GO CAM Data Model (Python)
https://geneontology.github.io/gocam-py
Example yaml/json
id: gomodel:568b0f9600000284
title: Antibacterial innate immune response in the intestine via MAPK cascade (C.
elegans)
taxon: NCBITaxon:6239
status: production
comments:
- 'Automated change 2023-03-16: RO:0002212 replaced by RO:0002630'
- 'Automated change 2023-03-16: RO:0002213 replaced by RO:0002629'
activities:
- id: gomodel:568b0f9600000284/57ec3a7e00000079
enabled_by: WB:WBGene00006575
molecular_function:
evidence:
- term: ECO:0000314
reference: PMID:15625192
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2019-09-23'
provenances: []
term: GO:0035591
occurs_in:
evidence:
- term: ECO:0000314
reference: PMID:15625192
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-06-28'
term: GO:0005737
part_of:
evidence:
- term: ECO:0000315
reference: PMID:19837372
with_objects:
- WB:WBVar00241222|WB:WBVar00241223
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2021-07-08'
term: GO:0140367
causal_associations:
- evidence:
- term: ECO:0000315
reference: PMID:15123841
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-05-31'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/57ec3a7e00000109
- id: gomodel:568b0f9600000284/580685bd00000135
enabled_by: WB:WBGene00011979
molecular_function:
evidence:
- term: ECO:0000307
reference: GO_REF:0000015
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-11-12'
provenances: []
term: GO:0003674
occurs_in:
evidence:
- term: ECO:0000307
reference: GO_REF:0000015
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2021-11-29'
term: GO:0110165
part_of:
evidence:
- term: ECO:0000270
reference: PMID:17096597
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2021-07-08'
term: GO:0140367
- id: gomodel:568b0f9600000284/5745387b00000588
enabled_by: WB:WBGene00012019
molecular_function:
evidence:
- term: ECO:0000314
reference: PMID:17728253
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2019-09-23'
provenances: []
term: GO:0004674
occurs_in:
evidence:
- term: ECO:0000314
reference: PMID:17728253
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-07-01'
term: GO:0009898
part_of:
evidence:
- term: ECO:0000315
reference: PMID:19371715
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2016-10-19'
term: GO:0140367
causal_associations:
- evidence:
- term: ECO:0000315
reference: PMID:19371715
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-07-02'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/568b0f9600000285
- id: gomodel:568b0f9600000284/5b528b1100002286
enabled_by: WB:WBGene00006599
molecular_function:
evidence:
- term: ECO:0000501
reference: GO_REF:0000037
with_objects:
- UniProtKB-KW:KW-0723
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-09-06'
- term: ECO:0000315
reference: PMID:23072806
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-09-06'
- term: ECO:0000501
reference: GO_REF:0000002
with_objects:
- InterPro:IPR000961
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-09-06'
- term: ECO:0000318
reference: PAINT_REF:24356
with_objects:
- PANTHER:PTN000683254
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-09-06'
provenances: []
term: GO:0004674
part_of:
evidence:
- term: ECO:0000315
reference: PMID:22470487
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-09-06'
term: GO:0002225
causal_associations:
- evidence:
- term: ECO:0000316
reference: PMID:19371715
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-07-01'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/5745387b00000588
- id: gomodel:568b0f9600000284/57ec3a7e00000119
enabled_by: WB:WBGene00004758
molecular_function:
evidence:
- term: ECO:0000314
reference: PMID:11751572
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2019-09-23'
provenances: []
term: GO:0004708
occurs_in:
evidence:
- term: ECO:0000318
reference: PMID:21873635
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-06-28'
term: GO:0005737
part_of:
evidence:
- term: ECO:0000315
reference: PMID:12142542
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2020-10-28'
term: GO:0140367
causal_associations:
- evidence:
- term: ECO:0000315
reference: PMID:12142542
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-05-31'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/568b0f9600000285
- id: gomodel:568b0f9600000284/568b0f9600000285
enabled_by: WB:WBGene00004055
molecular_function:
evidence:
- term: ECO:0000314
reference: PMID:20369020
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2020-10-28'
provenances: []
term: GO:0004707
occurs_in:
evidence:
- term: ECO:0000314
reference: PMID:20133945
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-07-01'
term: GO:0005829
part_of:
evidence:
- term: ECO:0000315
reference: PMID:12142542
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2020-10-28'
term: GO:0140367
causal_associations:
- evidence:
- term: ECO:0000314
reference: PMID:20369020
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-05-31'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/568b0f9600000287
- id: gomodel:568b0f9600000284/57ec3a7e00000109
enabled_by: WB:WBGene00003822
molecular_function:
evidence:
- term: ECO:0000314
reference: PMID:11751572
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2019-09-23'
provenances: []
term: GO:0004709
occurs_in:
evidence:
- term: ECO:0000314
reference: PMID:15625192
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-06-28'
term: GO:0005737
part_of:
evidence:
- term: ECO:0000315
reference: PMID:12142542
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2020-10-28'
term: GO:0140367
causal_associations:
- evidence:
- term: ECO:0000315
reference: PMID:12142542
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-05-31'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/57ec3a7e00000119
- id: gomodel:568b0f9600000284/5b91dbd100000652
enabled_by: WB:WBGene00006923
molecular_function:
evidence:
- term: ECO:0000314
reference: PMID:15116070
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
provenances: []
term: GO:0017017
occurs_in:
evidence:
- term: ECO:0000250
reference: PMID:15116070
with_objects:
- UniProt:Q920R2
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-07-01'
term: GO:0005737
part_of:
evidence:
- term: ECO:0000316
reference: PMID:22554143
with_objects:
- WB:WBGene00002187
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
- term: ECO:0000315
reference: PMID:22554143
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
term: GO:1900425
causal_associations:
- evidence:
- term: ECO:0000315
reference: PMID:22554143
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-09'
predicate: RO:0002630
downstream_activity: gomodel:568b0f9600000284/5b91dbd100000659
- evidence:
- term: ECO:0000315
reference: PMID:15256594
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-06-20'
- term: ECO:0000315
reference: PMID:22554143
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2020-10-28'
predicate: RO:0002630
downstream_activity: gomodel:568b0f9600000284/568b0f9600000285
- id: gomodel:568b0f9600000284/5b91dbd100000659
enabled_by: WB:WBGene00002187
molecular_function:
evidence:
- term: ECO:0000353
reference: PMID:12435362
with_objects:
- WB:WBGene00001599
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
- term: ECO:0000353
reference: PMID:12435362
with_objects:
- WB:WBGene00001600
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
- term: ECO:0000353
reference: PMID:23437011
with_objects:
- WB:WBGene00001345
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
- term: ECO:0000353
reference: PMID:23437011
with_objects:
- WB:WBGene00001345
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
provenances: []
term: GO:0005515
occurs_in:
evidence:
- term: ECO:0000314
reference: PMID:17699606
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2019-07-01'
term: GO:0005737
part_of:
evidence:
- term: ECO:0000315
reference: PMID:22554143
with_objects:
- WB:WBGene00002187
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-08'
term: GO:1900181
- id: gomodel:568b0f9600000284/568b0f9600000287
enabled_by: WB:WBGene00000223
molecular_function:
evidence:
- term: ECO:0000250
reference: PMID:20369020
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-29'
provenances: []
term: GO:0000981
occurs_in:
evidence:
- term: ECO:0000314
reference: PMID:20369020
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-29'
term: GO:0005634
part_of:
evidence:
- term: ECO:0000315
reference: PMID:20369020
provenances:
- contributor: https://orcid.org/0000-0002-1706-4196
date: '2020-10-28'
term: GO:0140367
causal_associations:
- evidence:
- term: ECO:0000315
reference: PMID:20369020
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-09-26'
- term: ECO:0000315
reference: PMID:19837372
provenances:
- contributor: https://orcid.org/0000-0002-3013-9906
date: '2018-10-31'
predicate: RO:0002629
downstream_activity: gomodel:568b0f9600000284/580685bd00000135
objects:
- id: WB:WBGene00006599
label: tpa-1 Cele
- id: GO:0004674
label: protein serine/threonine kinase activity
- id: GO:0002225
label: positive regulation of antimicrobial peptide production
- id: ECO:0000501
label: evidence used in automatic assertion
- id: ECO:0000315
label: mutant phenotype evidence used in manual assertion
- id: ECO:0000318
label: biological aspect of ancestor evidence used in manual assertion
- id: WB:WBGene00006923
label: vhp-1 Cele
- id: GO:0017017
label: MAP kinase tyrosine/serine/threonine phosphatase activity
- id: GO:1900425
label: negative regulation of defense response to bacterium
- id: ECO:0000314
label: direct assay evidence used in manual assertion
- id: ECO:0000316
label: genetic interaction evidence used in manual assertion
- id: WB:WBGene00002187
label: kgb-1 Cele
- id: GO:0005515
label: protein binding
- id: GO:1900181
label: negative regulation of protein localization to nucleus
- id: ECO:0000353
label: physical interaction evidence used in manual assertion
- id: ECO:0000250
label: sequence similarity evidence used in manual assertion
- id: ECO:0000307
label: no evidence data found used in manual assertion
- id: GO:0005737
label: cytoplasm
- id: GO:0005829
label: cytosol
- id: GO:0009898
label: cytoplasmic side of plasma membrane
- id: WB:WBGene00000223
label: atf-7 Cele
- id: WB:WBGene00004055
label: pmk-1 Cele
- id: WB:WBGene00004758
label: sek-1 Cele
- id: GO:0004707
label: MAP kinase activity
- id: GO:0000981
label: DNA-binding transcription factor activity, RNA polymerase II-specific
- id: GO:0005634
label: nucleus
- id: GO:0016045
label: detection of bacterium
- id: GO:0003674
label: molecular_function
- id: GO:0035591
label: signaling adaptor activity
- id: WB:WBGene00006575
label: tir-1 Cele
- id: GO:0004709
label: MAP kinase kinase kinase activity
- id: WB:WBGene00003822
label: nsy-1 Cele
- id: GO:0004708
label: MAP kinase kinase activity
- id: WB:WBGene00012019
label: dkf-2 Cele
- id: GO:0140367
label: antibacterial innate immune response
- id: WB:WBGene00011979
label: sysm-1 Cele
- id: ECO:0000270
label: expression pattern evidence used in manual assertion
- id: GO:0110165
label: cellular anatomical entity
Additional dependencies are required for CX2 conversion. Install them with the cx2 extras:
pip install gocam-py[cx2]Important
This will attempt to install the pygraphviz package, which requires Graphviz (version 2.46 or later) to be installed. If you are on MacOS and you installed Graphviz with Homebrew, you may need to set the following environment variables first so that pygraphviz can find the Graphviz installation:
export GRAPHVIZ_PREFIX=$(brew --prefix graphviz)
export CFLAGS="-I${GRAPHVIZ_PREFIX}/include"
export LDFLAGS="-L${GRAPHVIZ_PREFIX}/lib"Then you can convert a GO-CAM model to CX2 with the convert subcommand:
gocam convert -O cx2 model.yamlSee the CLI help for more information and options:
gocam convert --help