Re: Digest for openbel-discuss@googlegroups.com - 1 update in 1 topic

[William Hayes]

Thanks Christian, I’ll make the changes unless you’d be willing to make a Pull request on the source document: https://github.com/OpenBEL/language/blob/master/version_1.0/bel_specification_version_1.0.adoc  I would still need to build the html document and re-publish.

On Jan 16, 2018, at 10:35 PM, openbel...@googlegroups.com wrote:

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• Wrong statement examples in specification BEL 1.0 - 1 Update

Wrong statement examples in specification BEL 1.0

Christian Ebeling <chr.e...@gmail.com>: Jan 16 12:40PM -0800 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

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