GAP/GPAD example, most basic, 57ea2dae00000004, regulation example

[ukemi]

GAF model 57ea2dae00000004
MGI MGI:1916888 Enho Mmus GO:0051055 PMID:22318315 IMP MGI:MGI:5781010 P gene taxon:10090 20160927 GO_Noctua
MGI MGI:1916888 Enho Mmus GO:0046676 PMID:22318315 IMP MGI:MGI:5781010 P gene taxon:10090 20160927 GO_Noctua
MGI MGI:1916888 Enho Mmus GO:0046627 PMID:22318315 IMP MGI:MGI:5781010 P gene taxon:10090 20160927 GO_Noctua
MGI MGI:107606 Srebf1 Mmus GO:0000978 PMID:17074803 IDA F gene taxon:10090 20160927 GO_Noctua
MGI MGI:98239 Scd1 Mmus GO:0004768 PMID:16443825 IDA F gene taxon:10090 20160927 GO_Noctua
MGI MGI:98239 Scd1 Mmus GO:0008610 PMID:16443825 TAS P gene taxon:10090 20160927 GO_Noctua
MGI MGI:1916888 Enho Mmus GO:0051354 PMID:22318315 IMP MGI:MGI:5781010 P gene taxon:10090 20160927 GO_Noctua negatively_regulates(GO:0004768) MGI MGI:1916888 Enho Mmus GO:0043433 PMID:22318315 IMP MGI:MGI:5781010 P gene taxon:10090 20160927 GO_Noctua negatively_regulates(GO:0000978) MGI MGI:107606 Srebf1 Mmus GO:0051353 PMID:22318315 TAS P gene taxon:10090 20160927 GO_Noctua positively_regulates(GO:0004768) MGI MGI:1916888 Enho Mmus GO:0005179 PMID:22318315 IMP MGI:MGI:5781010 F gene taxon:10090 20160927 GO_Noctua

GPAD model 57ea2dae00000004
MGI MGI:1916888 GO:0051055 PMID:22318315 MGI:MGI:5781010 20160927 GO_Noctua
MGI MGI:1916888 GO:0046676 PMID:22318315 MGI:MGI:5781010 20160927 GO_Noctua
MGI MGI:1916888 GO:0046627 PMID:22318315 MGI:MGI:5781010 20160927 GO_Noctua
MGI MGI:107606 GO:0000978 PMID:17074803 20160927 GO_Noctua
MGI MGI:98239 GO:0004768 PMID:16443825 20160927 GO_Noctua
MGI MGI:98239 GO:0008610 PMID:16443825 20160927 GO_Noctua
MGI MGI:1916888 GO:0051354 PMID:22318315 MGI:MGI:5781010 20160927 GO_Noctua
MGI MGI:1916888 GO:0043433 PMID:22318315 MGI:MGI:5781010 20160927 GO_Noctua
MGI MGI:107606 GO:0051353 PMID:22318315 20160927 GO_Noctua
MGI MGI:1916888 GO:0005179 PMID:22318315 MGI:MGI:5781010 20160927 GO_Noctua

[balhoff]

I'm getting 36 lines out of this one. Sorry about the duplicates within the annotation extension; there are some problems with extra labels in the graphstore.

 "pr_type" , "rel_label" , "target_type" , "target_type_label" , "extensions" , "evidence_type" , "with" , "contributor" , "date" , "source" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "enables" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "enables" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "MGI:MGI:5426758" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "enables" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22331133" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "enables" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in regulation of" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process),enabled by(Srebf1 Mmus),enabled by(Srebf1)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in regulation of" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process),enabled by(Srebf1 Mmus),enabled by(Srebf1)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "MGI:MGI:5426758" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in regulation of" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process),enabled by(Srebf1 Mmus),enabled by(Srebf1)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22331133" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in regulation of" , "http://purl.obolibrary.org/obo/GO_0000978" , "RNA polymerase II core promoter proximal region sequence-specific DNA binding" , "causally downstream of(insulin receptor signaling pathway),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),positively regulated by(insulin receptor signaling pathway),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),directly activates(stearoyl-CoA 9-desaturase activity),regulated by(hormone activity),positively regulates(lipid biosynthetic process),enabled by(Srebf1 Mmus),enabled by(Srebf1)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0042593" , "glucose homeostasis" , "has part(protein serine/threonine kinase activity),has_part(protein serine/threonine kinase activity),overlaps(protein serine/threonine kinase activity),has part(protein phosphorylation),has_part(protein phosphorylation),has part(peptidyl-serine phosphorylation),has_part(peptidyl-serine phosphorylation),has part(peptidyl-threonine phosphorylation),has_part(peptidyl-threonine phosphorylation),overlaps(glucose homeostasis),has part(insulin receptor signaling pathway),has_part(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),has participant(AKT kinase)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0008286" , "insulin receptor signaling pathway" , "has part(protein serine/threonine kinase activity),has_part(protein serine/threonine kinase activity),overlaps(protein serine/threonine kinase activity),positively regulates(RNA polymerase II core promoter proximal region sequence-specific DNA binding),has part(peptidyl-serine phosphorylation),has_part(peptidyl-serine phosphorylation),has part(peptidyl-threonine phosphorylation),has_part(peptidyl-threonine phosphorylation),part of(glucose homeostasis),part_of(glucose homeostasis),overlaps(insulin receptor signaling pathway),has part(protein phosphorylation),has_part(protein phosphorylation),regulates(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),regulates(lipid biosynthetic process),causally downstream of(insulin secretion),has participant(AKT kinase)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0008286" , "insulin receptor signaling pathway" , "has part(protein serine/threonine kinase activity),has_part(protein serine/threonine kinase activity),overlaps(protein serine/threonine kinase activity),positively regulates(RNA polymerase II core promoter proximal region sequence-specific DNA binding),has part(peptidyl-serine phosphorylation),has_part(peptidyl-serine phosphorylation),has part(peptidyl-threonine phosphorylation),has_part(peptidyl-threonine phosphorylation),part of(glucose homeostasis),part_of(glucose homeostasis),overlaps(insulin receptor signaling pathway),has part(protein phosphorylation),has_part(protein phosphorylation),regulates(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),regulates(lipid biosynthetic process),causally downstream of(insulin secretion),has participant(AKT kinase)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0008286" , "insulin receptor signaling pathway" , "has part(protein serine/threonine kinase activity),has_part(protein serine/threonine kinase activity),overlaps(protein serine/threonine kinase activity),positively regulates(RNA polymerase II core promoter proximal region sequence-specific DNA binding),has part(peptidyl-serine phosphorylation),has_part(peptidyl-serine phosphorylation),has part(peptidyl-threonine phosphorylation),has_part(peptidyl-threonine phosphorylation),part of(glucose homeostasis),part_of(glucose homeostasis),overlaps(insulin receptor signaling pathway),has part(protein phosphorylation),has_part(protein phosphorylation),regulates(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),regulates(lipid biosynthetic process),causally downstream of(insulin secretion),has participant(AKT kinase)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "involved in positive regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Enho Mmus),has causal agent(Enho),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "involved in positive regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Enho Mmus),has causal agent(Enho),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "involved in positive regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Enho Mmus),has causal agent(Enho),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "MGI:MGI:3623168" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "involved in positive regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Enho Mmus),has causal agent(Enho),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:16443825" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "MGI:MGI:3623168" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),enabled by(Scd1 Mmus),enabled by(Scd1),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:16443825" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:98239" , "enables" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Enho Mmus),has causal agent(Enho)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:98239" , "enables" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Enho Mmus),has causal agent(Enho)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:98239" , "enables" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Enho Mmus),has causal agent(Enho)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "MGI:MGI:3623168" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:98239" , "enables" , "http://purl.obolibrary.org/obo/GO_0004768" , "stearoyl-CoA 9-desaturase activity" , "positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),immediately causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),part of(lipid biosynthetic process),part_of(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),has causal agent(Enho Mmus),has causal agent(Enho)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:16443825" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "enables" , "http://purl.obolibrary.org/obo/GO_0005179" , "hormone activity" , "precedes(protein serine/threonine kinase activity),regulates(RNA polymerase II core promoter proximal region sequence-specific DNA binding),precedes(peptidyl-serine phosphorylation),precedes(peptidyl-threonine phosphorylation),negatively regulates(glucose homeostasis),negatively regulates(insulin receptor signaling pathway),precedes(protein phosphorylation),negatively regulates(stearoyl-CoA 9-desaturase activity),negatively regulates(lipid biosynthetic process),negatively regulates(insulin secretion)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "enables" , "http://purl.obolibrary.org/obo/GO_0005179" , "hormone activity" , "precedes(protein serine/threonine kinase activity),regulates(RNA polymerase II core promoter proximal region sequence-specific DNA binding),precedes(peptidyl-serine phosphorylation),precedes(peptidyl-threonine phosphorylation),negatively regulates(glucose homeostasis),negatively regulates(insulin receptor signaling pathway),precedes(protein phosphorylation),negatively regulates(stearoyl-CoA 9-desaturase activity),negatively regulates(lipid biosynthetic process),negatively regulates(insulin secretion)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "involved in positive regulation of" , "http://purl.obolibrary.org/obo/GO_0008610" , "lipid biosynthetic process" , "preceded_by(protein serine/threonine kinase activity),preceded by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),has part(stearoyl-CoA 9-desaturase activity),has_part(stearoyl-CoA 9-desaturase activity),overlaps(lipid biosynthetic process),positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:107606" , "involved in positive regulation of" , "http://purl.obolibrary.org/obo/GO_0008610" , "lipid biosynthetic process" , "preceded_by(protein serine/threonine kinase activity),preceded by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),has part(stearoyl-CoA 9-desaturase activity),has_part(stearoyl-CoA 9-desaturase activity),overlaps(lipid biosynthetic process),positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0008610" , "lipid biosynthetic process" , "preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),has part(stearoyl-CoA 9-desaturase activity),has_part(stearoyl-CoA 9-desaturase activity),overlaps(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0008610" , "lipid biosynthetic process" , "preceded by(protein serine/threonine kinase activity),preceded_by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),has part(stearoyl-CoA 9-desaturase activity),has_part(stearoyl-CoA 9-desaturase activity),overlaps(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Scd1 Mmus),has causal agent(Scd1)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:98239" , "involved in" , "http://purl.obolibrary.org/obo/GO_0008610" , "lipid biosynthetic process" , "preceded_by(protein serine/threonine kinase activity),preceded by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),has part(stearoyl-CoA 9-desaturase activity),has_part(stearoyl-CoA 9-desaturase activity),overlaps(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho)" , "http://purl.obolibrary.org/obo/ECO_0000304" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:98239" , "involved in" , "http://purl.obolibrary.org/obo/GO_0008610" , "lipid biosynthetic process" , "preceded_by(protein serine/threonine kinase activity),preceded by(protein serine/threonine kinase activity),preceded by(peptidyl-serine phosphorylation),preceded_by(peptidyl-serine phosphorylation),preceded by(peptidyl-threonine phosphorylation),preceded_by(peptidyl-threonine phosphorylation),preceded by(protein phosphorylation),preceded_by(protein phosphorylation),has part(stearoyl-CoA 9-desaturase activity),has_part(stearoyl-CoA 9-desaturase activity),overlaps(lipid biosynthetic process),has causal agent(Srebf1 Mmus),has causal agent(Srebf1),positively regulated by(RNA polymerase II core promoter proximal region sequence-specific DNA binding),causally downstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),regulated by(insulin receptor signaling pathway),causally downstream of(insulin receptor signaling pathway),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally downstream of(insulin secretion),has causal agent(Enho Mmus),has causal agent(Enho)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-28" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0030073" , "insulin secretion" , "causally upstream of(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally upstream of(lipid biosynthetic process),precedes(protein serine/threonine kinase activity),causally upstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),precedes(peptidyl-serine phosphorylation),precedes(peptidyl-threonine phosphorylation),causally upstream of(insulin receptor signaling pathway),precedes(protein phosphorylation)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0030073" , "insulin secretion" , "causally upstream of(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally upstream of(lipid biosynthetic process),precedes(protein serine/threonine kinase activity),causally upstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),precedes(peptidyl-serine phosphorylation),precedes(peptidyl-threonine phosphorylation),causally upstream of(insulin receptor signaling pathway),precedes(protein phosphorylation)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0030073" , "insulin secretion" , "precedes(protein serine/threonine kinase activity),causally upstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),precedes(peptidyl-serine phosphorylation),precedes(peptidyl-threonine phosphorylation),causally upstream of(insulin receptor signaling pathway),precedes(protein phosphorylation),causally upstream of(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally upstream of(lipid biosynthetic process)" , "http://purl.obolibrary.org/obo/ECO_0000315" , "MGI:MGI:5781010" , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,
 "http://www.informatics.jax.org/accession/MGI:MGI:1916888" , "involved in negative regulation of" , "http://purl.obolibrary.org/obo/GO_0030073" , "insulin secretion" , "precedes(protein serine/threonine kinase activity),causally upstream of(RNA polymerase II core promoter proximal region sequence-specific DNA binding),precedes(peptidyl-serine phosphorylation),precedes(peptidyl-threonine phosphorylation),causally upstream of(insulin receptor signaling pathway),precedes(protein phosphorylation),causally upstream of(stearoyl-CoA 9-desaturase activity),negatively regulated by(hormone activity),causally downstream of(hormone activity),causally upstream of(lipid biosynthetic process)" , "http://purl.obolibrary.org/obo/ECO_0000314" ,  , "http://orcid.org/0000-0001-7476-6306" , "2016-09-27" , "PMID:22318315" ,

[balhoff]

Output from test job: https://build.berkeleybop.org/job/export-lego-to-gpad-sparql/lastSuccessfulBuild/artifact/legacy/gpad/57ea2dae00000004.gpad/*view*/

[ukemi]

Sooooo close, but:

MGI MGI:1916888 involved_in_negative_regulation_of GO:0030073 PMID:22318315 ECO:0000314 20160927 GO_Noctua precedes(GO:0004674),precedes(GO:0006468),precedes(GO:0018105),precedes(GO:0018107),causally_upstream_of(GO:0000978),causally_upstream_of(GO:0004768),causally_upstream_of(GO:0008286),causally_upstream_of(GO:0008610) contributor=http://orcid.org/0000-0001-7476-6306

should be (I think):

MGI MGI:1916888 involved_in GO:0046676 MGI:MGI:3623168 ECO:0000314 20160927 GO_Noctua part_of(GO:0008610)|preceded_by(GO:0004674)|preceded_by(GO:0006468)|preceded_by(GO:0018105)|preceded_by(GO:0018107)|regulated_by(GO:0008286) contributor=http://orcid.org/0000-0001-7476-6306

Since the negative regulation of GO:0030073 term exists in the ontology.

Will look at this more closely tomorrow.

[balhoff]

Thanks! That link should continue to update as the code changes.

[balhoff]

This is a potential example for needed annotation deepening. Currently missing "involved_in negative regulation of..."

[balhoff]

@ukemi I updated your comment to put the right ID for 'insulin secretion'—you had grabbed a different row. If you run ELK in Noctua right now, is there a node which you expect to be inferred as 'negative regulation of insulin secretion'? Right now there is:

'hormone activity' enabled_by 'Enho Mmus' 'hormone activity' negatively_regulates 'insulin secretion'

Via ELK this 'hormone activity' is inferred to also be a 'molecular function regulator'.

RDFox/Jena infer that 'Enho Mmus' involved_in_negative_regulation_of 'insulin secretion'. So my question is, do you think one of the individuals in the model should be inferred to be a 'negative regulation of insulin secretion', or instead you're thinking that the model entails the existence of an unstated 'negative regulation of insulin secretion'? Hope that makes sense.

[balhoff]

'negative regulation of insulin secretion' == 'biological regulation' and (negatively_regulates some 'insulin secretion')

But 'hormone activity' is not under 'biological regulation' and it doesn't look like this is inferred from any property domains.

[cmungall]

@balhoff brings up a good point. Any idea how to handle this @dosumis

[ukemi]

I think at one point we had thought about something like biological regulation = BFO process and regulates some BFO process I think I played around with it, but can't remember the results.

[ukemi]

but that wouldn't include regulation qualities and wouldn't restrict biological regulation to a BP.

[ukemi]

Thinking about this again last night, maybe we approaching it from the wrong end. Maybe we shouldn't try to make the ontology fit the model, maybe the model needs to fit the ontology. In the current model, we have a function directly regulating a process. As Jim discovered, this doesn't fit the definition of regulation in GO since biological regulation is a BP and regulation of X is a biologcal regulation that regulates some X. What if in the model, whenever we wanted to express the regulation of a BP, we required that it be done by another BP? This would match the structure of the ontology. See this test model gomodel:586fc17a00000366

[cmungall]

Let's leave aside qualities for the moment; but yes, you have it right. Either the modeling patterns have to change or the ontology axioms have to change. If the ontology axiom changes such that the genus is a BFO process then we suddenly get lots of is-a crossings between MF and BP. Not necessarily bad, but a big change.

I think the model-level change would be fine, it seems logical. It may be seen as 'busy work'. We also need conventions as to where to put the evidence.

NOTE I just updated this ticket, ignore my previous comments about property chains which I've removed

[ukemi]

Shall we put this on the agenda for Wednesday's GPAD call?

[dosumis]

Shall we put this on the agenda for Wednesday's GPAD call?

Yes please, but can you put together a quick summary or the issue. I've been trying to get a clear picture of the issue, but finding the ticket a bit hard to follow.

Cheers.

[balhoff]

Basically, from an assertion:

[a 'Enho'] involved_in_negative_regulation_of [a 'insulin secretion']

how can you infer:

[a 'Enho'] involved_in [a 'negative regulation of insulin secretion']

For one thing there is no instance of 'negative regulation of insulin secretion' in the model, asserted or inferred.

[dosumis]

Why would a model assert involved_in_negative_regulation_of rather than than asserting that an instance of some class (call it X) 'negatively regulates' 'insulin secretion' => inference 'negative regulation of insulin secretion' on node X.

[balhoff]

Sorry, I was too terse. The involved_in_negative_regulation_of statement is inferred from these asserted statements:

[a 'hormone activity'] enabled_by [a 'Enho'];
    negatively_regulates [a 'insulin secretion'] .

So node X, the 'hormone activity', is a 'molecular function', while 'negative regulation of insulin secretion' is a 'biological process'.

[vanaukenk]

The issue here is related to changes in the genus of regulation terms in the ontology. Needs further investigation.