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Specification for the Biological Expression Language
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Default namespace implementation for BEL 2.0 #10

Open abargnesi opened 8 years ago

abargnesi commented 8 years ago

Protein modification and activity types are now namespace values. The specification mentions a default namespace and implies that it should have both sets of protein modification and activity types.

Set of values:

# Protein Modification types
Ac
acetylation
ADPRib  
ADP-ribosylation
ADP-rybosylation
adenosine diphosphoribosyl
Farn
farnesylation
Gerger  
geranylgeranylation
Glyco   
glycosylation
Hy  
hydroxylation
ISG 
ISGylation
ISG15-protein conjugation
Me  
methylation
Me1 
monomethylation
mono-methylation
Me2 
dimethylation
di-methylation
Me3 
trimethylation
tri-methylation
Myr 
myristoylation
Nedd    
neddylation
NGlyco  
N-linked glycosylation
NO  
Nitrosylation
OGlyco  
O-linked glycosylation
Palm    
palmitoylation
Ph  
phosphorylation
Sulf    
sulfation
sulphation
sulfur addition
sulphur addition
sulfonation
sulphonation
Sumo    
SUMOylation
Ub  
ubiquitination
ubiquitinylation
ubiquitylation
UbK48   
Lysine 48-linked polyubiquitination
UbK63   
Lysine 63-linked polyubiquitination
UbMono  
monoubiquitination
UbPoly  
polyubiquitination

# Activity types (BEL 1.0 functions)
act
molecularActivity
cat
catalyticActivity
chap
chaperoneActivity
gtp
gtpBoundActivity
kin
kinaseActivity
pep
peptidaseActivity
phos
phosphataseActivity
ribo
ribosylationActivity
tscript
transcriptionalActivity
tport
transportActivity

Is this set accurate with respect to the BEL 2.0 specification? This default namespace is not defined as part of the specification so I'm unsure.

Also it seems reasonable to implement this as a namespace supported by OpenBEL. Users could then use this namespace as the DEFAULT in BEL Script using:

DEFINE DEFAULT NAMESPACE AS URI "http://www.openbel.org/bel/namespace/default"

act(p(HGNC:AKT1), ma(kin))
p(HGNC:AKT1, pmod(phosphorylation, Ser, 473))

What about the amino acid? Should the usual suspects be included in the default namespace?

/cc @ncatlett @wshayes

ncatlett commented 8 years ago

The protein modification and activity types were moved out of the specification to a namespace to facilitate the addition of new modifications and activities without requiring a BEL version change.

It should be OK to leave the amino acids as part of the BEL specification because they are unlikely to change. The intent is to support both 1 letter and 3 letter amino acid codes (and treat as equivalent, similar to function short/long forms).