sharks and relatives

• The six letter combination AbcXyz is a species/strain designator. In most cases, this will be GenSpe for Genus/Species but that is not required (see below for how to resolve clashes).

• {#} is an incremental number per individual specimen from the same species.

For each species in the VGP ordinal project, the 7-letter prefix [abfmrs]AbcXyz will be pre-assigned to avoid conflicts. Across all species, there will be clashes for this 7-letter prefix. There are a few options for dealing with these:

1. Allow the clashes and with individuals/species disambiguated by the final incremental number.
2. Allow variation within the six letter species designator, e.g. a 2-4 split (GeSpec), or modified capitalisation (GENSpe)

The EBI are in the process of setting up a registry where VGP IDs can be assigned and avoid individual IDs clashing between centres.

Examples

VGP ID	Species and common name
fGouWil2	Gouania willdenowi; blunt-snouted clingfish
mLemCat1	Lemur catta; ring-tailed lemur
aRhiDar3	Rhinoderma darwinii; Darwin's frog
bCalAnn1	Calypte anna; Anna's hummingbird
rDerCor1	Dermochelys coriacea; leatherback sea turtle
sCarCar1	Carcharodon carcharias; great-white shark

Tissue samples

For a single individual, there may be multiple tissue samples used for transcriptome sequencing. The proposed scheme to distinguish these samples is:

[abfmrs]AbcXyz{#}.tissue{#}

where tissue should come from an agreed list of terms (to be decided). Examples: fGouWil2.brain1, fGouWil2.eye2.

If the tissue used for transcriptome sequencing is from a different indiviual than the one sequenced to produce the assembly, then an new individual VGP ID should registered.

Biosamples

Having assigned VGP IDs, a BioSamples accession ID should also be generated for the individual. Agreed metadata (to be decided) should be attached to the BioSamples entries. Tissue samples should be assigned metadata based on an agreed ontology such as Uberon and should used the Derived from linking facility in BioSamples to indicate the individual source of that tissue sample.

Extension beyond vertebrates

If this scheme were to extend beyond vertebrates in the VGP, the below is a proposal which would use all the letters of the alphabet to cover the Tree of Life. This is meant as a pragmatic division rather then a strict taxonomic one.

prefix	class	count	group	notes
a	amphibians	6439	chordates
b	birds	10301	chordates
c	non-vascular plants	14222	plants
d	dicotyledons	200000	plants	not monophyletic
e	echinoderm	6753	other animals
f	fishes	31862	chordates	lobe-finned and ray finned = Osteichthyes = Teleostomi (excluding tetrapods)
g	fungi	123126	other eukaryotes
h	platyhelminths	9164	other animals
i	insects	795000	other animals
j	jellyfish and other cnidaria	9747	other animals
k	other chordates	1926	chordates	cephalochordates, urochordates (tunicates), jawless fish; not monophyletic
l	monocotyledons (lilies etc.)	51595	plants	'l' for lily
m	mammals	4863	chordates
n	nematodes	3455	other animals
o	sponges	8499	other animals
p	protists	12695	other eukaryotes	defined here as eukaryotes not animals or plants or fungi; not monophyletic
q	other arthropods	120000	other animals	not insects; not monophyletic
r	reptiles	9789	chordates	excluding birds
s	sharks and relatives	1149	chordates	Chondricthyes = Elasmobranchs and Chimaeras
t	other animal phyla	165	other animals
u	algae	2056	plants	not monophyletic
v	other vascular plants	66717	plants	ferns, cycads, conifers, gingko etc.; not monophyletic
w	annelids (worms)	12738	other animals
x	molluscs	41646	other animals	the "scs" in "moluscs" sounds a bit like it contains an 'x'
y	bacteria	6468	prokaryotes
z	archea	281	prokaryotes	mosses, liverworts, hornworts; not monophyletic
-	viruses			'-' for missing

Equivalently, presented by group:

group	prefix	class
chordates (including vertebrates)	m	mammals
	b	birds
	r	reptiles
	a	amphibians
	f	fishes
	s	sharks
	k	other chordates
other animals	e	echinoderms
	x	molluscs
	i	insects
	q	other arthropods
	w	annelids (worms)
	n	nematodes
	h	platyhelminths
	j	jellyfish and other cnidaria
	o	sponges
	t	other animal phyla
plants	d	dicotyledons
	l	monocotyledons
	v	other vascular plants
	c	non-vascular plants
	u	algae
other eukaryotes	g	fungi
	p	protists
prokaryotes	y	bacteria
	z	archaea