├── .github └── workflows │ ├── goex.yml │ ├── qc.yml │ ├── refresh-readmes.yaml │ └── trigger-website-rebuild.yaml ├── .gitignore ├── LICENSE ├── README.goex.yaml ├── README.md ├── configurations ├── jenkins │ └── artifacts │ │ └── index.html └── supervisord │ ├── README.org │ ├── barista.conf │ ├── minerva.conf │ └── owlservices.conf ├── docs ├── gaf_validation.md ├── go-arch-2018.graffle ├── go-arch-2018.png ├── go-consortium-dataflow.graffle │ ├── data.plist │ ├── image1.tiff │ └── image3.tiff ├── go-consortium-dataflow.png ├── gorules_test_errors.gaf └── gorules_test_errors.gpad ├── documentation ├── application-logins.md ├── how-do-i-edit-metadata.md └── images │ ├── authorize-tg-screenshot.png │ └── login-tg-screenshot.png ├── drupal7 ├── bootstrap │ ├── amigo.css │ ├── amigo2.js │ ├── bbop.css │ ├── bbop.js │ ├── bootstrap.info │ ├── go-overlay.css │ ├── go-overlay.js │ └── jquery.tablesorter.min.js ├── migrate.org └── update.org ├── fs-to-s3 ├── README.org ├── fs-to-s3.js └── package.json ├── graphstore ├── gocam.svg ├── graphstore.svg ├── load_cam.svg ├── noctua_load.svg ├── rdf-graph.svg ├── rule-runner │ ├── README.md │ ├── example.yml │ ├── requirements.txt │ ├── rulerunner │ │ ├── __init__.py │ │ ├── main.py │ │ └── rule.py │ ├── setup.py │ └── tests │ │ ├── __init__.py │ │ ├── data │ │ ├── gorule-0000006-test.ttl │ │ ├── gorule-0000007-test.ttl │ │ └── gorule-0000014-test.ttl │ │ └── test_rules.py ├── simple_load.svg └── triplestore_info.md ├── metadata ├── README.md ├── biological_entity_mapping.schema.yaml ├── biological_entity_mapping.yaml ├── datasets.schema.yaml ├── datasets │ ├── README.md │ ├── cgd.yaml │ ├── dictybase.yaml │ ├── ecocyc.yaml │ ├── fb.yaml │ ├── genedb.yaml │ ├── goa.yaml │ ├── japonicusdb.yaml │ ├── mgi.yaml │ ├── noctua.yaml │ ├── paint.yaml │ ├── pombase.yaml │ ├── pseudocap.yaml │ ├── reactome.yaml │ ├── rgd.yaml │ ├── rnacentral.yaml │ ├── sgd.yaml │ ├── sgn.yaml │ ├── tair.yaml │ ├── wb.yaml │ ├── xenbase.yaml │ ├── xenbase_xlae.yaml │ ├── xenbase_xtro.yaml │ └── zfin.yaml ├── db-xrefs.md ├── db-xrefs.schema.yaml ├── db-xrefs.yaml ├── eco-usage-constraints.schema.yaml ├── eco-usage-constraints.yaml ├── extensions-constraints.schema.yaml ├── extensions-constraints.yaml ├── go-reference-species.schema.yaml ├── go-reference-species.yaml ├── goex.linkmlschema.yaml ├── goex.yaml ├── gorefs.schema.yaml ├── gorefs.yaml ├── group-contacts.csv ├── groups.schema.yaml ├── groups.yaml ├── retracted-publications.txt ├── rules.schema.yaml ├── rules │ ├── ABOUT.md │ ├── Makefile │ ├── README.md │ ├── SOP.md │ ├── gorule-0000001.md │ ├── gorule-0000002.md │ ├── gorule-0000003.md │ ├── gorule-0000004.md │ ├── gorule-0000005.md │ ├── gorule-0000006.md │ ├── gorule-0000007.md │ ├── gorule-0000008.md │ ├── gorule-0000009.md │ ├── gorule-0000010.md │ ├── gorule-0000011.md │ ├── gorule-0000013.md │ ├── gorule-0000014.md │ ├── gorule-0000015.md │ ├── gorule-0000016.md │ ├── gorule-0000017.md │ ├── gorule-0000018.md │ ├── gorule-0000019.md │ ├── gorule-0000020.md │ ├── gorule-0000021.md │ ├── gorule-0000022.md │ ├── gorule-0000023.md │ ├── gorule-0000024.md │ ├── gorule-0000025.md │ ├── gorule-0000026.md │ ├── gorule-0000027.md │ ├── gorule-0000028.md │ ├── gorule-0000029.md │ ├── gorule-0000030.md │ ├── gorule-0000031.md │ ├── gorule-0000032.md │ ├── gorule-0000033.md │ ├── gorule-0000035.md │ ├── gorule-0000036.md │ ├── gorule-0000037.md │ ├── gorule-0000038.md │ ├── gorule-0000039.md │ ├── gorule-0000042.md │ ├── gorule-0000043.md │ ├── gorule-0000044.md │ ├── gorule-0000045.md │ ├── gorule-0000046.md │ ├── gorule-0000047.md │ ├── gorule-0000048.md │ ├── gorule-0000049.md │ ├── gorule-0000050.md │ ├── gorule-0000051.md │ ├── gorule-0000053.md │ ├── gorule-0000054.md │ ├── gorule-0000055.md │ ├── gorule-0000056.md │ ├── gorule-0000057.md │ ├── gorule-0000058.md │ ├── gorule-0000059.md │ ├── gorule-0000061.md │ ├── gorule-0000062.md │ ├── gorule-0000063.md │ ├── gorule-0000064.md │ └── gorule-0000065.md ├── users-groups-context.yaml ├── users.schema.yaml ├── users.yaml └── users_sf2gh.json ├── package.json ├── pipeline ├── Makefile ├── README.md ├── conf │ ├── blazegraph.properties │ └── readonly_cors.xml ├── environment.sh ├── exclude.txt ├── go-association-transit │ ├── Makefile │ ├── README.md │ ├── goat │ │ ├── __init__.py │ │ ├── cached_ontology.py │ │ ├── goat.py │ │ ├── parse_into_gpad.py │ │ └── sources.py │ ├── requirements.txt │ ├── requirements.txt.back │ └── setup.py ├── go-graphstore.owl ├── group-timing.py ├── pom.xml ├── requirements.txt ├── rules.dlog ├── sparql │ ├── delete │ │ └── delete_non_production.sparql │ ├── insert │ │ ├── insert_inferred_graph_link.sparql │ │ ├── insert_inferred_models_metadata.sparql │ │ ├── insert_noctua_metadata.sparql │ │ ├── insert_ontology_metadata.sparql │ │ └── insert_reflexive_subclass_closure.sparql │ └── reports │ │ ├── count_noctua.sparql │ │ └── count_ontologies.sparql ├── triplestore-rulecheck.sh └── util │ ├── filter-gaf.pl │ ├── goa_filter │ ├── model_organism.py │ ├── new-filter-gaf.pl │ └── paint_merge.py ├── releases ├── 2018-03-06 │ └── README.md ├── 2018-03-10 │ └── README.md ├── 2018-04-02 │ └── README.md ├── 2018-05-20 │ └── README.md ├── 2018-06-01 │ └── README.md ├── 2018-07-02 │ └── README.md ├── 2018-08-09 │ └── README.md ├── 2018-09-05 │ └── README.md ├── 2018-10-01 │ └── README.md ├── 2019-03-10 │ └── README.md ├── 2019-06-01 │ └── README.md ├── 2020-01-01 │ └── README.md ├── 2020-02-26 │ └── README.md ├── 2020-03-25 │ └── README.md ├── 2020-07-16 │ └── README.md ├── 2020-11-17 │ └── README.md ├── 2021-05-01 │ └── README.md ├── 2021-06-16 │ └── README.md ├── 2022-07-01 │ └── README.md ├── 2022-10-07 │ └── README.md ├── 2023-01-01 │ └── README.md ├── 2023-03-6 │ └── README.md ├── 2023-04-01 │ └── README.md ├── 2024-03-28 │ └── README.md ├── 2024-04-18 │ └── README.md ├── 2024-06-10 │ └── README.md ├── 2024-11-03 │ └── README.md ├── 2025-03-16 │ └── README.md └── README.md ├── scripts ├── GitHubIssueCreatorExp01.lambda.py ├── Makefile-gaf-reprocess ├── README.md ├── aggregate-json-reports.py ├── aggregate-stats.py ├── annotation-review-report.py ├── assigned-by-reports-page-template.html ├── bootstrap-dataset-yaml.pl ├── bucket-indexer.py ├── cloudfront-log-lister.js ├── collate-gpads.pl ├── combine-datasets-metadata.py ├── combined_assigned_by.py ├── correct_paint_symbols.py ├── create-bdbag-remote-file-manifest.py ├── datasets.py ├── db-xrefs-yaml2legacy.js ├── directory-index-template.html ├── directory_indexer.py ├── download-annotation-sources.py ├── download_goex_data.py ├── download_source_gafs.py ├── downloads-page-gen.py ├── downloads-page-template.html ├── fix-users.js ├── gaf_pmid_author_list.pl ├── gaferencer-by-metadata.py ├── gaferencer-reprocess.sh ├── gen-model-meta.py ├── generate-gorules-summary.pl ├── github_issue_summary.py ├── go-db-install-wrapper.pl ├── go-db-install.pl ├── go_annotation_changes.py ├── go_bootstrap.py ├── go_ontology_changes.py ├── go_refine_stats.py ├── go_reports.py ├── go_stats.py ├── go_stats_utils.py ├── install-bug-log-lister.js ├── jenkins │ ├── README.md │ ├── create-annotation-summary-statistics.js │ ├── markup-inference-report.pl │ ├── package.json │ ├── query-github-for-new-tickets.js │ └── query-sf-for-new-terms.js ├── json-concat-lists.py ├── json-syntax-check.el ├── legacy-sql │ ├── migrate │ │ ├── changes-2007-08-23.sh │ │ ├── changes-2007-08-23.sql │ │ ├── changes-2007-09-20.sql │ │ ├── changes-2007-10-08.sql │ │ ├── changes-2007-10-09.sh │ │ └── changes-2008-10-27.sql │ ├── util │ │ └── materialized_views_proc.sql │ └── view │ │ ├── AUTOLOAD_MATVIEWS │ │ ├── AUTOLOAD_VIEWS │ │ ├── Makefile │ │ ├── README │ │ ├── go-annotation-reports.sql │ │ ├── go-association-views.sql │ │ ├── go-database-integrity-checks.sql │ │ ├── go-evidence-views.sql │ │ ├── go-graph-views.sql │ │ ├── go-homolset-views.sql │ │ ├── go-information-content-views.sql │ │ ├── go-mart-views.sql │ │ ├── go-obd-bridge.sql │ │ ├── go-prejoined-views.sql │ │ ├── go-refgenomes-views.sql │ │ ├── go-seq-views.sql │ │ ├── go-stats-views.sql │ │ ├── go-taxon-views.sql │ │ ├── go-term-motif-correlation.sql │ │ ├── go-uniq-assoc.sql │ │ ├── materialize-go-annotation-reports.mysql │ │ ├── materialize-go-evidence-views.mysql │ │ ├── materialize-go-graph-views.mysql │ │ ├── materialize-go-homolset-views.mysql │ │ ├── materialize-go-information-content-views-opt.mysql │ │ ├── materialize-go-information-content-views.mysql │ │ ├── materialize-go-mart-views.mysql │ │ ├── materialize-go-obd-bridge.mysql │ │ ├── materialize-go-prejoined-views.mysql │ │ ├── materialize-go-refgenomes-views.mysql │ │ ├── materialize-go-seq-views.mysql │ │ ├── materialize-go-stats-views.mysql │ │ ├── materialize-go-taxon-views.mysql │ │ ├── mk-combined.pl │ │ ├── mk-materialize.pl │ │ ├── mk-recreate-view.pl │ │ ├── new-views.sql │ │ ├── write-all-matviews.sh │ │ └── write-all-views.sh ├── log-rat.py ├── merge-all-reports.py ├── minerva_to_gocam_yaml_converter.py ├── obo_parser.py ├── ontologies-to-s3.js ├── partition_and_merge_gaf.py ├── prepare-panther-arbre-directory.py ├── pyproject.toml ├── reports-page-gen.py ├── reports-page-template.html ├── requirements.txt ├── rule-example-validation.sh ├── s3-uploader.py ├── sanity-check-ann-report.py ├── sanity-check-users-and-groups.py ├── shex-reports-page-gen.py ├── shex-reports-page-template.html ├── twitter-pull.pl ├── unify-gpads.pl ├── yaml2turtle.sh ├── zenodo-ops.py └── zenodo-version-update.py ├── static └── pages │ ├── README-annotation-downloads.txt │ └── blocked.html └── tests ├── behave ├── golr.feature ├── panther.feature └── steps │ └── basic.py └── panther-hammer.py /.github/workflows/goex.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/geneontology/go-site/HEAD/.github/workflows/goex.yml 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