Wrong statement examples in specification BEL 1.0

[Christian Ebeling]

Dear all,

I found following errors in examples of the BEL 1.0 specification document:
http://openbel.org/language/version_1.0/bel_specification_version_1.0.html

If this is not the offical link to the BEL 1.0, please delete this document and provide the correct link. If this is the correct link please correct the errors or comment if I'm wrong.

Many thanks in advance
Christian Ebeling


1. kinase() not exists, only kinaseActivity() or kin()

http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_line_continuation_operator


kinase(p(HGNC:IGFI1R)) -| (p(HGNC:BNIP3) -> bp(GO:apoptosis))

should be:

kin(p(HGNC:IGFI1R)) -| (p(HGNC:BNIP3) -> bp(GO:apoptosis))



kinase(p(HGNC:IGFI1R)) -| \
 (p(HGNC:BNIP3) -> bp(GO:apoptosis))
 
should be:

kin(p(HGNC:IGFI1R)) -| \
 (p(HGNC:BNIP3) -> bp(GO:apoptosis))


2. example statement not follows defined rule

rule: translocation(A, ns1:v1, ns2:v2)
http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_translocations
Here are addtional round brackets around  GO:"cell surface" and GO:endosome which infringe the rule


translocation(p(HGNC:EGFR), (GO:"cell surface"), (GO:endosome))

should be:

translocation(p(HGNC:EGFR), GO:"cell surface", GO:endosome)


3. Closing bracket is missing

reaction(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide"), a(CHEBI: "oxygen"))

should be:

reaction(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide"), a(CHEBI: "oxygen")))



http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_protein_protein_interactions

complexAbundance(proteinAbundance(HGNC:AKT1S1), proteinAbundance(HGNC:MTOR)

should be:

complexAbundance(proteinAbundance(HGNC:AKT1S1), proteinAbundance(HGNC:MTOR))


4. p is missing in pmod

p(HGNC:CLSPN) => (kin(p(HGNC:ATR)) => p(HGNC:CHEK1, mod(P)))

should be:

p(HGNC:CLSPN) => (kin(p(HGNC:ATR)) => p(HGNC:CHEK1, pmod(P)))


p(HGNC:GSK3B, mod(P, S, 9)) =| kin(p(HGNC:GSK3B))

should be:

p(HGNC:GSK3B, pmod(P, S, 9)) =| kin(p(HGNC:GSK3B))


5. Missing quotation marks

http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_complexes

complexAbundance(NCH:IkappaB Kinase Complex)

should be:

complexAbundance(NCH:"IkappaB Kinase Complex")


6. Misspelling

proteinAbudance instead of proteinAbundance
cellSurfaceExpression instead of cellSurface


http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_translocations_2

cellSurface(proteinAbudance(RGD:Fas))

should be:

cellSurfaceExpression(proteinAbundance(RGD:Fas))



http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_ligand_and_receptor

proteinAbundance(HGNC:AREG) directlyIncreases \
 kinaseActivity(proteinAbudance(HGNC:EGFR))

should be:

proteinAbundance(HGNC:AREG) directlyIncreases \
 kinaseActivity(proteinAbundance(HGNC:EGFR))
 


7. CLEAR is no BEL keyword


http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_biomarkers

CLEAR CardiovascularSystem

should be:

UNSET CardiovascularSystem



8. Set value without surrounding quotation marks


It's not complitly clear if value needs surrounding quotation marks because this is not defined in ...
http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_set
But all examples have surrounding quotation marks. Please clarify this.

http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_prognostic_biomarkers
SET BodyRegion = Mouth

should be:

SET BodyRegion = "Mouth"


9. p is missing

http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#situation_one_protein_modification_initiates_additional_modifications

p(HGNC:CTNNB1, pmod(P, S, 45)) => \
    (kin(p(PFH:"GSK3 Family")) => (HGNC:CTNNB1, pmod(P, T, 41)))

should be:

p(HGNC:CTNNB1, pmod(P, S, 45)) => \
    (kin(p(PFH:"GSK3 Family")) => p(HGNC:CTNNB1, pmod(P, T, 41)))


10. value should be in quotation marks


http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#reversible_metabolic_reaction

cat(p(HGNC:HSD11B1)) => \
 rxn(reactants(a(CHEBI:NADPH), a(CHEBI:cortisone)), products(a(CHEBI:NADP(+)), a(CHEBI:cortisol)))

should be:

cat(p(HGNC:HSD11B1)) => \
 rxn(reactants(a(CHEBI:NADPH), a(CHEBI:cortisone)), products(a(CHEBI:"NADP(+)"), a(CHEBI:cortisol))
 
 
cat(p(HGNC:HSD11B1)) => \
 rxn(reactants(a(CHEBI:NADP(+)), a(CHEBI:cortisol)), products(a(CHEBI:NADPH), a(CHEBI:cortisone)))
 
should be:

cat(p(HGNC:HSD11B1)) => \
 rxn(reactants(a(CHEBI:"NADP(+)"), a(CHEBI:cortisol)), products(a(CHEBI:NADPH), a(CHEBI:cortisone)))
 
Can you please link me to the rule in the specification where it is defined when I can skip the surrounding quotation marks

[William Hayes]

Hi Christian,

All mistakes pointed out and the missing quote specification for SET Control Records were fixed/added and updates were published.  You can review the changes here:  https://github.com/OpenBEL/language/issues/18

Thanks for taking the time to find and report these.

Best,

Wm

[William Hayes]

When to quote and not quote Namespace values:  http://openbel.org/language/version_1.0/bel_specification_version_1.0.html#_quotes

On Tuesday, January 16, 2018 at 3:40:09 PM UTC-5, Christian Ebeling wrote:

[Christian Ebeling]

Dear William,

many thanks for the hint, I missed that.

Best regards
Christian

[Natalie Catlett]

Christian and William,

There are a few values that need to be quoted as well, that don't appear to be documented in William's link. I am not sure on the full list, but MGI 'a' and HGNC 'SET' both require quotes.

This may be useful (includes my function to add quotations for values that caused trouble) -  https://github.com/OpenBEL/resource-generator/blob/master/bel_functions.py

Best,

Natalie

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[Natalie Catlett]

I found the documentation on the reserved control words in the BEL Script 1.0 section of the OpenBEL wiki - https://wiki.openbel.org/display/BLD/Language+Characteristics

I'm pretty sure that all of these would require quotations, if they are used as namespace values in BEL terms.

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