gocam 0.0.1__tar.gz

gocam-0.0.1/LICENSE

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+
+Copyright (c) 2024, My Name
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of pytest-gocam nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

gocam-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: gocam
+Version: 0.0.1
+Summary: GO CAM Data Model (Python)
+License: BSD-3
+Author: The Gene Ontology Consortium
+Author-email: help@geneontology.org
+Requires-Python: >=3.9,<4.0
+Classifier: License :: Other/Proprietary License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: click (>=8,<9)
+Requires-Dist: linkml-runtime (>=1.1.24,<2.0.0)
+Requires-Dist: pydantic (>=2,<3)
+Requires-Dist: pyyaml (>=6,<7)
+Requires-Dist: requests (>=2,<3)
+Description-Content-Type: text/markdown
+
+# gocam
+
+GO CAM Data Model (Python)
+
+## Website
+
+[https://geneontology.github.io/gocam-py](https://geneontology.github.io/gocam-py)
+
+## About
+
+Example yaml/json
+
+```yaml
+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
+
+```
+
+