From 2653043a8cc1269c8ba4b7569330f2b039fa0c7c Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Wed, 30 Nov 2022 13:11:47 -0800 Subject: [PATCH 01/30] Added gitignore to the python folder --- python/.gitignore | 138 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 138 insertions(+) create mode 100644 python/.gitignore diff --git a/python/.gitignore b/python/.gitignore new file mode 100644 index 0000000..9168c40 --- /dev/null +++ b/python/.gitignore @@ -0,0 +1,138 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ \ No newline at end of file From bb1607599d33ae87958d20cf9282c458fb85aacd Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Wed, 30 Nov 2022 13:37:13 -0800 Subject: [PATCH 02/30] fix: exclude_from_extensions to boolean from list of booleans --- python/json_export.py | 14 +- shapes/json/shex_dump.json | 283 +-- .../{look_table.json => terms_metadata.json} | 1543 +++++++++-------- 3 files changed, 961 insertions(+), 879 deletions(-) rename shapes/json/{look_table.json => terms_metadata.json} (90%) diff --git a/python/json_export.py b/python/json_export.py index c725562..3b80e67 100644 --- a/python/json_export.py +++ b/python/json_export.py @@ -45,7 +45,7 @@ def get_shape_name(self, uri, clean=False): name = 'GO' + name return self.pref_dict.get(name, None if clean else uri) - def gen_lookup_table(self): + def gen_terms_metadata(self): goApi = 'http://api.geneontology.org/api/ontology/term/' table = list() for k, v in self.pref_dict.items(): @@ -91,7 +91,7 @@ def _load_triple_expr(self, subject: str, expr: Union[tripleExpr, tripleExprLabe objects = [] self._load_expr(subject, expr.valueExpr, objects) - exclude_from_extensions = "" + exclude_from_extensions = False if isinstance(expr.annotations, list): exclude_from_extensions = self._load_annotation( expr, self.exclude_ext_pred) @@ -105,11 +105,11 @@ def _load_triple_expr(self, subject: str, expr: Union[tripleExpr, tripleExprLabe object=objects, predicate=predicate, is_multivalued=is_multivalued, + exclude_from_extensions=exclude_from_extensions, is_required=False, context="" ) - if exclude_from_extensions != "": - goshape.exclude_from_extensions = exclude_from_extensions, + self.json_shapes.append(goshape) return preds @@ -146,7 +146,7 @@ def parse(self): base_path = Path(__file__).parent shex_fp = (base_path / "../shapes/go-cam-shapes.shex").resolve() json_shapes_fp = (base_path / "../shapes/json/shex_dump.json").resolve() - look_table_fp = (base_path / "../shapes/json/look_table.json").resolve() + terms_metadata_fp = (base_path / "../shapes/json/terms_metadata.json").resolve() shex_full_fp = (base_path / "../shapes/json/shex_full.json").resolve() with open(shex_fp) as f: @@ -160,8 +160,8 @@ def parse(self): coll = AssociationCollection(goshapes=nfShex.json_shapes) jd.dump(coll, to_file=OUT_JSON) - """ with open(look_table_fp, "w") as sf: - json.dump(nfShex.gen_lookup_table(), sf, indent=2) """ + with open(terms_metadata_fp, "w") as sf: + json.dump(nfShex.gen_terms_metadata(), sf, indent=2) with open(shex_full_fp, "w") as sf: json.dump(nfShex.parse_raw(), sf, indent=2) diff --git a/shapes/json/shex_dump.json b/shapes/json/shex_dump.json index 2c06fff..329185d 100644 --- a/shapes/json/shex_dump.json +++ b/shapes/json/shex_dump.json @@ -9,9 +9,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000050", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -24,7 +22,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002233" + "predicate": "RO:0002233", + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -36,7 +35,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002234" + "predicate": "RO:0002234", + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -47,9 +47,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000066", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -60,7 +58,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002313" + "predicate": "RO:0002313", + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -70,7 +69,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002339" + "predicate": "RO:0002339", + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -80,7 +80,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002338" + "predicate": "RO:0002338", + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -93,9 +94,7 @@ "is_required": false, "context": "", "predicate": "RO:0002411", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -108,9 +107,7 @@ "is_required": false, "context": "", "predicate": "RO:0002305", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -123,9 +120,7 @@ "is_required": false, "context": "", "predicate": "RO:0002304", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -136,9 +131,7 @@ "is_required": false, "context": "", "predicate": "RO:0002211", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -149,9 +142,7 @@ "is_required": false, "context": "", "predicate": "RO:0002212", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -162,9 +153,7 @@ "is_required": false, "context": "", "predicate": "RO:0002213", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -175,7 +164,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0012003" + "predicate": "RO:0012003", + "exclude_from_extensions": false }, { "subject": "GO:0048856", @@ -185,7 +175,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002296" + "predicate": "RO:0002296", + "exclude_from_extensions": false }, { "subject": "GO:0048646", @@ -195,7 +186,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002297" + "predicate": "RO:0002297", + "exclude_from_extensions": false }, { "subject": "GO:0009653", @@ -205,7 +197,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002298" + "predicate": "RO:0002298", + "exclude_from_extensions": false }, { "subject": "GO:0030154", @@ -215,7 +208,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002315" + "predicate": "RO:0002315", + "exclude_from_extensions": false }, { "subject": "GO:0051301", @@ -225,7 +219,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002233" + "predicate": "RO:0002233", + "exclude_from_extensions": false }, { "subject": "GO:0045165", @@ -235,7 +230,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002348" + "predicate": "RO:0002348", + "exclude_from_extensions": false }, { "subject": "GO:0001709", @@ -245,7 +241,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002349" + "predicate": "RO:0002349", + "exclude_from_extensions": false }, { "subject": "GO:0001708", @@ -255,7 +252,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002356" + "predicate": "RO:0002356", + "exclude_from_extensions": false }, { "subject": "GO:0022607", @@ -265,7 +263,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002588" + "predicate": "RO:0002588", + "exclude_from_extensions": false }, { "subject": "GO:0022411", @@ -275,7 +274,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002590" + "predicate": "RO:0002590", + "exclude_from_extensions": false }, { "subject": "GO:0016043", @@ -285,7 +285,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002592" + "predicate": "RO:0002592", + "exclude_from_extensions": false }, { "subject": "GO:0021700", @@ -295,7 +296,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002299" + "predicate": "RO:0002299", + "exclude_from_extensions": false }, { "subject": "GO:0040007", @@ -305,7 +307,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002343" + "predicate": "RO:0002343", + "exclude_from_extensions": false }, { "subject": "GO:0051179", @@ -318,7 +321,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002313" + "predicate": "RO:0002313", + "exclude_from_extensions": false }, { "subject": "GO:0051179", @@ -328,7 +332,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002339" + "predicate": "RO:0002339", + "exclude_from_extensions": false }, { "subject": "GO:0051179", @@ -338,7 +343,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002338" + "predicate": "RO:0002338", + "exclude_from_extensions": false }, { "subject": "GO:0040011", @@ -348,7 +354,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002565" + "predicate": "RO:0002565", + "exclude_from_extensions": false }, { "subject": "GO:0008152", @@ -358,7 +365,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0004009" + "predicate": "RO:0004009", + "exclude_from_extensions": false }, { "subject": "GO:0008152", @@ -368,7 +376,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0004008" + "predicate": "RO:0004008", + "exclude_from_extensions": false }, { "subject": "GO:0034367", @@ -378,7 +387,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002591" + "predicate": "RO:0002591", + "exclude_from_extensions": false }, { "subject": "GO:0007389", @@ -388,7 +398,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002356" + "predicate": "RO:0002356", + "exclude_from_extensions": false }, { "subject": "GO:0006810", @@ -400,7 +411,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0004009" + "predicate": "RO:0004009", + "exclude_from_extensions": false }, { "subject": "GO:0006810", @@ -412,7 +424,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0004008" + "predicate": "RO:0004008", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -423,7 +436,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002333" + "predicate": "RO:0002333", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -434,9 +448,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000050", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -446,7 +458,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "BFO:0000051" + "predicate": "BFO:0000051", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -457,9 +470,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000066", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -470,7 +481,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002234" + "predicate": "RO:0002234", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -481,7 +493,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002233" + "predicate": "RO:0002233", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -493,9 +506,7 @@ "is_required": false, "context": "", "predicate": "RO:0002413", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -507,9 +518,7 @@ "is_required": false, "context": "", "predicate": "RO:0002211", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -521,9 +530,7 @@ "is_required": false, "context": "", "predicate": "RO:0002212", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -535,9 +542,7 @@ "is_required": false, "context": "", "predicate": "RO:0002213", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -549,9 +554,7 @@ "is_required": false, "context": "", "predicate": "RO:0002578", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -563,9 +566,7 @@ "is_required": false, "context": "", "predicate": "RO:0002630", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -577,9 +578,7 @@ "is_required": false, "context": "", "predicate": "RO:0002629", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -590,7 +589,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0012012" + "predicate": "RO:0012012", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -602,9 +602,7 @@ "is_required": false, "context": "", "predicate": "RO:0002407", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -616,9 +614,7 @@ "is_required": false, "context": "", "predicate": "RO:0002409", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -629,7 +625,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0012009" + "predicate": "RO:0012009", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -640,7 +637,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0012010" + "predicate": "RO:0012010", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -653,9 +651,7 @@ "is_required": false, "context": "", "predicate": "RO:0002418", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -666,9 +662,7 @@ "is_required": false, "context": "", "predicate": "RO:0004046", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -679,9 +673,7 @@ "is_required": false, "context": "", "predicate": "RO:0004047", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -694,9 +686,7 @@ "is_required": false, "context": "", "predicate": "RO:0002411", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -709,9 +699,7 @@ "is_required": false, "context": "", "predicate": "RO:0002305", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -724,9 +712,7 @@ "is_required": false, "context": "", "predicate": "RO:0002304", - "exclude_from_extensions": [ - true - ] + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -738,7 +724,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002092" + "predicate": "RO:0002092", + "exclude_from_extensions": false }, { "subject": "GO:0005215", @@ -750,7 +737,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002313" + "predicate": "RO:0002313", + "exclude_from_extensions": false }, { "subject": "GO:0005215", @@ -760,7 +748,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002339" + "predicate": "RO:0002339", + "exclude_from_extensions": false }, { "subject": "GO:0005215", @@ -770,7 +759,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002338" + "predicate": "RO:0002338", + "exclude_from_extensions": false }, { "subject": "CARO:0000000", @@ -780,7 +770,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "BFO:0000050" + "predicate": "BFO:0000050", + "exclude_from_extensions": false }, { "subject": "CARO:0000000", @@ -791,7 +782,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0001015" + "predicate": "RO:0001015", + "exclude_from_extensions": false }, { "subject": "CL:0000003", @@ -801,7 +793,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "BFO:0000050" + "predicate": "BFO:0000050", + "exclude_from_extensions": false }, { "subject": "GO:0005575", @@ -811,7 +804,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "BFO:0000050" + "predicate": "BFO:0000050", + "exclude_from_extensions": false }, { "subject": "GO:0005575", @@ -821,7 +815,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002220" + "predicate": "RO:0002220", + "exclude_from_extensions": false }, { "subject": "GO:0005575", @@ -831,7 +826,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002131" + "predicate": "RO:0002131", + "exclude_from_extensions": false }, { "subject": "GO:0005575", @@ -843,7 +839,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002490" + "predicate": "RO:0002490", + "exclude_from_extensions": false }, { "subject": "GO:0005575", @@ -855,7 +852,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002491" + "predicate": "RO:0002491", + "exclude_from_extensions": false }, { "subject": "GO:0032991", @@ -865,7 +863,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0001025" + "predicate": "RO:0001025", + "exclude_from_extensions": false }, { "subject": "GO:0032991", @@ -876,7 +875,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002432" + "predicate": "RO:0002432", + "exclude_from_extensions": false }, { "subject": "GO:0032991", @@ -887,7 +887,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "BFO:0000051" + "predicate": "BFO:0000051", + "exclude_from_extensions": false }, { "subject": "GO:0032991", @@ -899,7 +900,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002490" + "predicate": "RO:0002490", + "exclude_from_extensions": false }, { "subject": "GO:0032991", @@ -911,7 +913,8 @@ "is_multivalued": true, "is_required": false, "context": "", - "predicate": "RO:0002491" + "predicate": "RO:0002491", + "exclude_from_extensions": false }, { "subject": "CHEBI:36080", @@ -921,7 +924,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0001025" + "predicate": "RO:0001025", + "exclude_from_extensions": false }, { "subject": "CHEBI:36080", @@ -932,7 +936,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002432" + "predicate": "RO:0002432", + "exclude_from_extensions": false }, { "subject": "CHEBI:36080", @@ -942,7 +947,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "BFO:0000050" + "predicate": "BFO:0000050", + "exclude_from_extensions": false }, { "subject": "CHEBI:36080", @@ -952,7 +958,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002326" + "predicate": "RO:0002326", + "exclude_from_extensions": false }, { "subject": "CHEBI:33695", @@ -962,7 +969,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0001025" + "predicate": "RO:0001025", + "exclude_from_extensions": false }, { "subject": "CHEBI:33695", @@ -973,7 +981,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002432" + "predicate": "RO:0002432", + "exclude_from_extensions": false }, { "subject": "CHEBI:33695", @@ -983,7 +992,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "BFO:0000050" + "predicate": "BFO:0000050", + "exclude_from_extensions": false }, { "subject": "CHEBI:33695", @@ -993,7 +1003,8 @@ "is_multivalued": false, "is_required": false, "context": "", - "predicate": "RO:0002326" + "predicate": "RO:0002326", + "exclude_from_extensions": false } ], "@type": "AssociationCollection" diff --git a/shapes/json/look_table.json b/shapes/json/terms_metadata.json similarity index 90% rename from shapes/json/look_table.json rename to shapes/json/terms_metadata.json index c4ed2a7..bbeb58a 100644 --- a/shapes/json/look_table.json +++ b/shapes/json/terms_metadata.json @@ -1,737 +1,808 @@ -[ - { - "id": "CHEBI:33695", - "label": "information biomacromolecule", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "CHEBI:36080", - "label": "protein", - "definition": "A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.", - "comment": "", - "synonyms": [ - "proteins" - ] - }, - { - "id": "GO:0032991", - "label": "protein-containing complex", - "definition": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", - "comment": "A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.", - "synonyms": [ - "macromolecular complex", - "macromolecule complex", - "protein containing complex" - ] - }, - { - "id": "GO:0005575", - "label": "cellular_component", - "definition": "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).", - "comment": "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", - "synonyms": [ - "cell or subcellular entity", - "cellular component" - ] - }, - { - "id": "GO:0008150", - "label": "biological_process", - "definition": "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", - "comment": "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", - "synonyms": [ - "biological process", - "physiological process" - ] - }, - { - "id": "GO:0048856", - "label": "anatomical structure development", - "definition": "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.", - "comment": "", - "synonyms": [ - "development of an anatomical structure" - ] - }, - { - "id": "GO:0048646", - "label": "anatomical structure formation involved in morphogenesis", - "definition": "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.", - "comment": "Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.", - "synonyms": [ - "formation of an anatomical structure involved in morphogenesis" - ] - }, - { - "id": "GO:0009653", - "label": "anatomical structure morphogenesis", - "definition": "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.", - "comment": "", - "synonyms": [ - "anatomical structure organization", - "morphogenesis" - ] - }, - { - "id": "GO:0030154", - "label": "cell differentiation", - "definition": "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0051301", - "label": "cell division", - "definition": "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.", - "comment": "Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0045165", - "label": "cell fate commitment", - "definition": "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.", - "comment": "Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created.", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0001709", - "label": "cell fate determination", - "definition": "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0001708", - "label": "cell fate specification", - "definition": "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0022607", - "label": "cellular component assembly", - "definition": "The aggregation, arrangement and bonding together of a cellular component.", - "comment": "", - "synonyms": [ - "cell structure assembly", - "cellular component assembly at cellular level" - ] - }, - { - "id": "GO:0022411", - "label": "cellular component disassembly", - "definition": "A cellular process that results in the breakdown of a cellular component.", - "comment": "", - "synonyms": [ - "cell structure disassembly", - "cellular component disassembly at cellular level" - ] - }, - { - "id": "GO:0016043", - "label": "cellular component organization", - "definition": "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.", - "comment": "", - "synonyms": [ - "cell organisation", - "cellular component organisation at cellular level", - "cellular component organisation in other organism", - "cellular component organization at cellular level", - "cellular component organization in other organism" - ] - }, - { - "id": "GO:0021700", - "label": "developmental maturation", - "definition": "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0040007", - "label": "growth", - "definition": "The increase in size or mass of an entire organism, a part of an organism or a cell.", - "comment": "See also the biological process term 'cell growth ; GO:0016049'.", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0051179", - "label": "localization", - "definition": "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.", - "comment": "", - "synonyms": [ - "establishment and maintenance of localization", - "establishment and maintenance of position", - "localisation" - ] - }, - { - "id": "GO:0040011", - "label": "locomotion", - "definition": "Self-propelled movement of a cell or organism from one location to another.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0006928", - "label": "obsolete movement of cell or subcellular component", - "definition": "OBSOLETE. The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.", - "comment": "This term was obsoleted because it mixes cellular and subcellular processes.", - "synonyms": [ - "cellular component motion", - "cellular component movement" - ] - }, - { - "id": "GO:0034367", - "label": "protein-containing complex remodeling", - "definition": "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0007389", - "label": "pattern specification process", - "definition": "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0003674", - "label": "molecular_function", - "definition": "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", - "comment": "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", - "synonyms": [ - "molecular function" - ] - }, - { - "id": "GO:0005215", - "label": "transporter activity", - "definition": "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.", - "comment": "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.", - "synonyms": [ - "" - ] - }, - { - "id": "CHEBI:24431", - "label": "chemical entity", - "definition": "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.", - "comment": "", - "synonyms": [ - "chemical entity" - ] - }, - { - "id": "ECO:0000000", - "label": "evidence", - "definition": "A type of information that is used to support an assertion.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "CARO:0000000", - "label": "anatomical entity", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "CL:0000003", - "label": "native cell", - "definition": "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "NCBITaxon:1", - "label": "root", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "GO:0044848", - "label": "biological phase", - "definition": "A distinct period or stage in a biological process or cycle.", - "comment": "Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.", - "synonyms": [ - "" - ] - }, - { - "id": "UBERON:0000105", - "label": "life cycle stage", - "definition": "A spatiotemporal region encompassing some part of the life cycle of an organism.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "PO:0009012", - "label": "plant structure development stage", - "definition": "A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.", - "comment": "", - "synonyms": [ - "etapa de desarrollo de estructura vegetal (Spanish, exact)", - "plant growth and development stage (exact)" - ] - }, - { - "id": "BFO:0000050", - "label": "part of", - "definition": "a core relation that holds between a part and its whole", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "BFO:0000051", - "label": "has part", - "definition": "a core relation that holds between a whole and its part", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "BFO:0000066", - "label": "occurs in", - "definition": "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s\u2019 where & b spatially_projects_onto s at t& c is occupies_spatial_region s\u2019 at t& s is a proper_continuant_part_of s\u2019 at t", - "comment": "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002220", - "label": "adjacent to", - "definition": "x adjacent to y if and only if x and y share a boundary.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002131", - "label": "overlaps", - "definition": "x overlaps y if and only if there exists some z such that x has part z and z part of y", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002490", - "label": "existence overlaps", - "definition": "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (\u03b1(x) >= \u03b1(y) & \u03b1(x) <= \u03c9(y)) OR (\u03c9(x) <= \u03c9(y) & \u03c9(x) >= \u03b1(y))", - "comment": "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002491", - "label": "existence starts and ends during", - "definition": "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff \u03b1(x) >= \u03b1(y) & \u03b1(x) <= \u03c9(y) & \u03c9(x) <= \u03c9(y) & \u03c9(x) >= \u03b1(y)", - "comment": "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.", - "synonyms": [ - "exists during" - ] - }, - { - "id": "RO:0002333", - "label": "enabled by", - "definition": "inverse of enables", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002326", - "label": "contributes to", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002233", - "label": "has input", - "definition": "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002234", - "label": "has output", - "definition": "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002339", - "label": "has target end location", - "definition": "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002338", - "label": "has target start location", - "definition": "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002313", - "label": "transports or maintains localization of", - "definition": "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002413", - "label": "directly provides input for", - "definition": "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002629", - "label": "directly positively regulates", - "definition": "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0001025", - "label": "located in", - "definition": "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0001015", - "label": "location of", - "definition": "a relation between two independent continuants, the location and the target, in which the target is entirely within the location", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002432", - "label": "is active in", - "definition": "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "comment": "", - "synonyms": [ - "enables activity in" - ] - }, - { - "id": "RO:0002092", - "label": "happens during", - "definition": "", - "comment": "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002211", - "label": "regulates", - "definition": "process(P1) regulates process(P2) iff:\u00a0P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002212", - "label": "negatively regulates", - "definition": "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002213", - "label": "positively regulates", - "definition": "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002578", - "label": "directly regulates", - "definition": "p directly regulates q iff p is immediately causally upstream of q and p regulates q.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002630", - "label": "directly negatively regulates", - "definition": "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002406", - "label": "directly activates", - "definition": "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q", - "comment": "This term was obsoleted because it has the same meaning as 'directly positively regulates'.", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002418", - "label": "causally upstream of or within", - "definition": "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0004046", - "label": "causally upstream of or within, negative effect", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0004047", - "label": "causally upstream of or within, positive effect", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002411", - "label": "causally upstream of", - "definition": "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002305", - "label": "causally upstream of, negative effect", - "definition": "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", - "comment": "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002304", - "label": "causally upstream of, positive effect", - "definition": "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.", - "comment": "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0012003", - "label": "acts on population of", - "definition": "p acts on population of c iff c' is a collection, has members of type c, and p has participant c", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002296", - "label": "results in development of", - "definition": "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002297", - "label": "results in formation of", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002298", - "label": "results in morphogenesis of", - "definition": "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002315", - "label": "results in acquisition of features of", - "definition": "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002348", - "label": "results in commitment to", - "definition": "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002349", - "label": "results in determination of", - "definition": "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002356", - "label": "results in specification of", - "definition": "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. ", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002588", - "label": "results in assembly of", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002590", - "label": "results in disassembly of", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002592", - "label": "results in organization of", - "definition": "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002299", - "label": "results in maturation of", - "definition": "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002343", - "label": "results in growth of", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002565", - "label": "results in movement of", - "definition": "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c", - "comment": "", - "synonyms": [ - "" - ] - }, - { - "id": "RO:0002591", - "label": "results in remodeling of", - "definition": "", - "comment": "", - "synonyms": [ - "" - ] - } +[ + { + "id": "CHEBI:33695", + "label": "information biomacromolecule", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "CHEBI:36080", + "label": "protein", + "definition": "A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.", + "comment": "", + "synonyms": [ + "proteins" + ] + }, + { + "id": "GO:0032991", + "label": "protein-containing complex", + "definition": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", + "comment": "A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.", + "synonyms": [ + "macromolecular complex", + "macromolecule complex", + "protein containing complex" + ] + }, + { + "id": "GO:0005575", + "label": "cellular_component", + "definition": "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).", + "comment": "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", + "synonyms": [ + "cell or subcellular entity", + "cellular component" + ] + }, + { + "id": "GO:0008150", + "label": "biological_process", + "definition": "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", + "comment": "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", + "synonyms": [ + "biological process", + "physiological process" + ] + }, + { + "id": "GO:0048856", + "label": "anatomical structure development", + "definition": "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.", + "comment": "", + "synonyms": [ + "development of an anatomical structure" + ] + }, + { + "id": "GO:0048646", + "label": "anatomical structure formation involved in morphogenesis", + "definition": "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.", + "comment": "Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.", + "synonyms": [ + "formation of an anatomical structure involved in morphogenesis" + ] + }, + { + "id": "GO:0009653", + "label": "anatomical structure morphogenesis", + "definition": "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.", + "comment": "", + "synonyms": [ + "anatomical structure organization", + "morphogenesis" + ] + }, + { + "id": "GO:0030154", + "label": "cell differentiation", + "definition": "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0051301", + "label": "cell division", + "definition": "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.", + "comment": "Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0045165", + "label": "cell fate commitment", + "definition": "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.", + "comment": "Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created.", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0001709", + "label": "cell fate determination", + "definition": "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0001708", + "label": "cell fate specification", + "definition": "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0022607", + "label": "cellular component assembly", + "definition": "The aggregation, arrangement and bonding together of a cellular component.", + "comment": "", + "synonyms": [ + "cell structure assembly", + "cellular component assembly at cellular level" + ] + }, + { + "id": "GO:0022411", + "label": "cellular component disassembly", + "definition": "A cellular process that results in the breakdown of a cellular component.", + "comment": "", + "synonyms": [ + "cell structure disassembly", + "cellular component disassembly at cellular level" + ] + }, + { + "id": "GO:0016043", + "label": "cellular component organization", + "definition": "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.", + "comment": "", + "synonyms": [ + "cell organisation", + "cellular component organisation at cellular level", + "cellular component organisation in other organism", + "cellular component organization at cellular level", + "cellular component organization in other organism" + ] + }, + { + "id": "GO:0021700", + "label": "developmental maturation", + "definition": "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0040007", + "label": "growth", + "definition": "The increase in size or mass of an entire organism, a part of an organism or a cell.", + "comment": "See also the biological process term 'cell growth ; GO:0016049'.", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0051179", + "label": "localization", + "definition": "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.", + "comment": "", + "synonyms": [ + "establishment and maintenance of localization", + "establishment and maintenance of position", + "localisation" + ] + }, + { + "id": "GO:0040011", + "label": "locomotion", + "definition": "Self-propelled movement of a cell or organism from one location to another.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0034367", + "label": "protein-containing complex remodeling", + "definition": "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0007389", + "label": "pattern specification process", + "definition": "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0008152", + "label": "metabolic process", + "definition": "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.", + "comment": "Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.", + "synonyms": [ + "metabolism" + ] + }, + { + "id": "GO:0006810", + "label": "transport", + "definition": "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.", + "comment": "Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0003674", + "label": "molecular_function", + "definition": "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "comment": "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", + "synonyms": [ + "molecular function" + ] + }, + { + "id": "GO:0005215", + "label": "transporter activity", + "definition": "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.", + "comment": "Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.", + "synonyms": [ + "" + ] + }, + { + "id": "CHEBI:24431", + "label": "chemical entity", + "definition": "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.", + "comment": "", + "synonyms": [ + "chemical entity" + ] + }, + { + "id": "ECO:0000000", + "label": "evidence", + "definition": "A type of information that is used to support an assertion.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "CARO:0000000", + "label": "anatomical entity", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "CL:0000003", + "label": "native cell", + "definition": "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "NCBITaxon:1", + "label": "root", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "GO:0044848", + "label": "biological phase", + "definition": "A distinct period or stage in a biological process or cycle.", + "comment": "Note that phases are is_a disjoint from other biological processes. happens_during relationships can operate between phases and other biological processes e.g. DNA replication happens_during S phase.", + "synonyms": [ + "" + ] + }, + { + "id": "UBERON:0000105", + "label": "life cycle stage", + "definition": "A spatiotemporal region encompassing some part of the life cycle of an organism.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "PO:0009012", + "label": "plant structure development stage", + "definition": "A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.", + "comment": "", + "synonyms": [ + "etapa de desarrollo de estructura vegetal (Spanish, exact)", + "plant growth and development stage (exact)" + ] + }, + { + "id": "BFO:0000050", + "label": "part of", + "definition": "a core relation that holds between a part and its whole", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "BFO:0000051", + "label": "has part", + "definition": "a core relation that holds between a whole and its part", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "BFO:0000066", + "label": "occurs in", + "definition": "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s\u2019 where & b spatially_projects_onto s at t& c is occupies_spatial_region s\u2019 at t& s is a proper_continuant_part_of s\u2019 at t", + "comment": "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002220", + "label": "adjacent to", + "definition": "x adjacent to y if and only if x and y share a boundary.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002131", + "label": "overlaps", + "definition": "x overlaps y if and only if there exists some z such that x has part z and z part of y", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002490", + "label": "existence overlaps", + "definition": "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (\u03b1(x) >= \u03b1(y) & \u03b1(x) <= \u03c9(y)) OR (\u03c9(x) <= \u03c9(y) & \u03c9(x) >= \u03b1(y))", + "comment": "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002491", + "label": "existence starts and ends during", + "definition": "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff \u03b1(x) >= \u03b1(y) & \u03b1(x) <= \u03c9(y) & \u03c9(x) <= \u03c9(y) & \u03c9(x) >= \u03b1(y)", + "comment": "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.", + "synonyms": [ + "exists during" + ] + }, + { + "id": "RO:0002333", + "label": "enabled by", + "definition": "inverse of enables", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002326", + "label": "contributes to", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002233", + "label": "has input", + "definition": "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002234", + "label": "has output", + "definition": "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0004009", + "label": "has primary input", + "definition": "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0004008", + "label": "has primary output", + "definition": "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002339", + "label": "has target end location", + "definition": "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002338", + "label": "has target start location", + "definition": "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002313", + "label": "transports or maintains localization of", + "definition": "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002413", + "label": "directly provides input for", + "definition": "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002629", + "label": "directly positively regulates", + "definition": "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0001025", + "label": "located in", + "definition": "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0001015", + "label": "location of", + "definition": "a relation between two independent continuants, the location and the target, in which the target is entirely within the location", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002432", + "label": "is active in", + "definition": "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "comment": "", + "synonyms": [ + "enables activity in" + ] + }, + { + "id": "RO:0002092", + "label": "happens during", + "definition": "", + "comment": "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002211", + "label": "regulates", + "definition": "process(P1) regulates process(P2) iff:\u00a0P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002212", + "label": "negatively regulates", + "definition": "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002213", + "label": "positively regulates", + "definition": "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002578", + "label": "directly regulates", + "definition": "p directly regulates q iff p is immediately causally upstream of q and p regulates q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002630", + "label": "directly negatively regulates", + "definition": "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002406", + "label": "directly activates", + "definition": "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q", + "comment": "This term was obsoleted because it has the same meaning as 'directly positively regulates'.", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012012", + "label": "indirectly regulates", + "definition": "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002407", + "label": "indirectly activates", + "definition": "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002409", + "label": "indirectly inhibits", + "definition": "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012009", + "label": "constitutively upstream of", + "definition": "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012010", + "label": "removes input for", + "definition": "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002418", + "label": "causally upstream of or within", + "definition": "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0004046", + "label": "causally upstream of or within, negative effect", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0004047", + "label": "causally upstream of or within, positive effect", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002411", + "label": "causally upstream of", + "definition": "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002305", + "label": "causally upstream of, negative effect", + "definition": "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", + "comment": "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002304", + "label": "causally upstream of, positive effect", + "definition": "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.", + "comment": "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012003", + "label": "acts on population of", + "definition": "p acts on population of c iff c' is a collection, has members of type c, and p has participant c", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002296", + "label": "results in development of", + "definition": "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002297", + "label": "results in formation of", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002298", + "label": "results in morphogenesis of", + "definition": "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002315", + "label": "results in acquisition of features of", + "definition": "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002348", + "label": "results in commitment to", + "definition": "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002349", + "label": "results in determination of", + "definition": "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002356", + "label": "results in specification of", + "definition": "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. ", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002588", + "label": "results in assembly of", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002590", + "label": "results in disassembly of", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002592", + "label": "results in organization of", + "definition": "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002299", + "label": "results in maturation of", + "definition": "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002343", + "label": "results in growth of", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002565", + "label": "results in movement of", + "definition": "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0002591", + "label": "results in remodeling of", + "definition": "", + "comment": "", + "synonyms": [ + "" + ] + } ] \ No newline at end of file From fe59fb4dd4197497d0d41a3fa673221ea075f3f5 Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Wed, 30 Nov 2022 19:59:21 -0800 Subject: [PATCH 03/30] inits on adding linkml for shex term metadata --- .../shex_terms_metadata_json_linkml.yaml | 80 +++++++++++ python/shex_terms_metadata_linkml.py | 134 ++++++++++++++++++ 2 files changed, 214 insertions(+) create mode 100644 python/schema/shex_terms_metadata_json_linkml.yaml create mode 100644 python/shex_terms_metadata_linkml.py diff --git a/python/schema/shex_terms_metadata_json_linkml.yaml b/python/schema/shex_terms_metadata_json_linkml.yaml new file mode 100644 index 0000000..93baeae --- /dev/null +++ b/python/schema/shex_terms_metadata_json_linkml.yaml @@ -0,0 +1,80 @@ +id: shex-term-metadata +name: ShexTermMetadataModel +description: a schema for metadata of the terms used in the shex schema +license: https://creativecommons.org/publicdomain/zero/1.0/ +version: 0.1.0 + +default_prefix: GO +default_range: string + +imports: + - linkml:types + +default_curi_maps: + - obo_context + - idot_context + - monarch_context + - semweb_context + +prefixes: + biolink: https://w3id.org/biolink/vocab/ + linkml: https://w3id.org/linkml/ + +classes: + Term: + description: >- + A term metadata + slots: + - id + - label + - definition + - comment + - synonyms + close_mappings: + - schema:Thing + + TermCollection: + tree_root: true + slots: + - terms + description: >- + A collection of terms + +slots: + + id: + range: uriorcurie + description: >- + The term id. It can be a GO Term, RO term + required: true + + label: + range: string + description: >- + The term label + required: true + + definition: + range: string + description: >- + The term definition + + comment: + range: string + description: >- + The term comment + + synonyms: + range: string + description: >- + The term synonyms + + terms: + multivalued: true + range: TermCollection + inlined: true + inlined_as_list: true + description: >- + A collection of terms + + \ No newline at end of file diff --git a/python/shex_terms_metadata_linkml.py b/python/shex_terms_metadata_linkml.py new file mode 100644 index 0000000..eee690f --- /dev/null +++ b/python/shex_terms_metadata_linkml.py @@ -0,0 +1,134 @@ +# Auto generated from shex_terms_metadata_json_linkml.yaml by pythongen.py version: 0.9.0 +# Generation date: 2022-11-30T19:57:14 +# Schema: ShexTermMetadataModel +# +# id: shex-term-metadata +# description: a schema for metadata of the terms used in the shex schema +# license: https://creativecommons.org/publicdomain/zero/1.0/ + +import dataclasses +import sys +import re +from jsonasobj2 import JsonObj, as_dict +from typing import Optional, List, Union, Dict, ClassVar, Any +from dataclasses import dataclass +from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions + +from linkml_runtime.utils.slot import Slot +from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode +from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int +from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs +from linkml_runtime.utils.formatutils import camelcase, underscore, sfx +from linkml_runtime.utils.enumerations import EnumDefinitionImpl +from rdflib import Namespace, URIRef +from linkml_runtime.utils.curienamespace import CurieNamespace +from linkml_runtime.linkml_model.types import String, Uriorcurie +from linkml_runtime.utils.metamodelcore import URIorCURIE + +metamodel_version = "1.7.0" +version = "0.1.0" + +# Overwrite dataclasses _init_fn to add **kwargs in __init__ +dataclasses._init_fn = dataclasses_init_fn_with_kwargs + +# Namespaces +GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') +BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') +LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') +SCHEMA = CurieNamespace('schema', 'http://example.org/UNKNOWN/schema/') +DEFAULT_ = GO + + +# Types + +# Class references + + + +@dataclass +class Term(YAMLRoot): + """ + A term metadata + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = GO.Term + class_class_curie: ClassVar[str] = "GO:Term" + class_name: ClassVar[str] = "Term" + class_model_uri: ClassVar[URIRef] = GO.Term + + id: Union[str, URIorCURIE] = None + label: str = None + definition: Optional[str] = None + comment: Optional[str] = None + synonyms: Optional[str] = None + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if self._is_empty(self.id): + self.MissingRequiredField("id") + if not isinstance(self.id, URIorCURIE): + self.id = URIorCURIE(self.id) + + if self._is_empty(self.label): + self.MissingRequiredField("label") + if not isinstance(self.label, str): + self.label = str(self.label) + + if self.definition is not None and not isinstance(self.definition, str): + self.definition = str(self.definition) + + if self.comment is not None and not isinstance(self.comment, str): + self.comment = str(self.comment) + + if self.synonyms is not None and not isinstance(self.synonyms, str): + self.synonyms = str(self.synonyms) + + super().__post_init__(**kwargs) + + +@dataclass +class TermCollection(YAMLRoot): + """ + A collection of terms + """ + _inherited_slots: ClassVar[List[str]] = [] + + class_class_uri: ClassVar[URIRef] = GO.TermCollection + class_class_curie: ClassVar[str] = "GO:TermCollection" + class_name: ClassVar[str] = "TermCollection" + class_model_uri: ClassVar[URIRef] = GO.TermCollection + + terms: Optional[Union[Union[dict, "TermCollection"], List[Union[dict, "TermCollection"]]]] = empty_list() + + def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): + if not isinstance(self.terms, list): + self.terms = [self.terms] if self.terms is not None else [] + self.terms = [v if isinstance(v, TermCollection) else TermCollection(**as_dict(v)) for v in self.terms] + + super().__post_init__(**kwargs) + + +# Enumerations + + +# Slots +class slots: + pass + +slots.id = Slot(uri=GO.id, name="id", curie=GO.curie('id'), + model_uri=GO.id, domain=None, range=Union[str, URIorCURIE]) + +slots.label = Slot(uri=GO.label, name="label", curie=GO.curie('label'), + model_uri=GO.label, domain=None, range=str) + +slots.definition = Slot(uri=GO.definition, name="definition", curie=GO.curie('definition'), + model_uri=GO.definition, domain=None, range=Optional[str]) + +slots.comment = Slot(uri=GO.comment, name="comment", curie=GO.curie('comment'), + model_uri=GO.comment, domain=None, range=Optional[str]) + +slots.synonyms = Slot(uri=GO.synonyms, name="synonyms", curie=GO.curie('synonyms'), + model_uri=GO.synonyms, domain=None, range=Optional[str]) + +slots.terms = Slot(uri=GO.terms, name="terms", curie=GO.curie('terms'), + model_uri=GO.terms, domain=None, range=Optional[Union[Union[dict, TermCollection], List[Union[dict, TermCollection]]]]) From 78652125facebb96d6b5082d890ab928ffca9ef7 Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Thu, 1 Dec 2022 11:10:12 -0800 Subject: [PATCH 04/30] added more excluded from extension from noctua workbench call --- shapes/go-cam-shapes.shex | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 35ed12b..6c0f99b 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -184,10 +184,12 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - part_of: @ * // true; - has_input: ( @ OR @ OR @ OR @ ) *; - has_output: ( @ OR @ OR @ ) *; - occurs_in: @ {0,1} // true; + part_of: @ *; + has_input: ( @ OR @ OR @ OR @ ) * // true; + has_output: ( @ OR @ OR @ ) * // true; + has_primary_input: ( @ OR @ OR @ OR @ ) *; + has_primary_output: ( @ OR @ OR @ ) *; + occurs_in: @ {0,1}; transports_or_maintains_localization_of: ( @ OR @ ) *; has_target_end_location: @ {0,1}; has_target_start_location: @ {0,1}; @@ -398,7 +400,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - enabled_by: ( @ OR @ ) {0,1}; + enabled_by: ( @ OR @ ) {0,1} // true; part_of: @ * // true; has_part: @ *; occurs_in: @ {0,1} // true; @@ -411,11 +413,11 @@ PREFIX results_in_remodeling_of: directly_regulates: ( @ OR @ ) * // true; directly_negatively_regulates: ( @ OR @ ) * // true; directly_positively_regulates: ( @ OR @ ) * // true; - indirectly_regulates: ( @ OR @) *; + indirectly_regulates: ( @ OR @) * // true; indirectly_positively_regulates: ( @ OR @ ) * // true; indirectly_negatively_regulates: ( @ OR @ ) * // true; - constitutively_upstream_of: ( @ OR @ ) *; - removes_input_for: ( @ OR @ ) *; + constitutively_upstream_of: ( @ OR @ ) * // true; + removes_input_for: ( @ OR @ ) * // true; causally_upstream_of_or_within: ( @ OR @ OR @ ) * // true; causally_upstream_of_or_within_negative_effect: @ * // true; causally_upstream_of_or_within_positive_effect: @ * // true; From 29287755ed687ed64552c5eab1a1a6830b6311dd Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 1 Dec 2022 13:02:25 -0800 Subject: [PATCH 05/30] fix actions syntax errors --- .github/workflows/gen-project-linkml.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gen-project-linkml.yaml b/.github/workflows/gen-project-linkml.yaml index dfbdc7a..1cd89b6 100644 --- a/.github/workflows/gen-project-linkml.yaml +++ b/.github/workflows/gen-project-linkml.yaml @@ -22,10 +22,10 @@ jobs: - name: Check out repository uses: actions/checkout@v2 - - name: Set up Python ${{ "{{" }} matrix.python-version {{ "}}" }} + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: - python-version: ${{ "{{" }} matrix.python-version {{ "}}" }} + python-version: ${{ matrix.python-version }} #---------------------------------------------- # install & configure poetry From c065ee854fa08a8174d999ba66e49f79cfc90835 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 1 Dec 2022 13:14:39 -0800 Subject: [PATCH 06/30] add schema prefix --- python/schema/shex_json_linkml.yaml | 1 + python/shex_json_linkml.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/python/schema/shex_json_linkml.yaml b/python/schema/shex_json_linkml.yaml index 0858375..f2789a5 100644 --- a/python/schema/shex_json_linkml.yaml +++ b/python/schema/shex_json_linkml.yaml @@ -19,6 +19,7 @@ default_curi_maps: prefixes: biolink: https://w3id.org/biolink/vocab/ linkml: https://w3id.org/linkml/ + schema: 'http://schema.org/' classes: Association: diff --git a/python/shex_json_linkml.py b/python/shex_json_linkml.py index e740c57..0c947e5 100644 --- a/python/shex_json_linkml.py +++ b/python/shex_json_linkml.py @@ -1,5 +1,5 @@ # Auto generated from shex_json_linkml.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-11-18T12:44:53 +# Generation date: 2022-12-01T13:14:33 # Schema: GODomainRangeConstraintsModel # # id: go-shex-domain-range-constraints @@ -35,7 +35,7 @@ GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -SCHEMA = CurieNamespace('schema', 'http://example.org/UNKNOWN/schema/') +SCHEMA = CurieNamespace('schema', 'http://schema.org/') DEFAULT_ = GO From fd4db539c2ee0526966d36c5f4a87e8f103cfc5a Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 1 Dec 2022 13:20:39 -0800 Subject: [PATCH 07/30] add an import for shex_json_linkml --- python/Makefile | 6 +- python/schema/shex_json_linkml.yaml | 2 +- .../shex_terms_metadata_json_linkml.yaml | 8 +- .../target/jsonschema/shex_json_linkml.json | 83 ------------------- 4 files changed, 6 insertions(+), 93 deletions(-) delete mode 100644 python/target/jsonschema/shex_json_linkml.json diff --git a/python/Makefile b/python/Makefile index 24b2fea..d7c1e8d 100644 --- a/python/Makefile +++ b/python/Makefile @@ -42,16 +42,16 @@ f-%: tests/data/f-%.ttl python ./gocam_validator.py $< && exit -1 || echo FAILED AS EXPECTED gen-python: - rm -f shex_json_linkml.py && gen-python schema/shex_json_linkml.yaml > shex_json_linkml.py + rm -f shex_json_linkml.py && gen-python schema/shex_term_metadata_json_linkml.yaml > shex_term_metadata_json_linkml.py #gen-pydantic: # rm -f shex_json_linkml.py && gen-pydantic schema/shex_json_linkml.yaml > shex_json_linkml.py gen-jsonschema: - rm -f target/jsonschema/shex_json_linkml.json && gen-json-schema schema/shex_json_linkml.yaml > target/jsonschema/shex_json_linkml.json + rm -f target/jsonschema/shex_terms_metadata_json_linkml.json && gen-json-schema schema/shex_terms_metadata_json_linkml.yaml > target/jsonschema/shex_terms_metadata_json_linkml.json gen-typescript: - rm -f target/typescript/shex_json_linkml.ts && gen-typescript schema/shex_json_linkml.yaml > target/typescript/shex_json_linkml.ts + rm -f target/typescript/shex_terms_metadata_json_linkml.ts && gen-typescript schema/shex_terms_metadata_json_linkml.yaml > target/typescript/shex_terms_metadata_json_linkml.ts linkml: gen-python gen-jsonschema gen-typescript diff --git a/python/schema/shex_json_linkml.yaml b/python/schema/shex_json_linkml.yaml index f2789a5..aa310ec 100644 --- a/python/schema/shex_json_linkml.yaml +++ b/python/schema/shex_json_linkml.yaml @@ -19,7 +19,7 @@ default_curi_maps: prefixes: biolink: https://w3id.org/biolink/vocab/ linkml: https://w3id.org/linkml/ - schema: 'http://schema.org/' + schema: http://schema.org/ classes: Association: diff --git a/python/schema/shex_terms_metadata_json_linkml.yaml b/python/schema/shex_terms_metadata_json_linkml.yaml index 93baeae..ace96c2 100644 --- a/python/schema/shex_terms_metadata_json_linkml.yaml +++ b/python/schema/shex_terms_metadata_json_linkml.yaml @@ -9,6 +9,7 @@ default_range: string imports: - linkml:types + - shex_json_linkml default_curi_maps: - obo_context @@ -19,6 +20,7 @@ default_curi_maps: prefixes: biolink: https://w3id.org/biolink/vocab/ linkml: https://w3id.org/linkml/ + schema: http://schema.org/ classes: Term: @@ -42,12 +44,6 @@ classes: slots: - id: - range: uriorcurie - description: >- - The term id. It can be a GO Term, RO term - required: true - label: range: string description: >- diff --git a/python/target/jsonschema/shex_json_linkml.json b/python/target/jsonschema/shex_json_linkml.json deleted file mode 100644 index 1d02317..0000000 --- a/python/target/jsonschema/shex_json_linkml.json +++ /dev/null @@ -1,83 +0,0 @@ -{ - "$defs": { - "Association": { - "additionalProperties": false, - "description": "GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule", - "properties": { - "context": { - "description": "used to determine if this shape is used in the the visual pathway editor or the graphical editor. Those shapes annotated with like this https://github.com/geneontology/go-shapes/pull/285/files will be exlcuded from the visual pathway editor but still included in the file so this file can be used in the graphical editor as well.", - "type": "string" - }, - "exclude_from_extensions": { - "description": "used to determine if this shape is used in the the visual pathway editor or the graphical editor. Those shapes annotated with like this", - "type": "boolean" - }, - "is_multivalued": { - "description": "for this shape, the relationship in question supports multiple values in the object of the association.", - "type": "boolean" - }, - "is_required": { - "type": "boolean" - }, - "object": { - "description": "The range of the relationship identified by the Relationship.id parameter (This contains the values can be provided in the object of a statement)", - "items": { - "type": "string" - }, - "type": "array" - }, - "predicate": { - "description": "The predicate is the relationship between the domain and range of the GO shape expression rule.", - "type": "string" - }, - "subject": { - "description": "The domain of the GO shape expression rule, this is the subject of the relationship.", - "type": "string" - } - }, - "required": [ - "subject", - "object", - "is_multivalued", - "is_required", - "context" - ], - "title": "Association", - "type": "object" - }, - "Collection": { - "additionalProperties": false, - "description": "A collection of GO domain/range constraint shapes. This is primarily used in this schema to allow several test data objects to be submitted in a single file.", - "properties": { - "goshapes": { - "description": "A collectionm of GO domain/range constraint shapes where a GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule.", - "items": { - "$ref": "#/$defs/Association" - }, - "type": "array" - } - }, - "required": [], - "title": "Collection", - "type": "object" - } - }, - "$id": "go-shex-domain-range-constraints", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "goshapes": { - "description": "A collectionm of GO domain/range constraint shapes where a GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule.", - "items": { - "$ref": "#/$defs/Association" - }, - "type": "array" - } - }, - "required": [], - "title": "GODomainRangeConstraintsModel", - "type": "object", - "version": "0.1.0" -} - From 51496e2b03479e1c2c5d2edc3ef7e92601a5a45b Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Wed, 7 Dec 2022 18:47:46 -0800 Subject: [PATCH 08/30] Adding the shex shorthand for overriding the labels --- .vscode/launch.json | 16 +++ python/json_export.py | 3 +- python/schema/shex_json_linkml.yaml | 4 +- python/shex_json_linkml.py | 2 +- python/shex_to_json_playground.ipynb | 6 +- python/target/typescript/shex_json_linkml.ts | 57 ++------ shapes/json/shex_dump.json | 41 +++++- shapes/json/shex_full.json | 135 ++++++++++++++++--- shapes/json/terms_shorthand.json | 34 +++++ 9 files changed, 220 insertions(+), 78 deletions(-) create mode 100644 .vscode/launch.json create mode 100644 shapes/json/terms_shorthand.json diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 0000000..7e7c6f7 --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,16 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "Python: Current File", + "type": "python", + "request": "launch", + "program": "${file}", + "console": "integratedTerminal", + "justMyCode": true + } + ] +} \ No newline at end of file diff --git a/python/json_export.py b/python/json_export.py index 3b80e67..58836b5 100644 --- a/python/json_export.py +++ b/python/json_export.py @@ -147,6 +147,7 @@ def parse(self): shex_fp = (base_path / "../shapes/go-cam-shapes.shex").resolve() json_shapes_fp = (base_path / "../shapes/json/shex_dump.json").resolve() terms_metadata_fp = (base_path / "../shapes/json/terms_metadata.json").resolve() + terms_shorthand_fp = (base_path / "../shapes/json/terms_shorthand.json").resolve() shex_full_fp = (base_path / "../shapes/json/shex_full.json").resolve() with open(shex_fp) as f: @@ -162,6 +163,6 @@ def parse(self): with open(terms_metadata_fp, "w") as sf: json.dump(nfShex.gen_terms_metadata(), sf, indent=2) - + with open(shex_full_fp, "w") as sf: json.dump(nfShex.parse_raw(), sf, indent=2) diff --git a/python/schema/shex_json_linkml.yaml b/python/schema/shex_json_linkml.yaml index 0858375..1217fce 100644 --- a/python/schema/shex_json_linkml.yaml +++ b/python/schema/shex_json_linkml.yaml @@ -84,7 +84,7 @@ slots: inlined: true inlined_as_list: true description: >- - A collectionm of GO domain/range constraint shapes where a GO domain/range constraint shape + A collection of GO domain/range constraint shapes where a GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule. is_required: @@ -95,7 +95,7 @@ slots: range: string description: >- used to determine if this shape is used in the the visual pathway editor or the graphical editor. Those shapes - annotated with like this https://github.com/geneontology/go-shapes/pull/285/files will be exlcuded from the + annotated with like this https://github.com/geneontology/go-shapes/pull/285/files will be excluded from the visual pathway editor but still included in the file so this file can be used in the graphical editor as well. required: true diff --git a/python/shex_json_linkml.py b/python/shex_json_linkml.py index e740c57..e160013 100644 --- a/python/shex_json_linkml.py +++ b/python/shex_json_linkml.py @@ -1,5 +1,5 @@ # Auto generated from shex_json_linkml.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-11-18T12:44:53 +# Generation date: 2022-11-30T19:55:17 # Schema: GODomainRangeConstraintsModel # # id: go-shex-domain-range-constraints diff --git a/python/shex_to_json_playground.ipynb b/python/shex_to_json_playground.ipynb index 9c52124..f89418d 100644 --- a/python/shex_to_json_playground.ipynb +++ b/python/shex_to_json_playground.ipynb @@ -191,7 +191,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "Python 3.8.10 ('venv': venv)", "language": "python", "name": "python3" }, @@ -205,11 +205,11 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.9" + "version": "3.8.10" }, "vscode": { "interpreter": { - "hash": "88953039a69fbc3cee158df0a3647530aed876ec4de7d6bab7db32384164d671" + "hash": "fd3b897b1e7df8fe01541c1cc54eb2b15faa6ce950f05eeae4aaf5e5940a405f" } } }, diff --git a/python/target/typescript/shex_json_linkml.ts b/python/target/typescript/shex_json_linkml.ts index 2860b65..f9b779d 100644 --- a/python/target/typescript/shex_json_linkml.ts +++ b/python/target/typescript/shex_json_linkml.ts @@ -1,70 +1,33 @@ - - - - - /** * GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule */ - export interface Association { - - /** * The domain of the GO shape expression rule, this is the subject of the relationship. - */ - subject?: string, - - + */subject?: string, /** * The predicate is the relationship between the domain and range of the GO shape expression rule. - */ - predicate?: string, - - + */predicate?: string, /** * The range of the relationship identified by the Relationship.id parameter (This contains the values can be provided in the object of a statement) - */ - object?: string, - - + */object?: string, /** * for this shape, the relationship in question supports multiple values in the object of the association. - */ - is_multivalued?: boolean, - - - /** - * None - */ + */is_multivalued?: boolean, is_required?: boolean, - - /** - * used to determine if this shape is used in the the visual pathway editor or the graphical editor. Those shapes annotated with like this https://github.com/geneontology/go-shapes/pull/285/files will be exlcuded from the visual pathway editor but still included in the file so this file can be used in the graphical editor as well. - */ - context?: string, - - + * used to determine if this shape is used in the the visual pathway editor or the graphical editor. Those shapes annotated with like this https://github.com/geneontology/go-shapes/pull/285/files will be excluded from the visual pathway editor but still included in the file so this file can be used in the graphical editor as well. + */context?: string, /** * used to determine if this shape is used in the the visual pathway editor or the graphical editor. Those shapes annotated with like this - */ - exclude_from_extensions?: boolean, - + */exclude_from_extensions?: boolean, } - - /** * A collection of GO domain/range constraint shapes. This is primarily used in this schema to allow several test data objects to be submitted in a single file. */ - -export interface Collection { - - +export interface AssociationCollection { /** - * A collectionm of GO domain/range constraint shapes where a GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule. - */ - goshapes?: Association[], - + * A collection of GO domain/range constraint shapes where a GO domain/range constraint shape is defined as the domain, relationship, and range of a GO shape expression rule. + */goshapes?: Association[], } diff --git a/shapes/json/shex_dump.json b/shapes/json/shex_dump.json index 329185d..b7b740a 100644 --- a/shapes/json/shex_dump.json +++ b/shapes/json/shex_dump.json @@ -9,7 +9,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000050", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -23,7 +23,7 @@ "is_required": false, "context": "", "predicate": "RO:0002233", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0008150", @@ -36,6 +36,33 @@ "is_required": false, "context": "", "predicate": "RO:0002234", + "exclude_from_extensions": true + }, + { + "subject": "GO:0008150", + "object": [ + "CHEBI:24431", + "CARO:0000000", + "GO:0032991", + "NCBITaxon:1" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0004009", + "exclude_from_extensions": false + }, + { + "subject": "GO:0008150", + "object": [ + "CHEBI:24431", + "CARO:0000000", + "GO:0032991" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0004008", "exclude_from_extensions": false }, { @@ -47,7 +74,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000066", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -437,7 +464,7 @@ "is_required": false, "context": "", "predicate": "RO:0002333", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -590,7 +617,7 @@ "is_required": false, "context": "", "predicate": "RO:0012012", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -626,7 +653,7 @@ "is_required": false, "context": "", "predicate": "RO:0012009", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", @@ -638,7 +665,7 @@ "is_required": false, "context": "", "predicate": "RO:0012010", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", diff --git a/shapes/json/shex_full.json b/shapes/json/shex_full.json index ea7149c..2d13730 100644 --- a/shapes/json/shex_full.json +++ b/shapes/json/shex_full.json @@ -589,6 +589,21 @@ "predicate": "http://purl.obolibrary.org/obo/BFO_0000050", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0002233", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex", + "http://purl.obolibrary.org/obo/go/shapes/Organism" + ] + }, + "min": 0, "max": -1, "annotations": [ { @@ -603,7 +618,31 @@ }, { "type": "TripleConstraint", - "predicate": "http://purl.obolibrary.org/obo/RO_0002233", + "predicate": "http://purl.obolibrary.org/obo/RO_0002234", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" + ] + }, + "min": 0, + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0004009", "valueExpr": { "type": "ShapeOr", "shapeExprs": [ @@ -618,7 +657,7 @@ }, { "type": "TripleConstraint", - "predicate": "http://purl.obolibrary.org/obo/RO_0002234", + "predicate": "http://purl.obolibrary.org/obo/RO_0004008", "valueExpr": { "type": "ShapeOr", "shapeExprs": [ @@ -635,17 +674,7 @@ "predicate": "http://purl.obolibrary.org/obo/BFO_0000066", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", "min": 0, - "max": 1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": 1 }, { "type": "TripleConstraint", @@ -2500,7 +2529,17 @@ ] }, "min": 0, - "max": 1 + "max": 1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2741,7 +2780,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2800,7 +2849,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2813,7 +2872,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -3098,6 +3167,38 @@ "type": "http://www.w3.org/2001/XMLSchema#boolean" } }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, { "type": "Annotation", "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", diff --git a/shapes/json/terms_shorthand.json b/shapes/json/terms_shorthand.json new file mode 100644 index 0000000..c9967b9 --- /dev/null +++ b/shapes/json/terms_shorthand.json @@ -0,0 +1,34 @@ +[ + { + "label": "Protein", + "shorthand": "Protein" + }, + { + "label": "Protein Containing Complex", + "shorthand": "Protein Complex" + }, + { + "label": "Anatomical", + "shorthand": "Anatomy" + }, + { + "label": "Native Cell", + "shorthand": "Cell" + }, + { + "label": "Organism", + "shorthand": "Organism" + }, + { + "label": "Biological Phase", + "shorthand": "Biological Phase" + }, + { + "label": "Life Cycle Stage", + "shorthand": "Stage" + }, + { + "label": "Plant Structure Development Stage", + "shorthand": "Stage" + } +] \ No newline at end of file From 9e692ab253dc312edc5b7f93952e345d22068bec Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Thu, 8 Dec 2022 13:11:25 -0800 Subject: [PATCH 09/30] Added root_subject on linkml and json export.py --- python/json_export.py | 32 +++++++---- python/schema/shex_json_linkml.yaml | 8 +++ python/shex_json_linkml.py | 11 +++- shapes/json/shex_dump.json | 88 +++++++++++++++++++++++++++++ 4 files changed, 127 insertions(+), 12 deletions(-) diff --git a/python/json_export.py b/python/json_export.py index 58836b5..da433c3 100644 --- a/python/json_export.py +++ b/python/json_export.py @@ -59,8 +59,16 @@ def gen_terms_metadata(self): 'synonyms': term.get('synonyms', "") }) return table + + def _load_root_subject_expr(self, expr: Optional[Union[shapeExprLabel, shapeExpr]]) -> str: + + if expr is not None and len(expr)>0 and isinstance(expr[0], str): + return self.get_shape_name(expr[0]) + + return None + - def _load_expr(self, subject: str, expr: Optional[Union[shapeExprLabel, shapeExpr]], preds=None) -> List: + def _load_expr(self, root_subject: str, subject: str, expr: Optional[Union[shapeExprLabel, shapeExpr]], preds=None) -> List: if preds is None: preds = {} @@ -68,20 +76,20 @@ def _load_expr(self, subject: str, expr: Optional[Union[shapeExprLabel, shapeExp preds.append(self.get_shape_name(expr)) if isinstance(expr, (ShapeOr, ShapeAnd)): for expr2 in expr.shapeExprs: - self._load_expr(subject, expr2, preds) + self._load_expr(root_subject, subject, expr2, preds) elif isinstance(expr, ShapeNot): - self._load_expr(subject, expr.shapeExpr, preds) + self._load_expr(root_subject, subject, expr.shapeExpr, preds) elif isinstance(expr, Shape) and expr.expression is not None: - self._load_triple_expr(subject, expr.expression, preds) + self._load_triple_expr(root_subject, subject, expr.expression, preds) # throw an error here if pred list is empty return preds - def _load_triple_expr(self, subject: str, expr: Union[tripleExpr, tripleExprLabel], preds=None) -> None: + def _load_triple_expr(self, root_subject: str, subject: str, expr: Union[tripleExpr, tripleExprLabel], preds=None) -> None: if isinstance(expr, (OneOf, EachOf)): for expr2 in expr.expressions: - self._load_triple_expr(subject, expr2, preds) + self._load_triple_expr(root_subject, subject, expr2, preds) elif isinstance(expr, TripleConstraint) and expr.valueExpr is not None: predicate = get_suffix(expr.predicate) @@ -89,7 +97,7 @@ def _load_triple_expr(self, subject: str, expr: Union[tripleExpr, tripleExprLabe return preds objects = [] - self._load_expr(subject, expr.valueExpr, objects) + self._load_expr(root_subject, subject, expr.valueExpr, objects) exclude_from_extensions = False if isinstance(expr.annotations, list): @@ -101,6 +109,7 @@ def _load_triple_expr(self, subject: str, expr: Union[tripleExpr, tripleExprLabe is_multivalued = True goshape = Association( + root_subject=root_subject, subject=subject, object=objects, predicate=predicate, @@ -129,7 +138,8 @@ def parse(self): for shape in shapes: shape_name = self.get_shape_name(shape['id'], True) - + root_subject = self._load_root_subject_expr(shape.shapeExprs) + if shape_name is None: continue @@ -138,7 +148,7 @@ def parse(self): shexps = shape.shapeExprs or [] for expr in shexps: - self._load_expr(shape_name, expr) + self._load_expr(root_subject, shape_name, expr) if __name__ == "__main__": @@ -161,8 +171,8 @@ def parse(self): coll = AssociationCollection(goshapes=nfShex.json_shapes) jd.dump(coll, to_file=OUT_JSON) - with open(terms_metadata_fp, "w") as sf: - json.dump(nfShex.gen_terms_metadata(), sf, indent=2) + """ with open(terms_metadata_fp, "w") as sf: + json.dump(nfShex.gen_terms_metadata(), sf, indent=2) """ with open(shex_full_fp, "w") as sf: json.dump(nfShex.parse_raw(), sf, indent=2) diff --git a/python/schema/shex_json_linkml.yaml b/python/schema/shex_json_linkml.yaml index 6fde0e4..a22b906 100644 --- a/python/schema/shex_json_linkml.yaml +++ b/python/schema/shex_json_linkml.yaml @@ -28,6 +28,7 @@ classes: expression rule slots: - subject + - root_subject - predicate - object - is_multivalued @@ -73,6 +74,13 @@ slots: description: >- The domain of the GO shape expression rule, this is the subject of the relationship. + root_subject: + range: uriorcurie + required: true + description: >- + The domain of the GO shape expression rule, this is the root subject of the relationship. + + is_multivalued: range: boolean required: true diff --git a/python/shex_json_linkml.py b/python/shex_json_linkml.py index 0c947e5..9cc6e6e 100644 --- a/python/shex_json_linkml.py +++ b/python/shex_json_linkml.py @@ -1,5 +1,5 @@ # Auto generated from shex_json_linkml.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-12-01T13:14:33 +# Generation date: 2022-12-07T23:52:38 # Schema: GODomainRangeConstraintsModel # # id: go-shex-domain-range-constraints @@ -58,6 +58,7 @@ class Association(YAMLRoot): class_model_uri: ClassVar[URIRef] = GO.Association subject: Union[str, URIorCURIE] = None + root_subject: Union[str, URIorCURIE] = None object: Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]] = None is_multivalued: Union[bool, Bool] = None is_required: Union[bool, Bool] = None @@ -71,6 +72,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.subject, URIorCURIE): self.subject = URIorCURIE(self.subject) + if self._is_empty(self.root_subject): + self.MissingRequiredField("root_subject") + if not isinstance(self.root_subject, URIorCURIE): + self.root_subject = URIorCURIE(self.root_subject) + if self._is_empty(self.object): self.MissingRequiredField("object") if not isinstance(self.object, list): @@ -143,6 +149,9 @@ class slots: slots.subject = Slot(uri=GO.subject, name="subject", curie=GO.curie('subject'), model_uri=GO.subject, domain=None, range=Union[str, URIorCURIE]) +slots.root_subject = Slot(uri=GO.root_subject, name="root_subject", curie=GO.curie('root_subject'), + model_uri=GO.root_subject, domain=None, range=Union[str, URIorCURIE]) + slots.is_multivalued = Slot(uri=GO.is_multivalued, name="is_multivalued", curie=GO.curie('is_multivalued'), model_uri=GO.is_multivalued, domain=None, range=Union[bool, Bool]) diff --git a/shapes/json/shex_dump.json b/shapes/json/shex_dump.json index b7b740a..cb75396 100644 --- a/shapes/json/shex_dump.json +++ b/shapes/json/shex_dump.json @@ -2,6 +2,7 @@ "goshapes": [ { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -13,6 +14,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:24431", "CARO:0000000", @@ -27,6 +29,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:24431", "CARO:0000000", @@ -40,6 +43,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:24431", "CARO:0000000", @@ -54,6 +58,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:24431", "CARO:0000000", @@ -67,6 +72,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -78,6 +84,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:33695", "GO:0032991" @@ -90,6 +97,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -101,6 +109,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -112,6 +121,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "GO:0003674", @@ -125,6 +135,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "GO:0003674", @@ -138,6 +149,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "GO:0003674", @@ -151,6 +163,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -162,6 +175,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -173,6 +187,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -184,6 +199,7 @@ }, { "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000", "NCBITaxon:1" @@ -196,6 +212,7 @@ }, { "subject": "GO:0048856", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -207,6 +224,7 @@ }, { "subject": "GO:0048646", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -218,6 +236,7 @@ }, { "subject": "GO:0009653", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -229,6 +248,7 @@ }, { "subject": "GO:0030154", + "root_subject": "GO:0008150", "object": [ "CL:0000003" ], @@ -240,6 +260,7 @@ }, { "subject": "GO:0051301", + "root_subject": "GO:0008150", "object": [ "CL:0000003" ], @@ -251,6 +272,7 @@ }, { "subject": "GO:0045165", + "root_subject": "GO:0008150", "object": [ "CL:0000003" ], @@ -262,6 +284,7 @@ }, { "subject": "GO:0001709", + "root_subject": "GO:0008150", "object": [ "CL:0000003" ], @@ -273,6 +296,7 @@ }, { "subject": "GO:0001708", + "root_subject": "GO:0008150", "object": [ "CL:0000003" ], @@ -284,6 +308,7 @@ }, { "subject": "GO:0022607", + "root_subject": "GO:0008150", "object": [ "GO:0005575" ], @@ -295,6 +320,7 @@ }, { "subject": "GO:0022411", + "root_subject": "GO:0008150", "object": [ "GO:0005575" ], @@ -306,6 +332,7 @@ }, { "subject": "GO:0016043", + "root_subject": "GO:0008150", "object": [ "GO:0005575" ], @@ -317,6 +344,7 @@ }, { "subject": "GO:0021700", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -328,6 +356,7 @@ }, { "subject": "GO:0040007", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -339,6 +368,7 @@ }, { "subject": "GO:0051179", + "root_subject": "GO:0008150", "object": [ "CARO:0000000", "CHEBI:24431", @@ -353,6 +383,7 @@ }, { "subject": "GO:0051179", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -364,6 +395,7 @@ }, { "subject": "GO:0051179", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -375,6 +407,7 @@ }, { "subject": "GO:0040011", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -386,6 +419,7 @@ }, { "subject": "GO:0008152", + "root_subject": "GO:0008150", "object": [ "CHEBI:24431" ], @@ -397,6 +431,7 @@ }, { "subject": "GO:0008152", + "root_subject": "GO:0008150", "object": [ "CHEBI:24431" ], @@ -408,6 +443,7 @@ }, { "subject": "GO:0034367", + "root_subject": "GO:0008150", "object": [ "GO:0032991" ], @@ -419,6 +455,7 @@ }, { "subject": "GO:0007389", + "root_subject": "GO:0008150", "object": [ "CARO:0000000" ], @@ -430,6 +467,7 @@ }, { "subject": "GO:0006810", + "root_subject": "GO:0008150", "object": [ "CHEBI:24431", "CARO:0000000", @@ -443,6 +481,7 @@ }, { "subject": "GO:0006810", + "root_subject": "GO:0008150", "object": [ "CHEBI:24431", "CARO:0000000", @@ -456,6 +495,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:33695", "GO:0032991" @@ -468,6 +508,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -479,6 +520,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674" ], @@ -490,6 +532,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -501,6 +544,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:24431", "GO:0032991" @@ -513,6 +557,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:24431", "GO:0032991" @@ -525,6 +570,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -537,6 +583,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -549,6 +596,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -561,6 +609,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -573,6 +622,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -585,6 +635,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -597,6 +648,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -609,6 +661,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -621,6 +674,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -633,6 +687,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -645,6 +700,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -657,6 +713,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -669,6 +726,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent", @@ -682,6 +740,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -693,6 +752,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150" ], @@ -704,6 +764,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "GO:0003674", @@ -717,6 +778,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "GO:0003674", @@ -730,6 +792,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "GO:0003674", @@ -743,6 +806,7 @@ }, { "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0044848", "UBERON:0000105", @@ -756,6 +820,7 @@ }, { "subject": "GO:0005215", + "root_subject": "GO:0003674", "object": [ "CHEBI:24431", "CHEBI:33695", @@ -769,6 +834,7 @@ }, { "subject": "GO:0005215", + "root_subject": "GO:0003674", "object": [ "GO:0005575" ], @@ -780,6 +846,7 @@ }, { "subject": "GO:0005215", + "root_subject": "GO:0003674", "object": [ "GO:0005575" ], @@ -791,6 +858,7 @@ }, { "subject": "CARO:0000000", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -802,6 +870,7 @@ }, { "subject": "CARO:0000000", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:33695", "GO:0032991" @@ -814,6 +883,7 @@ }, { "subject": "CL:0000003", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -825,6 +895,7 @@ }, { "subject": "GO:0005575", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -836,6 +907,7 @@ }, { "subject": "GO:0005575", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -847,6 +919,7 @@ }, { "subject": "GO:0005575", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -858,6 +931,7 @@ }, { "subject": "GO:0005575", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "UBERON:0000105", @@ -871,6 +945,7 @@ }, { "subject": "GO:0005575", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "UBERON:0000105", @@ -884,6 +959,7 @@ }, { "subject": "GO:0032991", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" ], @@ -895,6 +971,7 @@ }, { "subject": "GO:0032991", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000", "http://purl.obolibrary.org/obo/go/shapes/RootCellularComponent" @@ -907,6 +984,7 @@ }, { "subject": "GO:0032991", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CHEBI:33695", "GO:0032991" @@ -919,6 +997,7 @@ }, { "subject": "GO:0032991", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "UBERON:0000105", @@ -932,6 +1011,7 @@ }, { "subject": "GO:0032991", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "GO:0008150", "UBERON:0000105", @@ -945,6 +1025,7 @@ }, { "subject": "CHEBI:36080", + "root_subject": "CHEBI:24431", "object": [ "CARO:0000000" ], @@ -956,6 +1037,7 @@ }, { "subject": "CHEBI:36080", + "root_subject": "CHEBI:24431", "object": [ "CARO:0000000", "http://purl.obolibrary.org/obo/go/shapes/RootCellularComponent" @@ -968,6 +1050,7 @@ }, { "subject": "CHEBI:36080", + "root_subject": "CHEBI:24431", "object": [ "GO:0032991" ], @@ -979,6 +1062,7 @@ }, { "subject": "CHEBI:36080", + "root_subject": "CHEBI:24431", "object": [ "GO:0003674" ], @@ -990,6 +1074,7 @@ }, { "subject": "CHEBI:33695", + "root_subject": "CHEBI:24431", "object": [ "CARO:0000000" ], @@ -1001,6 +1086,7 @@ }, { "subject": "CHEBI:33695", + "root_subject": "CHEBI:24431", "object": [ "CARO:0000000", "http://purl.obolibrary.org/obo/go/shapes/RootCellularComponent" @@ -1013,6 +1099,7 @@ }, { "subject": "CHEBI:33695", + "root_subject": "CHEBI:24431", "object": [ "GO:0032991" ], @@ -1024,6 +1111,7 @@ }, { "subject": "CHEBI:33695", + "root_subject": "CHEBI:24431", "object": [ "GO:0003674" ], From 75935b337f90129200a8540f15a961b20a5865fc Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Tue, 20 Dec 2022 13:34:10 -0500 Subject: [PATCH 10/30] Adding has_primary_input and has_primary_output to MF shape --- shapes/go-cam-shapes.shex | 2 ++ 1 file changed, 2 insertions(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 9bc3ad7..6bf6200 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -404,6 +404,8 @@ PREFIX results_in_remodeling_of: occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; + has_primary_input: ( @ OR @ ) *; + has_primary_output: ( @ OR @ ) *; directly_provides_input_for: ( @ OR @ ) *; regulates: ( @ OR @ ) *; negatively_regulates: ( @ OR @ ) *; From 6c0ccd28f733558edb0b547358d1ffd3f1313a0c Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Tue, 20 Dec 2022 13:49:58 -0500 Subject: [PATCH 11/30] Adding has_primary_input and has_primary_output to transporter activity shape --- shapes/go-cam-shapes.shex | 2 ++ 1 file changed, 2 insertions(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 6bf6200..85a9a65 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -434,6 +434,8 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ {1}; transports_or_maintains_localization_of: ( @ OR @ OR @ ) *; + has_primary_input: ( @ OR @ ) *; + has_primary_output: ( @ OR @ ) *; has_target_end_location: @ *; has_target_start_location: @ *; } // rdfs:comment "a transporter activity GO molecular function or child" From f83e745a6c434905ac3bce81395ce105da0cf5f4 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 2 Feb 2023 10:37:36 -0500 Subject: [PATCH 12/30] Update go-cam-shapes.shex Adding happens_during to BP shape --- shapes/go-cam-shapes.shex | 1 + 1 file changed, 1 insertion(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 85a9a65..678d8f7 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -198,6 +198,7 @@ PREFIX results_in_remodeling_of: negatively_regulates: @ *; positively_regulates: @ *; acts_on_population_of: ( @ OR @ ) *; + happens_during: ( @ OR @ OR @ ) *; } // rdfs:comment "A biological process" From bc20e6e39da15742fae3dc7bcad66550dd2b4479 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 9 Mar 2023 15:54:09 -0500 Subject: [PATCH 13/30] Update go-cam-shapes.shex Adding small molecule relation terms to MF and chemical entity shapes. --- shapes/go-cam-shapes.shex | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 678d8f7..4820566 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -86,6 +86,12 @@ PREFIX has_target_start_location: PREFIX transports_or_maintains_localization_of: PREFIX directly_provides_input_for: PREFIX directly_positively_regulates: +PREFIX has_small_molecule_regulator: +PREFIX has_small_molecule_activator: +PREFIX has_small_molecule_inhibitor: +PREFIX is_small_molecule_regulator_of: +PREFIX is_small_molecule_activator_of: +PREFIX is_small_molecule_inhibitor_of: PREFIX located_in: PREFIX location_of: PREFIX is_active_in: @@ -419,6 +425,9 @@ PREFIX results_in_remodeling_of: indirectly_negatively_regulates: ( @ OR @ ) *; constitutively_upstream_of: ( @ OR @ ) *; removes_input_for: ( @ OR @ ) *; + has_small_molecule_regulator: @ *; + has_small_molecule_activator: @ *; + has_small_molecule_inhibitor: @ *; causally_upstream_of_or_within: ( @ OR @ OR @ ) *; causally_upstream_of_or_within_negative_effect: @ *; causally_upstream_of_or_within_positive_effect: @ *; @@ -525,6 +534,9 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ +; + is_small_molecule_regulator_of: @ *; + is_small_molecule_activator_of: @ *; + is_small_molecule_inhibitor_of: @ *; }// rdfs:comment "a molecular entity (a gene product, chemical, or complex typically)" IRI @ AND EXTRA rdfs:subClassOf { From 75106963ef0b657f803d8b54f26057508d291f08 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Tue, 5 Dec 2023 11:50:31 -0500 Subject: [PATCH 14/30] Allow multiple enablers --- shapes/go-cam-shapes.shex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 4820566..b9f9196 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -405,7 +405,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - enabled_by: ( @ OR @ ) {0,1}; + enabled_by: ( @ OR @ ) *; part_of: @ *; has_part: @ *; occurs_in: @ {0,1}; From 878330e30d334a09c0ea7243db17120686be4f23 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Tue, 5 Dec 2023 11:54:37 -0500 Subject: [PATCH 15/30] Replace obsolete native cell with cell --- shapes/go-cam-shapes.shex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 4820566..256b056 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -62,7 +62,7 @@ PREFIX GoTransporterActivity: PREFIX GoChemicalEntity: PREFIX GoEvidence: PREFIX GoAnatomicalEntity: -PREFIX GoNativeCell: +PREFIX GoCell: PREFIX GoOrganism: PREFIX GoBiologicalPhase: PREFIX GoLifeCycleStage: @@ -489,7 +489,7 @@ PREFIX results_in_remodeling_of: } // rdfs:comment "an anatomical entity" IRI @ AND EXTRA rdfs:subClassOf { - rdfs:subClassOf [ GoNativeCell: ]; + rdfs:subClassOf [ GoCell: ]; } @ AND EXTRA a { From c3c6a74c206007b9ba334e1dd1bffc0603a1fd5e Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Tue, 5 Dec 2023 12:10:03 -0500 Subject: [PATCH 16/30] Fix additional mentions of native cell --- shapes/go-cam-shapes.shex | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 256b056..4a49796 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -241,7 +241,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ {1}; - results_in_acquisition_of_features_of: @ {0,1}; + results_in_acquisition_of_features_of: @ {0,1}; } // rdfs:comment "a cell differentiation GO biological process or child" IRI @ AND EXTRA rdfs:subClassOf { @@ -250,7 +250,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ {1}; - has_input: @ {0,1}; + has_input: @ {0,1}; } // rdfs:comment "a cell division GO biological process or child" IRI @ AND EXTRA rdfs:subClassOf { @@ -259,7 +259,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ {1}; - results_in_commitment_to: @ {0,1}; + results_in_commitment_to: @ {0,1}; } // rdfs:comment "a cell fate commitment GO biological process or child" IRI @ AND EXTRA rdfs:subClassOf { @@ -268,7 +268,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ {1}; - results_in_determination_of: @ {0,1}; + results_in_determination_of: @ {0,1}; } // rdfs:comment "a cell fate determination GO biological process or child" IRI @ AND EXTRA rdfs:subClassOf { @@ -277,7 +277,7 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @ {1}; - results_in_specification_of: @ {0,1}; + results_in_specification_of: @ {0,1}; } // rdfs:comment "a cell fate specification GO biological process or child" IRI @ AND EXTRA rdfs:subClassOf { @@ -488,14 +488,14 @@ PREFIX results_in_remodeling_of: location_of: ( @ OR @ ) {0,1}; } // rdfs:comment "an anatomical entity" - IRI @ AND EXTRA rdfs:subClassOf { + IRI @ AND EXTRA rdfs:subClassOf { rdfs:subClassOf [ GoCell: ]; } - @ AND EXTRA a { - a @ {1}; + @ AND EXTRA a { + a @ {1}; part_of: @ {0,1}; -} // rdfs:comment "a native cell or child" +} // rdfs:comment "a cell or child" IRI @ AND EXTRA rdfs:subClassOf { rdfs:subClassOf [ GoCellularComponent: ]; From 292b1e003dc0ed2f6eee43441eb80a54d3d77ceb Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Thu, 14 Dec 2023 14:08:32 -0500 Subject: [PATCH 17/30] Replace CHEBI term in test. --- .../should_pass/Test027-has_input_2_MolecularEntity.ttl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl b/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl index 00de798..171fa5e 100644 --- a/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl +++ b/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl @@ -157,8 +157,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/CHEBI_60579 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/CHEBI_30623 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/ECO_0000314 @@ -467,7 +467,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000607/5d27d1cf00000626 rdf:type owl:NamedIndividual , - ; + ; "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; "2019-07-12"^^xsd:string ; "http://geneontology.org"^^xsd:string . From f017aae2f04fd4a5cbbe2ac98c24c1633e8ec5e1 Mon Sep 17 00:00:00 2001 From: Jim Balhoff Date: Wed, 6 Mar 2024 11:26:54 -0500 Subject: [PATCH 18/30] Fix obsolete GO terms in test models. (#308) --- test_ttl/go_cams/hold/Test009-has_output_GO_complex.ttl | 2 +- test_ttl/go_cams/hold/Test009b-has_output_complex.ttl | 2 +- .../go_cams/should_fail/Test001-bad-meta-no-contributor.ttl | 6 +++--- .../go_cams/should_fail/Test002-enabled_by_GO_complex.ttl | 6 +++--- .../should_fail/Test003-occurs_in_MolecularEntity.ttl | 6 +++--- .../go_cams/should_fail/Test004-occurs_in_GO_Complex.ttl | 6 +++--- .../should_fail/Test005-enabled_by_biological_process.ttl | 6 +++--- .../should_fail/Test006-occurs_in_BiologicalProcess.ttl | 6 +++--- .../should_fail/Test010-has_output-biological_process.ttl | 6 +++--- .../should_fail/Test011-has_output-molecular_function.ttl | 6 +++--- .../should_fail/Test012-has_input-complex_GO_complex.ttl | 6 +++--- .../go_cams/should_fail/Test012b-has_input-GoComplex.ttl | 6 +++--- .../should_fail/Test013-has_input-biological_process.ttl | 6 +++--- .../should_fail/Test014-has_input-molecular_function.ttl | 6 +++--- ...Test015-provides_direct_input_for-Biological_process.ttl | 6 +++--- ...Test016-provides_direct_input_for-cellular_component.ttl | 6 +++--- .../Test017-provides_direct_input_for-MolecularEntity.ttl | 6 +++--- .../Test020-happens_during_BP_not_a_biological_phase.ttl | 6 +++--- .../should_fail/Test021-happens_during_GOcomplex.ttl | 6 +++--- .../go_cams/should_fail/Test021b-happens_during-complex.ttl | 6 +++--- .../Test022-happens_during-molecular_function.ttl | 6 +++--- .../should_fail/Test023-enabled_by_2_MolecularEntity.ttl | 6 +++--- .../should_fail/Test024-part_of_2_biological_process.ttl | 6 +++--- .../should_fail/Test025-occurs_in_2_cellular_component.ttl | 6 +++--- ...028-directly_provides_input_for_2_molecular_function.ttl | 6 +++--- ...9-directly_positively_regulates_2_molecular_function.ttl | 6 +++--- ...-causally_upstream_of_or_within-2-biological_process.ttl | 6 +++--- .../Test000-Correct_and_complete_ActivityUnit_model.ttl | 6 +++--- test_ttl/go_cams/should_pass/Test001-missing_enabled_by.ttl | 6 +++--- ...t018-directly_positively_regulates_MolecularFunction.ttl | 6 +++--- .../should_pass/Test019-happens_during_BiologicalPhase.ttl | 6 +++--- .../should_pass/Test026-has_output_2_MolecularEntity.ttl | 6 +++--- .../should_pass/Test027-has_input_2_MolecularEntity.ttl | 6 +++--- 33 files changed, 95 insertions(+), 95 deletions(-) diff --git a/test_ttl/go_cams/hold/Test009-has_output_GO_complex.ttl b/test_ttl/go_cams/hold/Test009-has_output_GO_complex.ttl index c2cbf07..885b1cf 100644 --- a/test_ttl/go_cams/hold/Test009-has_output_GO_complex.ttl +++ b/test_ttl/go_cams/hold/Test009-has_output_GO_complex.ttl @@ -198,7 +198,7 @@ ### http://model.geneontology.org/5d27d1cf00000192/5d27d1cf00000204 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/hold/Test009b-has_output_complex.ttl b/test_ttl/go_cams/hold/Test009b-has_output_complex.ttl index d599b39..b0cecf5 100644 --- a/test_ttl/go_cams/hold/Test009b-has_output_complex.ttl +++ b/test_ttl/go_cams/hold/Test009b-has_output_complex.ttl @@ -163,7 +163,7 @@ ### http://model.geneontology.org/5d27d1cf00000211/5d27d1cf00000223 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test001-bad-meta-no-contributor.ttl b/test_ttl/go_cams/should_fail/Test001-bad-meta-no-contributor.ttl index a8663ba..fbdc0ad 100644 --- a/test_ttl/go_cams/should_fail/Test001-bad-meta-no-contributor.ttl +++ b/test_ttl/go_cams/should_fail/Test001-bad-meta-no-contributor.ttl @@ -166,8 +166,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -338,7 +338,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000038/5d27d1cf00000050 rdf:type owl:NamedIndividual , - ; + ; "148.75"^^xsd:string ; "55"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test002-enabled_by_GO_complex.ttl b/test_ttl/go_cams/should_fail/Test002-enabled_by_GO_complex.ttl index eb62fc3..cd37221 100644 --- a/test_ttl/go_cams/should_fail/Test002-enabled_by_GO_complex.ttl +++ b/test_ttl/go_cams/should_fail/Test002-enabled_by_GO_complex.ttl @@ -176,8 +176,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -367,7 +367,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000056/5d27d1cf00000068 rdf:type owl:NamedIndividual , - ; + ; "447.75"^^xsd:string ; "32.999996185302734"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test003-occurs_in_MolecularEntity.ttl b/test_ttl/go_cams/should_fail/Test003-occurs_in_MolecularEntity.ttl index 4ecf4d1..ff14492 100644 --- a/test_ttl/go_cams/should_fail/Test003-occurs_in_MolecularEntity.ttl +++ b/test_ttl/go_cams/should_fail/Test003-occurs_in_MolecularEntity.ttl @@ -176,8 +176,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -368,7 +368,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000078/5d27d1cf00000090 rdf:type owl:NamedIndividual , - ; + ; "218.75"^^xsd:string ; "21"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test004-occurs_in_GO_Complex.ttl b/test_ttl/go_cams/should_fail/Test004-occurs_in_GO_Complex.ttl index 5c52488..2905768 100644 --- a/test_ttl/go_cams/should_fail/Test004-occurs_in_GO_Complex.ttl +++ b/test_ttl/go_cams/should_fail/Test004-occurs_in_GO_Complex.ttl @@ -171,8 +171,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -367,7 +367,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000097/5d27d1cf00000109 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test005-enabled_by_biological_process.ttl b/test_ttl/go_cams/should_fail/Test005-enabled_by_biological_process.ttl index 140037d..f111771 100644 --- a/test_ttl/go_cams/should_fail/Test005-enabled_by_biological_process.ttl +++ b/test_ttl/go_cams/should_fail/Test005-enabled_by_biological_process.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -355,7 +355,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000116/5d27d1cf00000128 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test006-occurs_in_BiologicalProcess.ttl b/test_ttl/go_cams/should_fail/Test006-occurs_in_BiologicalProcess.ttl index 2d8a340..8d19ad5 100644 --- a/test_ttl/go_cams/should_fail/Test006-occurs_in_BiologicalProcess.ttl +++ b/test_ttl/go_cams/should_fail/Test006-occurs_in_BiologicalProcess.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -368,7 +368,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000135/5d27d1cf00000147 rdf:type owl:NamedIndividual , - ; + ; "468.75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test010-has_output-biological_process.ttl b/test_ttl/go_cams/should_fail/Test010-has_output-biological_process.ttl index cce1afd..fc46c86 100644 --- a/test_ttl/go_cams/should_fail/Test010-has_output-biological_process.ttl +++ b/test_ttl/go_cams/should_fail/Test010-has_output-biological_process.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -346,7 +346,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000231/5d27d1cf00000243 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test011-has_output-molecular_function.ttl b/test_ttl/go_cams/should_fail/Test011-has_output-molecular_function.ttl index 49f5f74..b6ade47 100644 --- a/test_ttl/go_cams/should_fail/Test011-has_output-molecular_function.ttl +++ b/test_ttl/go_cams/should_fail/Test011-has_output-molecular_function.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -346,7 +346,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000250/5d27d1cf00000262 rdf:type owl:NamedIndividual , - ; + ; "359.75"^^xsd:string ; "45"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test012-has_input-complex_GO_complex.ttl b/test_ttl/go_cams/should_fail/Test012-has_input-complex_GO_complex.ttl index 73b03c1..0673524 100644 --- a/test_ttl/go_cams/should_fail/Test012-has_input-complex_GO_complex.ttl +++ b/test_ttl/go_cams/should_fail/Test012-has_input-complex_GO_complex.ttl @@ -169,8 +169,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -345,7 +345,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000269/5d27d1cf00000281 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test012b-has_input-GoComplex.ttl b/test_ttl/go_cams/should_fail/Test012b-has_input-GoComplex.ttl index 74f0ff8..9aebaae 100644 --- a/test_ttl/go_cams/should_fail/Test012b-has_input-GoComplex.ttl +++ b/test_ttl/go_cams/should_fail/Test012b-has_input-GoComplex.ttl @@ -181,8 +181,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -252,7 +252,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000288/5d27d1cf00000293 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test013-has_input-biological_process.ttl b/test_ttl/go_cams/should_fail/Test013-has_input-biological_process.ttl index a7af5a0..af1c698 100644 --- a/test_ttl/go_cams/should_fail/Test013-has_input-biological_process.ttl +++ b/test_ttl/go_cams/should_fail/Test013-has_input-biological_process.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -346,7 +346,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000311/5d27d1cf00000323 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test014-has_input-molecular_function.ttl b/test_ttl/go_cams/should_fail/Test014-has_input-molecular_function.ttl index 8bfcb19..18acb62 100644 --- a/test_ttl/go_cams/should_fail/Test014-has_input-molecular_function.ttl +++ b/test_ttl/go_cams/should_fail/Test014-has_input-molecular_function.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -345,7 +345,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000330/5d27d1cf00000342 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test015-provides_direct_input_for-Biological_process.ttl b/test_ttl/go_cams/should_fail/Test015-provides_direct_input_for-Biological_process.ttl index 88845c1..260660f 100644 --- a/test_ttl/go_cams/should_fail/Test015-provides_direct_input_for-Biological_process.ttl +++ b/test_ttl/go_cams/should_fail/Test015-provides_direct_input_for-Biological_process.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -381,7 +381,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000349/5d27d1cf00000361 rdf:type owl:NamedIndividual , - ; + ; "155"^^xsd:string ; "60"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test016-provides_direct_input_for-cellular_component.ttl b/test_ttl/go_cams/should_fail/Test016-provides_direct_input_for-cellular_component.ttl index a88bdcd..e3b5110 100644 --- a/test_ttl/go_cams/should_fail/Test016-provides_direct_input_for-cellular_component.ttl +++ b/test_ttl/go_cams/should_fail/Test016-provides_direct_input_for-cellular_component.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -443,7 +443,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000368/5d27d1cf00000384 rdf:type owl:NamedIndividual , - ; + ; "155"^^xsd:string ; "60"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl b/test_ttl/go_cams/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl index 53a012e..9ac5cc4 100644 --- a/test_ttl/go_cams/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl +++ b/test_ttl/go_cams/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -404,7 +404,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000387/5d27d1cf00000399 rdf:type owl:NamedIndividual , - ; + ; "155"^^xsd:string ; "60"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl b/test_ttl/go_cams/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl index 218428b..a7fab4b 100644 --- a/test_ttl/go_cams/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl +++ b/test_ttl/go_cams/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0006352 @@ -447,7 +447,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000444/5d27d1cf00000461 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test021-happens_during_GOcomplex.ttl b/test_ttl/go_cams/should_fail/Test021-happens_during_GOcomplex.ttl index d4a89bb..6bb4b11 100644 --- a/test_ttl/go_cams/should_fail/Test021-happens_during_GOcomplex.ttl +++ b/test_ttl/go_cams/should_fail/Test021-happens_during_GOcomplex.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -250,7 +250,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000464/5d27d1cf00000468 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test021b-happens_during-complex.ttl b/test_ttl/go_cams/should_fail/Test021b-happens_during-complex.ttl index ef01652..3f0741b 100644 --- a/test_ttl/go_cams/should_fail/Test021b-happens_during-complex.ttl +++ b/test_ttl/go_cams/should_fail/Test021b-happens_during-complex.ttl @@ -189,8 +189,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -379,7 +379,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000484/5d27d1cf00000494 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test022-happens_during-molecular_function.ttl b/test_ttl/go_cams/should_fail/Test022-happens_during-molecular_function.ttl index 213e48a..3394244 100644 --- a/test_ttl/go_cams/should_fail/Test022-happens_during-molecular_function.ttl +++ b/test_ttl/go_cams/should_fail/Test022-happens_during-molecular_function.ttl @@ -185,8 +185,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -291,7 +291,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000509/5d27d1cf00000517 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test023-enabled_by_2_MolecularEntity.ttl b/test_ttl/go_cams/should_fail/Test023-enabled_by_2_MolecularEntity.ttl index cf4b302..73c031f 100644 --- a/test_ttl/go_cams/should_fail/Test023-enabled_by_2_MolecularEntity.ttl +++ b/test_ttl/go_cams/should_fail/Test023-enabled_by_2_MolecularEntity.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -380,7 +380,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000531/5d27d1cf00000543 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test024-part_of_2_biological_process.ttl b/test_ttl/go_cams/should_fail/Test024-part_of_2_biological_process.ttl index d0dc3c8..f665b77 100644 --- a/test_ttl/go_cams/should_fail/Test024-part_of_2_biological_process.ttl +++ b/test_ttl/go_cams/should_fail/Test024-part_of_2_biological_process.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -380,7 +380,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000550/5d27d1cf00000562 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test025-occurs_in_2_cellular_component.ttl b/test_ttl/go_cams/should_fail/Test025-occurs_in_2_cellular_component.ttl index 992a646..e64662f 100644 --- a/test_ttl/go_cams/should_fail/Test025-occurs_in_2_cellular_component.ttl +++ b/test_ttl/go_cams/should_fail/Test025-occurs_in_2_cellular_component.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -381,7 +381,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000569/5d27d1cf00000581 rdf:type owl:NamedIndividual , - ; + ; "386.75"^^xsd:string ; "49"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl b/test_ttl/go_cams/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl index e07ed5e..a1b999c 100644 --- a/test_ttl/go_cams/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl +++ b/test_ttl/go_cams/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl @@ -181,8 +181,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -385,7 +385,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000627/5d27d1cf00000639 rdf:type owl:NamedIndividual , - ; + ; "409.75"^^xsd:string ; "51"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl b/test_ttl/go_cams/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl index 725b2ac..6ede813 100644 --- a/test_ttl/go_cams/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl +++ b/test_ttl/go_cams/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl @@ -189,8 +189,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -330,7 +330,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000666/5d27d1cf00000676 rdf:type owl:NamedIndividual , - ; + ; "49"^^xsd:string ; "69"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl b/test_ttl/go_cams/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl index a65c509..dad87a5 100644 --- a/test_ttl/go_cams/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl +++ b/test_ttl/go_cams/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl @@ -173,8 +173,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -375,7 +375,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000647/5d27d1cf00000659 rdf:type owl:NamedIndividual , - ; + ; "205.75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/test_ttl/go_cams/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl b/test_ttl/go_cams/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl index 59b5ee7..de9baf0 100644 --- a/test_ttl/go_cams/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl +++ b/test_ttl/go_cams/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl @@ -170,8 +170,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -268,7 +268,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d251e6800000000/5d251e6800000003 rdf:type owl:NamedIndividual , - ; + ; "434.9801025390625"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2019-07-11"^^xsd:string ; diff --git a/test_ttl/go_cams/should_pass/Test001-missing_enabled_by.ttl b/test_ttl/go_cams/should_pass/Test001-missing_enabled_by.ttl index 612a5fd..3bed7b2 100644 --- a/test_ttl/go_cams/should_pass/Test001-missing_enabled_by.ttl +++ b/test_ttl/go_cams/should_pass/Test001-missing_enabled_by.ttl @@ -168,8 +168,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -340,7 +340,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000038/5d27d1cf00000050 rdf:type owl:NamedIndividual , - ; + ; "148.75"^^xsd:string ; "55"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl b/test_ttl/go_cams/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl index 67778d8..13e78e9 100644 --- a/test_ttl/go_cams/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl +++ b/test_ttl/go_cams/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl @@ -185,8 +185,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -389,7 +389,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000407/5d27d1cf00000418 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_pass/Test019-happens_during_BiologicalPhase.ttl b/test_ttl/go_cams/should_pass/Test019-happens_during_BiologicalPhase.ttl index c12f339..2d7bbe8 100644 --- a/test_ttl/go_cams/should_pass/Test019-happens_during_BiologicalPhase.ttl +++ b/test_ttl/go_cams/should_pass/Test019-happens_during_BiologicalPhase.ttl @@ -185,8 +185,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -389,7 +389,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000408/5d27d1cf00000418 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_pass/Test026-has_output_2_MolecularEntity.ttl b/test_ttl/go_cams/should_pass/Test026-has_output_2_MolecularEntity.ttl index c92e650..f2efd83 100644 --- a/test_ttl/go_cams/should_pass/Test026-has_output_2_MolecularEntity.ttl +++ b/test_ttl/go_cams/should_pass/Test026-has_output_2_MolecularEntity.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -380,7 +380,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000588/5d27d1cf00000600 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl b/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl index 171fa5e..a542bd6 100644 --- a/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl +++ b/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl @@ -177,8 +177,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty . rdf:type owl:Class . -### http://purl.obolibrary.org/obo/GO_0006306 - rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0043414 + rdf:type owl:Class . ### http://purl.obolibrary.org/obo/GO_0009008 @@ -455,7 +455,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5d27d1cf00000607/5d27d1cf00000625 rdf:type owl:NamedIndividual , - ; + ; "75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , From 22fe43ab6c264d4963e40ba3ded96db199257e2f Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Tue, 19 Mar 2024 12:20:45 -0400 Subject: [PATCH 19/30] Create WIP_standard_annot_ShEx --- shapes/WIP_standard_annot_ShEx | 541 +++++++++++++++++++++++++++++++++ 1 file changed, 541 insertions(+) create mode 100644 shapes/WIP_standard_annot_ShEx diff --git a/shapes/WIP_standard_annot_ShEx b/shapes/WIP_standard_annot_ShEx new file mode 100644 index 0000000..dcfcfed --- /dev/null +++ b/shapes/WIP_standard_annot_ShEx @@ -0,0 +1,541 @@ +BASE +PREFIX obo: +PREFIX rdf: +PREFIX rdfs: +PREFIX owl: +PREFIX xsd: +PREFIX skos: +PREFIX prov: +#metadata +PREFIX bl: +PREFIX contributor: +PREFIX provided_by: +PREFIX modification_date: +PREFIX creation_date: +PREFIX import_date: +PREFIX xref: +PREFIX exact_match: +PREFIX source: +PREFIX evidence: +PREFIX with: +PREFIX x: +PREFIX y: +#model level annotations +PREFIX ontology: +PREFIX taxon: +PREFIX modelstate: +PREFIX templatestate: +PREFIX oboinowlid: +###contributor, date, providedBy reused +PREFIX title: +PREFIX imports: +# always limit imports to? ; +PREFIX in_taxon: +#semantic: classes +PREFIX GoInformationBiomacromolecule: +PREFIX GoProtein: +PREFIX GoProteinContainingComplex: +PREFIX GoCellularComponent: +PREFIX GoBiologicalProcess: +PREFIX GoAnatomicalStructureDevelopment: +PREFIX GoAnatomicalStructureFormationInvolvedInMorphogenesis: +PREFIX GoAnatomicalStructureMorphogenesis: +PREFIX GoCellDifferentiation: +PREFIX GoCellDivision: +PREFIX GoCellFateCommitment: +PREFIX GoCellFateDetermination: +PREFIX GoCellFateSpecification: +PREFIX GoCellularComponentAssembly: +PREFIX GoCellularComponentDisassembly: +PREFIX GoCellularComponentOrganization: +PREFIX GoDevelopmentalMaturation: +PREFIX GoGrowth: +PREFIX GoLocalization: +PREFIX GoLocomotion: +PREFIX GoProteinContainingComplexRemodeling: +PREFIX GoPatternSpecificationProcess: +PREFIX GoMetabolicProcess: +PREFIX GoTransport: +PREFIX GoMolecularFunction: +PREFIX GoTransporterActivity: +PREFIX GoChemicalEntity: +PREFIX GoEvidence: +PREFIX GoAnatomicalEntity: +PREFIX GoCell: +PREFIX GoOrganism: +PREFIX GoBiologicalPhase: +PREFIX GoLifeCycleStage: +PREFIX GoPlantStructureDevelopmentStage: +#semantic: relations +PREFIX acts_upstream_of: +PREFIX acts_upstream_of_negative_effect: +PREFIX acts_upstream_of_positive_effect: +PREFIX acts_upstream_of_or_within: +PREFIX acts_upstream_of_or_within_negative_effect: +PREFIX acts_upstream_of_or_within_positive_effect: +PREFIX involved_in: +PREFIX part_of: +PREFIX has_part: +PREFIX occurs_in: +PREFIX adjacent_to: +PREFIX overlaps: +PREFIX existence_overlaps: +PREFIX existence_starts_and_ends_during: +PREFIX enabled_by: +PREFIX contributes_to: +PREFIX has_input: +PREFIX has_output: +PREFIX has_primary_input: +PREFIX has_primary_output: +PREFIX has_target_end_location: +PREFIX has_target_start_location: +PREFIX located_in: +PREFIX is_active_in: +PREFIX happens_during: +PREFIX acts_on_population_of: +PREFIX results_in_development_of: +PREFIX results_in_formation_of: +PREFIX results_in_morphogenesis_of: +PREFIX results_in_acquisition_of_features_of: +PREFIX results_in_commitment_to: +PREFIX results_in_determination_of: +PREFIX results_in_specification_of: +PREFIX results_in_assembly_of: +PREFIX results_in_disassembly_of: +PREFIX results_in_organization_of: +PREFIX results_in_maturation_of: +PREFIX results_in_growth_of: +PREFIX results_in_movement_of: +PREFIX results_in_remodeling_of: + + { + a [owl:Ontology] + ; + contributor: xsd:string +; #TODO would be better as an IRI + modification_date: xsd:string {1}; #Use ISO 8601 as a standard. + creation_date: xsd:string {0,1}; #Use ISO 8601 as a standard. + import_date: xsd:string {0,1}; #Use ISO 8601 as a standard. + provided_by: xsd:string +; #TODO would be better as an IRI + rdfs:comment xsd:string *; + modelstate: xsd:string {1}; #TODO would be better as an IRI + templatestate: xsd:string {0,1}; #TODO should be modeled as xsd:boolean but currently a string. No value means false. + in_taxon: . *; + title: xsd:string {1}; + imports: . *; + oboinowlid: . *; #TODO not sure if we really want this? + owl:versionIRI . *; + prov:wasDerivedFrom IRI {0,1}; # for model copy +} + + { + contributor: xsd:string +; #TODO would be better as an IRI + modification_date: xsd:string {1}; #Use ISO 8601 as a standard. + creation_date: xsd:string {0,1}; #Use ISO 8601 as a standard. + import_date: xsd:string {0,1}; #Use ISO 8601 as a standard. + provided_by: xsd:string *; #TODO would be better as an IRI + rdfs:comment xsd:string *; + skos:note xsd:string *; +} + + IRI @ AND EXTRA a { + a [owl:NamedIndividual] * // rdfs:comment "Every entity we care about is a named individual"; + xref: . * // rdfs:comment "mappings for the entity. Value is typically a CURIE string. Currently this is only used for Reactome-derived models." ; + rdfs:label . {0,1} // rdfs:comment "the name of the entity. Currently this is only used for Reactome-derived models." ; + exact_match: . *; + x: . {0,1} // rdfs:comment "X coordinate for node. This is used for caching layouts in the Noctua Graph Editor."; + y: . {0,1} // rdfs:comment "Y coordinate for node. This is used for caching layouts in the Noctua Graph Editor."; + skos:narrower . * // rdfs:comment "This entity (e.g. a node representing a pathway) represents a narrower (in any sense) concept then the target node. "; + skos:broader . * // rdfs:comment "This entity (e.g. a node representing a pathway) represents a broader (in any sense) concept then the target node. "; +} // rdfs:comment "Default allowable metadata for GO-CAM entities" + + { + rdf:type [ owl:Class ] {1}; +} + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoBiologicalProcess: ] ; +} + + BNode @ AND { + owl:complementOf @ +} + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoOrganism: ] ; +} + + @ AND EXTRA a { + a @ ; +} // rdfs:comment "A member of a class of organisms defined in the NCBI taxonomy" + + @ AND EXTRA a { + a ( @ OR @ ) {1}; + part_of: @ *; + has_input: ( @ OR @ OR @ OR @ ) *; + has_output: ( @ OR @ OR @ ) *; + occurs_in: @ {0,1}; + has_target_end_location: @ {0,1}; + has_target_start_location: @ {0,1}; + acts_on_population_of: ( @ OR @ ) *; + happens_during: ( @ OR @ OR @ ) *; +} // rdfs:comment "A biological process" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoAnatomicalStructureDevelopment: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_development_of: @ {0,1}; +} // rdfs:comment "an anatomical structure development class GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoAnatomicalStructureFormationInvolvedInMorphogenesis: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_formation_of: @ {0,1}; +} // rdfs:comment "an anatomical structure formation involved in morphogenesis class GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoAnatomicalStructureMorphogenesis: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_morphogenesis_of: @ {0,1}; +} // rdfs:comment "an anatomical structure morphogenesis class GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellDifferentiation: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_acquisition_of_features_of: @ {0,1}; +} // rdfs:comment "a cell differentiation GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellDivision: ] ; +} + + @ AND EXTRA a { + a @ {1}; + occurs_in: @ {0,1}; +} // rdfs:comment "a cell division GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellFateCommitment: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_commitment_to: @ {0,1}; +} // rdfs:comment "a cell fate commitment GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellFateDetermination: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_determination_of: @ {0,1}; +} // rdfs:comment "a cell fate determination GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellFateSpecification: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_specification_of: @ {0,1}; +} // rdfs:comment "a cell fate specification GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellularComponentAssembly: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_assembly_of: @ {0,1}; +} // rdfs:comment "a cellular component assembly GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellularComponentDisassembly: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_disassembly_of: @ {0,1}; +} // rdfs:comment "a cellular component disassembly GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellularComponentOrganization: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_organization_of: @ {0,1}; +} // rdfs:comment "a cellular component organization GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoDevelopmentalMaturation: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_maturation_of: @ {0,1}; +} // rdfs:comment "a developmental maturation GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoGrowth: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_growth_of: @ {0,1}; +} // rdfs:comment "a growth GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoLocalization: ] ; +} + + @ AND EXTRA a { + a @ {1}; + has_primary_input: ( @ OR @ OR @ OR @ ) *; + has_target_end_location: @ {0,1}; + has_target_start_location: @ {0,1}; +} // rdfs:comment "a localization GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoLocomotion: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_movement_of: @ {0,1}; +} // rdfs:comment "a locomotion GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoMetabolicProcess: ] ; +} + + @ AND EXTRA a { + a @ {1}; + has_primary_input: @ *; + has_primary_output: @ *; +} // rdfs:comment "a metabolic process GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoProteinContainingComplexRemodeling: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_remodeling_of: @ {0,1}; +} // rdfs:comment "a protein containing complex remodeling GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoPatternSpecificationProcess: ] ; +} + + @ AND EXTRA a { + a @ {1}; + results_in_specification_of: @ {0,1}; +} // rdfs:comment "a pattern specification process GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoTransport: ] ; +} + + @ AND EXTRA a { + a @ {1}; + has_primary_input: ( @ OR @ OR @ OR @ ) *; + has_primary_output: ( @ OR @ OR @ OR @ ) *; +} // rdfs:comment "a transport GO biological process or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoMolecularFunction: ] ; +} + + BNode @ AND { + owl:complementOf @ +} + + @ AND EXTRA a { + a ( @ OR @ ) {1}; + part_of: @ *; + has_part: @ *; + occurs_in: @ {0,1}; + has_output: ( @ OR @ ) *; + has_input: ( @ OR @ ) *; + has_primary_input: ( @ OR @ ) *; + has_primary_output: ( @ OR @ ) *; + happens_during: ( @ OR @ OR @ ) *; +} // rdfs:comment "A molecular function" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoTransporterActivity: ]; +} + + @ AND EXTRA a { + a @ {1}; + has_primary_input: ( @ OR @ ) *; + has_primary_output: ( @ OR @ ) *; + has_target_end_location: @ *; + has_target_start_location: @ *; +} // rdfs:comment "a transporter activity GO molecular function or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoBiologicalPhase: ]; +} + + @ AND EXTRA a { + a @; +} // rdfs:comment "a biological phase" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoLifeCycleStage: ]; +} + + @ AND EXTRA a { + a @; +} // rdfs:comment "a lifecycle stage" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoPlantStructureDevelopmentStage: ]; +} + + @ AND EXTRA a { + a @; +} // rdfs:comment "a plant structure developmental stage" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoAnatomicalEntity: ]; +} + + BNode @ AND { + owl:complementOf @ +} + + @ AND EXTRA a { + a ( @ OR @ ); + part_of: @ {0,1}; +} // rdfs:comment "an anatomical entity" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCell: ]; +} + + @ AND EXTRA a { + a @ {1}; + part_of: @ {0,1}; +} // rdfs:comment "a cell or child" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoCellularComponent: ]; +} + + BNode @ AND { + owl:complementOf @ +} + + IRI @ AND EXTRA a { + a [ GoCellularComponent: ]; +} + +# @ AND EXTRA a { # If we want to intersect with anatomical entity, then GO cellular_component needs to subclass anatomical entity in go-lego + @ AND EXTRA a { + a ( @ OR @ ) {1}; + part_of: @ {0,1}; + adjacent_to: @ *; + overlaps: @ *; + existence_overlaps: ( @ OR @ OR @ ) *; + existence_starts_and_ends_during: ( @ OR @ OR @ ) *; +} // rdfs:comment "a cellular component" + + @ AND EXTRA a { + a @; + enables: ( @ OR @ ) {0,1}; + contributes_to: @ {0,1}; + located_in: ( @ OR @ ) {0,1}; + is_active_in: ( @ OR @ OR @VirionComponent> ) {0,1}; + part_of: @ *; + has_part: ( @ OR @ ) *; + existence_overlaps: ( @ OR @ OR @ ) *; + existence_starts_and_ends_during: ( @ OR @ OR @ ) *; + involved_in: ( @ OR @ ) {0,1}; + acts_upstream_of_negative_effect: @ {0,1}; + acts_upstream_of_positive_effect: @ {0,1}; + acts_upstream_of_or_within_negative_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; +} // rdfs:comment "a protein complex" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoProteinContainingComplex: ]; +} + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoProtein: ]; +} + @ AND EXTRA a { + a @ ; + enables: ( @ OR @ ) {0,1}; + contributes_to: @ {0,1}; + located_in: ( @ OR @ ) {0,1}; + is_active_in: ( @ OR @ OR @ ) {0,1}; + part_of: @ {0,1}; + involved_in: ( @ OR @ ) {0,1}; + acts_upstream_of_negative_effect: @ {0,1}; + acts_upstream_of_positive_effect: @ {0,1}; + acts_upstream_of_or_within_negative_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; +}// rdfs:comment "a protein" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoInformationBiomacromolecule: ]; +} + @ AND EXTRA a { + a @ +; + enables: ( @ OR @ ) {0,1}; + contributes_to: @ {0,1}; + located_in: ( @ OR @ ) {0,1}; + is_active_in: ( @ OR @ OR @ ) {0,1}; + part_of: @ {0,1}; + involved_in: ( @ OR @ ) {0,1}; + acts_upstream_of_negative_effect: @ {0,1}; + acts_upstream_of_positive_effect: @ {0,1}; + acts_upstream_of_or_within_negative_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; +}// rdfs:comment "an information biomacromolecule - e.g. a protein or RNA product" + + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoEvidence: ] ; +} + + @ AND EXTRA a { + a @ {1}; + source: xsd:string {1}; + with: xsd:string {0,1} +}// rdfs:comment "A kind of evidence" + + BNode @ AND { + a [ owl:Axiom ] ; + owl:annotatedSource @ ; + owl:annotatedProperty IRI ; + owl:annotatedTarget @ ; + evidence: @ * +} + +# { +# bl:category . {0} +# // rdfs:comment "has no type tag inside" ; +#} // rdfs:comment "has no type tag full rule" + +# { +# bl:category . {1} +#} // rdfs:comment "has exactly one type tag" + +# { +# bl:category . {2,} +#} // rdfs:comment "has multiple type tags" From c289f9ac401ab832046c7826ec09f4110c959c88 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Tue, 19 Mar 2024 12:26:05 -0400 Subject: [PATCH 20/30] Update WIP_standard_annot_ShEx --- shapes/WIP_standard_annot_ShEx | 46 +++++++++++++++++----------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/shapes/WIP_standard_annot_ShEx b/shapes/WIP_standard_annot_ShEx index dcfcfed..2439c83 100644 --- a/shapes/WIP_standard_annot_ShEx +++ b/shapes/WIP_standard_annot_ShEx @@ -456,19 +456,19 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @; - enables: ( @ OR @ ) {0,1}; - contributes_to: @ {0,1}; + enables: ( @ OR @ ) {0,1}; + contributes_to: @ {0,1}; located_in: ( @ OR @ ) {0,1}; is_active_in: ( @ OR @ OR @VirionComponent> ) {0,1}; - part_of: @ *; + part_of: @ *; has_part: ( @ OR @ ) *; existence_overlaps: ( @ OR @ OR @ ) *; existence_starts_and_ends_during: ( @ OR @ OR @ ) *; - involved_in: ( @ OR @ ) {0,1}; - acts_upstream_of_negative_effect: @ {0,1}; - acts_upstream_of_positive_effect: @ {0,1}; - acts_upstream_of_or_within_negative_effect: @ {0,1}; - acts_upstream_of_or_within_positive_effect: @ {0,1}; + involved_in: ( @ OR @ ) {0,1}; + acts_upstream_of_negative_effect: @ {0,1}; + acts_upstream_of_positive_effect: @ {0,1}; + acts_upstream_of_or_within_negative_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { @@ -480,33 +480,33 @@ PREFIX results_in_remodeling_of: } @ AND EXTRA a { a @ ; - enables: ( @ OR @ ) {0,1}; - contributes_to: @ {0,1}; + enables: ( @ OR @ ) {0,1}; + contributes_to: @ {0,1}; located_in: ( @ OR @ ) {0,1}; is_active_in: ( @ OR @ OR @ ) {0,1}; part_of: @ {0,1}; - involved_in: ( @ OR @ ) {0,1}; - acts_upstream_of_negative_effect: @ {0,1}; - acts_upstream_of_positive_effect: @ {0,1}; - acts_upstream_of_or_within_negative_effect: @ {0,1}; - acts_upstream_of_or_within_positive_effect: @ {0,1}; + involved_in: ( @ OR @ ) {0,1}; + acts_upstream_of_negative_effect: @ {0,1}; + acts_upstream_of_positive_effect: @ {0,1}; + acts_upstream_of_or_within_negative_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; }// rdfs:comment "a protein" IRI @ AND EXTRA rdfs:subClassOf { rdfs:subClassOf [ GoInformationBiomacromolecule: ]; } @ AND EXTRA a { - a @ +; - enables: ( @ OR @ ) {0,1}; - contributes_to: @ {0,1}; + a @ +; + enables: ( @ OR @ ) {0,1}; + contributes_to: @ {0,1}; located_in: ( @ OR @ ) {0,1}; is_active_in: ( @ OR @ OR @ ) {0,1}; part_of: @ {0,1}; - involved_in: ( @ OR @ ) {0,1}; - acts_upstream_of_negative_effect: @ {0,1}; - acts_upstream_of_positive_effect: @ {0,1}; - acts_upstream_of_or_within_negative_effect: @ {0,1}; - acts_upstream_of_or_within_positive_effect: @ {0,1}; + involved_in: ( @ OR @ ) {0,1}; + acts_upstream_of_negative_effect: @ {0,1}; + acts_upstream_of_positive_effect: @ {0,1}; + acts_upstream_of_or_within_negative_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; }// rdfs:comment "an information biomacromolecule - e.g. a protein or RNA product" IRI @ AND EXTRA rdfs:subClassOf { From 3bab2e794b5a213f99a8f261cf987ed2fafa6cd6 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Wed, 1 May 2024 09:35:23 -0400 Subject: [PATCH 21/30] Update go-cam-shapes.shex Adding primary input and primary output to main BP shape as a test of the reasoner. --- shapes/go-cam-shapes.shex | 2 ++ 1 file changed, 2 insertions(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 47201c5..0737686 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -193,6 +193,8 @@ PREFIX results_in_remodeling_of: part_of: @ *; has_input: ( @ OR @ OR @ OR @ ) *; has_output: ( @ OR @ OR @ ) *; + has_primary_input: @ *; + has_primary_output: @ *; occurs_in: @ {0,1}; transports_or_maintains_localization_of: ( @ OR @ ) *; has_target_end_location: @ {0,1}; From 3320990a2f60889d6a8a54162d4704a05374e245 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 2 May 2024 17:06:55 -0400 Subject: [PATCH 22/30] Update WIP_standard_annot_ShEx A few small modifications for workbenches discussion tomorrow --- shapes/WIP_standard_annot_ShEx | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/shapes/WIP_standard_annot_ShEx b/shapes/WIP_standard_annot_ShEx index 2439c83..1ec1503 100644 --- a/shapes/WIP_standard_annot_ShEx +++ b/shapes/WIP_standard_annot_ShEx @@ -172,6 +172,8 @@ PREFIX results_in_remodeling_of: part_of: @ *; has_input: ( @ OR @ OR @ OR @ ) *; has_output: ( @ OR @ OR @ ) *; + has_primary_input: ( @ OR @ OR @ OR @ ) *; + has_primary_output: ( @ OR @ OR @ ) *; occurs_in: @ {0,1}; has_target_end_location: @ {0,1}; has_target_start_location: @ {0,1}; @@ -457,18 +459,18 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @; enables: ( @ OR @ ) {0,1}; - contributes_to: @ {0,1}; located_in: ( @ OR @ ) {0,1}; is_active_in: ( @ OR @ OR @VirionComponent> ) {0,1}; part_of: @ *; - has_part: ( @ OR @ ) *; - existence_overlaps: ( @ OR @ OR @ ) *; - existence_starts_and_ends_during: ( @ OR @ OR @ ) *; involved_in: ( @ OR @ ) {0,1}; acts_upstream_of_negative_effect: @ {0,1}; acts_upstream_of_positive_effect: @ {0,1}; acts_upstream_of_or_within_negative_effect: @ {0,1}; - acts_upstream_of_or_within_positive_effect: @ {0,1}; + acts_upstream_of_or_within_positive_effect: @ {0,1}; + has_part: ( @ OR @ ) *; + existence_overlaps: ( @ OR @ OR @ ) *; + existence_starts_and_ends_during: ( @ OR @ OR @ ) *; + } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { From 675934dd43bebd607f4e63251a027a43a9135e96 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 9 May 2024 16:11:06 -0400 Subject: [PATCH 23/30] Update README.md Removed a new line genontology/noctua-standard-annotations#14 --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 39878ac..c50af18 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,6 @@ Using RDF Shapes to define the schema of Gene Ontology Causal Activity Models - # Schema See [shapes/go-cam-shapes.shex](shapes/go-cam-shapes.shex) From 7a87fd5d2199aa04142de4e90ab5261816423a50 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Thu, 9 May 2024 16:20:18 -0400 Subject: [PATCH 24/30] Update go-cam-shapes.shex Added an extra line --- shapes/go-cam-shapes.shex | 1 + 1 file changed, 1 insertion(+) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 0737686..dc5684b 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -129,6 +129,7 @@ PREFIX results_in_growth_of: PREFIX results_in_movement_of: PREFIX results_in_remodeling_of: + { a [owl:Ontology] + ; contributor: xsd:string +; #TODO would be better as an IRI From 3734d2e0f1d6adee71911c57dc98e989680f8a39 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Fri, 10 May 2024 17:01:49 -0400 Subject: [PATCH 25/30] Update go-cam-shapes.shex Adding // true; comment to constrain relations' use for standard annotations --- shapes/go-cam-shapes.shex | 37 ++++++++++++++++++++----------------- 1 file changed, 20 insertions(+), 17 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index dc5684b..82bc851 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -408,32 +408,32 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - enabled_by: ( @ OR @ ) *; + enabled_by: ( @ OR @ ) *; // true; part_of: @ *; - has_part: @ *; + has_part: @ *; // true; occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; has_primary_input: ( @ OR @ ) *; has_primary_output: ( @ OR @ ) *; - directly_provides_input_for: ( @ OR @ ) *; + directly_provides_input_for: ( @ OR @ ) *; // true; regulates: ( @ OR @ ) *; negatively_regulates: ( @ OR @ ) *; positively_regulates: ( @ OR @ ) *; directly_regulates: ( @ OR @ ) *; directly_negatively_regulates: ( @ OR @ ) *; directly_positively_regulates: ( @ OR @ ) *; - indirectly_regulates: ( @ OR @) *; - indirectly_positively_regulates: ( @ OR @ ) *; - indirectly_negatively_regulates: ( @ OR @ ) *; - constitutively_upstream_of: ( @ OR @ ) *; - removes_input_for: ( @ OR @ ) *; - has_small_molecule_regulator: @ *; - has_small_molecule_activator: @ *; - has_small_molecule_inhibitor: @ *; - causally_upstream_of_or_within: ( @ OR @ OR @ ) *; - causally_upstream_of_or_within_negative_effect: @ *; - causally_upstream_of_or_within_positive_effect: @ *; + indirectly_regulates: ( @ OR @) *; // true; + indirectly_positively_regulates: ( @ OR @ ) *; // true; + indirectly_negatively_regulates: ( @ OR @ ) *; // true; + constitutively_upstream_of: ( @ OR @ ) *; // true; + removes_input_for: ( @ OR @ ) *; // true; + has_small_molecule_regulator: @ *; // true; + has_small_molecule_activator: @ *; // true; + has_small_molecule_inhibitor: @ *; // true; + causally_upstream_of_or_within: ( @ OR @ OR @ ) *; // true; + causally_upstream_of_or_within_negative_effect: @ *; // true; + causally_upstream_of_or_within_positive_effect: @ *; // true; causally_upstream_of: ( @ OR @ OR @ ) *; causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; @@ -524,11 +524,14 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @; - located_in: @ {0,1}; - is_active_in: @ OR @ {0,1}; - has_part: ( @ OR @) *; + located_in: @ {0,1}; // true; + is_active_in: @ OR @ {0,1}; // true; + part_of: @ {0,1}; + adjacent_to: @ *; + overlaps: @ *; existence_overlaps: ( @ OR @ OR @ ) *; existence_starts_and_ends_during: ( @ OR @ OR @ ) *; + has_part: ( @ OR @) *; // true; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { From 967a11e0ae6737a6afe61f48a981ee721bdff966 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Fri, 10 May 2024 17:18:28 -0400 Subject: [PATCH 26/30] Update go-cam-shapes.shex Trying again with adding extensions rules. Spaces vs tabs? From f54cfdbf622cc98f6029264cff3a56e45ed695a1 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Mon, 13 May 2024 12:31:43 -0400 Subject: [PATCH 27/30] Update go-cam-shapes.shex Removing extra semi-colon --- shapes/go-cam-shapes.shex | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index 82bc851..e9690ec 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -408,32 +408,32 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - enabled_by: ( @ OR @ ) *; // true; + enabled_by: ( @ OR @ ) * // true; part_of: @ *; - has_part: @ *; // true; + has_part: @ * // true; occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; has_primary_input: ( @ OR @ ) *; has_primary_output: ( @ OR @ ) *; - directly_provides_input_for: ( @ OR @ ) *; // true; + directly_provides_input_for: ( @ OR @ ) * // true; regulates: ( @ OR @ ) *; negatively_regulates: ( @ OR @ ) *; positively_regulates: ( @ OR @ ) *; directly_regulates: ( @ OR @ ) *; directly_negatively_regulates: ( @ OR @ ) *; directly_positively_regulates: ( @ OR @ ) *; - indirectly_regulates: ( @ OR @) *; // true; - indirectly_positively_regulates: ( @ OR @ ) *; // true; - indirectly_negatively_regulates: ( @ OR @ ) *; // true; - constitutively_upstream_of: ( @ OR @ ) *; // true; - removes_input_for: ( @ OR @ ) *; // true; - has_small_molecule_regulator: @ *; // true; - has_small_molecule_activator: @ *; // true; - has_small_molecule_inhibitor: @ *; // true; - causally_upstream_of_or_within: ( @ OR @ OR @ ) *; // true; - causally_upstream_of_or_within_negative_effect: @ *; // true; - causally_upstream_of_or_within_positive_effect: @ *; // true; + indirectly_regulates: ( @ OR @) * // true; + indirectly_positively_regulates: ( @ OR @ ) * // true; + indirectly_negatively_regulates: ( @ OR @ ) * // true; + constitutively_upstream_of: ( @ OR @ ) * // true; + removes_input_for: ( @ OR @ ) * // true; + has_small_molecule_regulator: @ * // true; + has_small_molecule_activator: @ * // true; + has_small_molecule_inhibitor: @ * // true; + causally_upstream_of_or_within: ( @ OR @ OR @ ) * // true; + causally_upstream_of_or_within_negative_effect: @ * // true; + causally_upstream_of_or_within_positive_effect: @ * // true; causally_upstream_of: ( @ OR @ OR @ ) *; causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; @@ -524,14 +524,14 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a @; - located_in: @ {0,1}; // true; - is_active_in: @ OR @ {0,1}; // true; + located_in: @ {0,1} // true; + is_active_in: @ OR @ {0,1} // true; part_of: @ {0,1}; adjacent_to: @ *; overlaps: @ *; existence_overlaps: ( @ OR @ OR @ ) *; existence_starts_and_ends_during: ( @ OR @ OR @ ) *; - has_part: ( @ OR @) *; // true; + has_part: ( @ OR @) * // true; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { From 636ab2281c71489b382b80b66d5d069e5e0cd4e4 Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Tue, 21 May 2024 11:02:02 -0700 Subject: [PATCH 28/30] updated the json export code to use the curies lib --- python/json_export.py | 18 +- shapes/json/shex_dump.json | 219 ++++++++--- shapes/json/shex_full.json | 742 ++++++++----------------------------- 3 files changed, 345 insertions(+), 634 deletions(-) diff --git a/python/json_export.py b/python/json_export.py index da433c3..adf5244 100644 --- a/python/json_export.py +++ b/python/json_export.py @@ -1,7 +1,11 @@ from os import path import json +from pathlib import Path +import os from ontobio.rdfgen.assoc_rdfgen import prefix_context -from prefixcommons.curie_util import contract_uri +#from prefixcommons.curie_util import contract_uri + +from curies import Converter, Record from pyshexc.parser_impl import generate_shexj from typing import Optional, List, Union from ShExJSG.ShExJ import Shape, ShapeAnd, ShapeOr, ShapeNot, TripleConstraint, shapeExpr, \ @@ -11,18 +15,16 @@ from shex_json_linkml import Association, AssociationCollection from linkml_runtime.dumpers import JSONDumper from linkml_runtime.loaders import JSONLoader -from pathlib import Path -import os + OUT_JSON = os.path.join('../shapes/json/shex_dump.json') +converter = Converter.from_prefix_map(prefix_context) def get_suffix(uri): - suffix = contract_uri(uri, cmaps=[prefix_context]) - if len(suffix) > 0: - return suffix[0] - - return path.basename(uri) + suffix = converter.compress(uri) + + return suffix if suffix else uri class NoctuaFormShex: diff --git a/shapes/json/shex_dump.json b/shapes/json/shex_dump.json index cb75396..658d0a0 100644 --- a/shapes/json/shex_dump.json +++ b/shapes/json/shex_dump.json @@ -25,7 +25,7 @@ "is_required": false, "context": "", "predicate": "RO:0002233", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -39,16 +39,13 @@ "is_required": false, "context": "", "predicate": "RO:0002234", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ - "CHEBI:24431", - "CARO:0000000", - "GO:0032991", - "NCBITaxon:1" + "CHEBI:24431" ], "is_multivalued": true, "is_required": false, @@ -60,9 +57,7 @@ "subject": "GO:0008150", "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ - "CHEBI:24431", - "CARO:0000000", - "GO:0032991" + "CHEBI:24431" ], "is_multivalued": true, "is_required": false, @@ -131,7 +126,7 @@ "is_required": false, "context": "", "predicate": "RO:0002411", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -145,7 +140,7 @@ "is_required": false, "context": "", "predicate": "RO:0002305", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -159,7 +154,7 @@ "is_required": false, "context": "", "predicate": "RO:0002304", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -171,7 +166,7 @@ "is_required": false, "context": "", "predicate": "RO:0002211", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -183,7 +178,7 @@ "is_required": false, "context": "", "predicate": "RO:0002212", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -195,7 +190,7 @@ "is_required": false, "context": "", "predicate": "RO:0002213", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0008150", @@ -210,6 +205,20 @@ "predicate": "RO:0012003", "exclude_from_extensions": false }, + { + "subject": "GO:0008150", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "GO:0044848", + "UBERON:0000105", + "PO:0009012" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0002092", + "exclude_from_extensions": false + }, { "subject": "GO:0048856", "root_subject": "GO:0008150", @@ -250,7 +259,7 @@ "subject": "GO:0030154", "root_subject": "GO:0008150", "object": [ - "CL:0000003" + "CL:0000000" ], "is_multivalued": false, "is_required": false, @@ -262,7 +271,7 @@ "subject": "GO:0051301", "root_subject": "GO:0008150", "object": [ - "CL:0000003" + "CL:0000000" ], "is_multivalued": false, "is_required": false, @@ -274,7 +283,7 @@ "subject": "GO:0045165", "root_subject": "GO:0008150", "object": [ - "CL:0000003" + "CL:0000000" ], "is_multivalued": false, "is_required": false, @@ -286,7 +295,7 @@ "subject": "GO:0001709", "root_subject": "GO:0008150", "object": [ - "CL:0000003" + "CL:0000000" ], "is_multivalued": false, "is_required": false, @@ -298,7 +307,7 @@ "subject": "GO:0001708", "root_subject": "GO:0008150", "object": [ - "CL:0000003" + "CL:0000000" ], "is_multivalued": false, "is_required": false, @@ -500,11 +509,11 @@ "CHEBI:33695", "GO:0032991" ], - "is_multivalued": false, + "is_multivalued": true, "is_required": false, "context": "", "predicate": "RO:0002333", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -516,7 +525,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000050", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -540,7 +549,7 @@ "is_required": false, "context": "", "predicate": "BFO:0000066", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -568,6 +577,32 @@ "predicate": "RO:0002233", "exclude_from_extensions": false }, + { + "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "CHEBI:24431", + "GO:0032991" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0004009", + "exclude_from_extensions": false + }, + { + "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "CHEBI:24431", + "GO:0032991" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0004008", + "exclude_from_extensions": false + }, { "subject": "GO:0003674", "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", @@ -579,7 +614,7 @@ "is_required": false, "context": "", "predicate": "RO:0002413", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -592,7 +627,7 @@ "is_required": false, "context": "", "predicate": "RO:0002211", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -605,7 +640,7 @@ "is_required": false, "context": "", "predicate": "RO:0002212", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -618,7 +653,7 @@ "is_required": false, "context": "", "predicate": "RO:0002213", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -631,7 +666,7 @@ "is_required": false, "context": "", "predicate": "RO:0002578", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -644,7 +679,7 @@ "is_required": false, "context": "", "predicate": "RO:0002630", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -657,7 +692,7 @@ "is_required": false, "context": "", "predicate": "RO:0002629", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -670,7 +705,7 @@ "is_required": false, "context": "", "predicate": "RO:0012012", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -683,7 +718,7 @@ "is_required": false, "context": "", "predicate": "RO:0002407", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -696,7 +731,7 @@ "is_required": false, "context": "", "predicate": "RO:0002409", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -709,7 +744,7 @@ "is_required": false, "context": "", "predicate": "RO:0012009", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -722,7 +757,43 @@ "is_required": false, "context": "", "predicate": "RO:0012010", - "exclude_from_extensions": true + "exclude_from_extensions": false + }, + { + "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "CHEBI:24431" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0012000", + "exclude_from_extensions": false + }, + { + "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "CHEBI:24431" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0012001", + "exclude_from_extensions": false + }, + { + "subject": "GO:0003674", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "CHEBI:24431" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0012002", + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -736,7 +807,7 @@ "is_required": false, "context": "", "predicate": "RO:0002418", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -748,7 +819,7 @@ "is_required": false, "context": "", "predicate": "RO:0004046", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -760,7 +831,7 @@ "is_required": false, "context": "", "predicate": "RO:0004047", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -774,7 +845,7 @@ "is_required": false, "context": "", "predicate": "RO:0002411", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -788,7 +859,7 @@ "is_required": false, "context": "", "predicate": "RO:0002305", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -802,7 +873,7 @@ "is_required": false, "context": "", "predicate": "RO:0002304", - "exclude_from_extensions": true + "exclude_from_extensions": false }, { "subject": "GO:0003674", @@ -832,6 +903,32 @@ "predicate": "RO:0002313", "exclude_from_extensions": false }, + { + "subject": "GO:0005215", + "root_subject": "GO:0003674", + "object": [ + "CHEBI:24431", + "GO:0032991" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0004009", + "exclude_from_extensions": false + }, + { + "subject": "GO:0005215", + "root_subject": "GO:0003674", + "object": [ + "CHEBI:24431", + "GO:0032991" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0004008", + "exclude_from_extensions": false + }, { "subject": "GO:0005215", "root_subject": "GO:0003674", @@ -882,7 +979,7 @@ "exclude_from_extensions": false }, { - "subject": "CL:0000003", + "subject": "CL:0000000", "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", "object": [ "CARO:0000000" @@ -1023,6 +1120,42 @@ "predicate": "RO:0002491", "exclude_from_extensions": false }, + { + "subject": "CHEBI:24431", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "GO:0003674" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0012004", + "exclude_from_extensions": false + }, + { + "subject": "CHEBI:24431", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "GO:0003674" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0012005", + "exclude_from_extensions": false + }, + { + "subject": "CHEBI:24431", + "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "object": [ + "GO:0003674" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0012006", + "exclude_from_extensions": false + }, { "subject": "CHEBI:36080", "root_subject": "CHEBI:24431", diff --git a/shapes/json/shex_full.json b/shapes/json/shex_full.json index 2d13730..65af115 100644 --- a/shapes/json/shex_full.json +++ b/shapes/json/shex_full.json @@ -604,17 +604,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -628,44 +618,19 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0004009", - "valueExpr": { - "type": "ShapeOr", - "shapeExprs": [ - "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", - "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", - "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex", - "http://purl.obolibrary.org/obo/go/shapes/Organism" - ] - }, + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "min": 0, "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0004008", - "valueExpr": { - "type": "ShapeOr", - "shapeExprs": [ - "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", - "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", - "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" - ] - }, + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "min": 0, "max": -1 }, @@ -715,17 +680,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -739,17 +694,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -763,68 +708,28 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002211", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002212", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002213", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -838,74 +743,24 @@ }, "min": 0, "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0002092", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/BiologicalPhase", + "http://purl.obolibrary.org/obo/go/shapes/LifeCycleStage", + "http://purl.obolibrary.org/obo/go/shapes/PlantStructureDevelopmentStage" + ] + }, + "min": 0, + "max": -1 } ] }, "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, { "type": "Annotation", "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -1191,7 +1046,7 @@ { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002315", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/NativeCell", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/Cell", "min": 0, "max": 1 } @@ -1264,7 +1119,7 @@ { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002233", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/NativeCell", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/Cell", "min": 0, "max": 1 } @@ -1337,7 +1192,7 @@ { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002348", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/NativeCell", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/Cell", "min": 0, "max": 1 } @@ -1410,7 +1265,7 @@ { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002349", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/NativeCell", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/Cell", "min": 0, "max": 1 } @@ -1483,7 +1338,7 @@ { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002356", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/NativeCell", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/Cell", "min": 0, "max": 1 } @@ -2529,34 +2384,14 @@ ] }, "min": 0, - "max": 1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/BFO_0000050", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2570,17 +2405,7 @@ "predicate": "http://purl.obolibrary.org/obo/BFO_0000066", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", "min": 0, - "max": 1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": 1 }, { "type": "TripleConstraint", @@ -2608,6 +2433,32 @@ "min": 0, "max": -1 }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0004009", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" + ] + }, + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0004008", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" + ] + }, + "min": 0, + "max": -1 + }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002413", @@ -2619,17 +2470,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2642,17 +2483,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2665,17 +2496,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2688,17 +2509,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2711,17 +2522,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2734,17 +2535,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2757,17 +2548,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2780,17 +2561,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2803,17 +2574,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2826,17 +2587,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2849,17 +2600,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2872,17 +2613,28 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0012000", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0012001", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0012002", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "min": 0, + "max": -1 }, { "type": "TripleConstraint", @@ -2896,51 +2648,21 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0004046", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0004047", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2954,17 +2676,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -2978,17 +2690,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -3002,17 +2704,7 @@ ] }, "min": 0, - "max": -1, - "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - } - ] + "max": -1 }, { "type": "TripleConstraint", @@ -3031,174 +2723,6 @@ ] }, "annotations": [ - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, - { - "type": "Annotation", - "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", - "object": { - "value": "true", - "type": "http://www.w3.org/2001/XMLSchema#boolean" - } - }, { "type": "Annotation", "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -3276,6 +2800,32 @@ "min": 0, "max": -1 }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0004009", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" + ] + }, + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0004008", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" + ] + }, + "min": 0, + "max": -1 + }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0002339", @@ -3597,7 +3147,7 @@ }, { "type": "ShapeAnd", - "id": "http://purl.obolibrary.org/obo/go/shapes/NativeCellClass", + "id": "http://purl.obolibrary.org/obo/go/shapes/CellClass", "shapeExprs": [ { "type": "ShapeAnd", @@ -3620,7 +3170,7 @@ "valueExpr": { "type": "NodeConstraint", "values": [ - "http://purl.obolibrary.org/obo/CL_0000003" + "http://purl.obolibrary.org/obo/CL_0000000" ] } } @@ -3629,7 +3179,7 @@ }, { "type": "ShapeAnd", - "id": "http://purl.obolibrary.org/obo/go/shapes/NativeCell", + "id": "http://purl.obolibrary.org/obo/go/shapes/Cell", "shapeExprs": [ "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", { @@ -3643,7 +3193,7 @@ { "type": "TripleConstraint", "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/NativeCellClass", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/CellClass", "min": 1, "max": 1 }, @@ -3661,7 +3211,7 @@ "type": "Annotation", "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", "object": { - "value": "a native cell or child" + "value": "a cell or child" } } ] @@ -3981,11 +3531,37 @@ "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" ], "expression": { - "type": "TripleConstraint", - "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntityClass", - "min": 1, - "max": -1 + "type": "EachOf", + "expressions": [ + { + "type": "TripleConstraint", + "predicate": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntityClass", + "min": 1, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0012004", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0012005", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0012006", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction", + "min": 0, + "max": -1 + } + ] }, "annotations": [ { From 5db4d993b252527d1014d8d4336b8fe8ed192874 Mon Sep 17 00:00:00 2001 From: vanaukenk Date: Tue, 4 Jun 2024 09:26:56 -0400 Subject: [PATCH 29/30] Update go-cam-shapes.shex --- shapes/go-cam-shapes.shex | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex index e9690ec..dd61728 100644 --- a/shapes/go-cam-shapes.shex +++ b/shapes/go-cam-shapes.shex @@ -417,12 +417,12 @@ PREFIX results_in_remodeling_of: has_primary_input: ( @ OR @ ) *; has_primary_output: ( @ OR @ ) *; directly_provides_input_for: ( @ OR @ ) * // true; - regulates: ( @ OR @ ) *; - negatively_regulates: ( @ OR @ ) *; - positively_regulates: ( @ OR @ ) *; - directly_regulates: ( @ OR @ ) *; - directly_negatively_regulates: ( @ OR @ ) *; - directly_positively_regulates: ( @ OR @ ) *; + regulates: ( @ OR @ ) * // true; + negatively_regulates: ( @ OR @ ) * // true; + positively_regulates: ( @ OR @ ) * // true; + directly_regulates: ( @ OR @ ) * // true; + directly_negatively_regulates: ( @ OR @ ) * // true; + directly_positively_regulates: ( @ OR @ ) * // true; indirectly_regulates: ( @ OR @) * // true; indirectly_positively_regulates: ( @ OR @ ) * // true; indirectly_negatively_regulates: ( @ OR @ ) * // true; @@ -434,9 +434,9 @@ PREFIX results_in_remodeling_of: causally_upstream_of_or_within: ( @ OR @ OR @ ) * // true; causally_upstream_of_or_within_negative_effect: @ * // true; causally_upstream_of_or_within_positive_effect: @ * // true; - causally_upstream_of: ( @ OR @ OR @ ) *; - causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; - causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; + causally_upstream_of: ( @ OR @ OR @ ) * // true; + causally_upstream_of_negative_effect: ( @ OR @ OR @ ) * // true; + causally_upstream_of_positive_effect: ( @ OR @ OR @ ) * // true; happens_during: ( @ OR @ OR @ ) *; } // rdfs:comment "A molecular function" From 20f3b23f17011a0efcb53fe100da09592112e775 Mon Sep 17 00:00:00 2001 From: tmushayahama Date: Tue, 4 Jun 2024 18:15:37 -0700 Subject: [PATCH 30/30] Now using the curies lib --- python/go_context.json | 224 +++++++++++++++++++ python/json_export.py | 25 ++- python/shex_json_linkml.py | 2 - shapes/json/shex_dump.json | 198 ++++++++++------- shapes/json/shex_full.json | 373 ++++++++++++++++++++++++++++++-- shapes/json/terms_metadata.json | 152 ++++++++----- 6 files changed, 814 insertions(+), 160 deletions(-) create mode 100644 python/go_context.json diff --git a/python/go_context.json b/python/go_context.json new file mode 100644 index 0000000..57a27fb --- /dev/null +++ b/python/go_context.json @@ -0,0 +1,224 @@ +{ + "@context": { + "dc": "http://purl.org/dc/terms/", + "dcat": "http://www.w3.org/ns/dcat#", + "faldo": "http://biohackathon.org/resource/faldo#", + "foaf": "http://xmlns.com/foaf/0.1/", + "idot": "http://identifiers.org/", + "oa": "http://www.w3.org/ns/oa#", + "owl": "http://www.w3.org/2002/07/owl#", + "prov": "http://www.w3.org/ns/prov#", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "void": "http://rdfs.org/ns/void#", + "xsd": "http://www.w3.org/2001/XMLSchema#", + "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", + "gomodel": "http://model.geneontology.org/", + "CARO": "http://purl.obolibrary.org/obo/CARO_", + "BIOMD": "http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=", + "COG_Function": "http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=", + "WB": "http://identifiers.org/wormbase/", + "FBbt": "http://purl.obolibrary.org/obo/FBbt_", + "KEGG_LIGAND": "http://www.genome.jp/dbget-bin/www_bget?cpd:", + "PSO_GIT": "https://github.com/Planteome/plant-stress-ontology/issues/", + "MaizeGDB_stock": "http://maizegdb.org/data_center/stock?id=", + "EMAPA": "http://purl.obolibrary.org/obo/EMAPA_", + "GO": "http://purl.obolibrary.org/obo/GO_", + "NCBI_GP": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=", + "NMPDR": "http://www.nmpdr.org/linkin.cgi?id=", + "CASSPC": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=", + "TGD_REF": "http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=", + "NCBIGene": "http://identifiers.org/ncbigene/", + "KEGG_REACTION": "http://www.genome.jp/dbget-bin/www_bget?rn:", + "PseudoCAP": "http://v2.pseudomonas.com/getAnnotation.do?locusID=", + "UniPathway": "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=", + "MEROPS_fam": "http://merops.sanger.ac.uk/cgi-bin/famsum?family=", + "GO_REF": "http://purl.obolibrary.org/obo/go/references/", + "VEGA": "http://vega.sanger.ac.uk/id/", + "ZFIN": "http://identifiers.org/zfin/", + "AspGD_REF": "http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=", + "RO": "http://purl.obolibrary.org/obo/RO_", + "Pfam": "http://pfam.xfam.org/family/", + "UBERON": "http://purl.obolibrary.org/obo/UBERON_", + "GR": "http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=", + "PDB": "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=", + "CORIELL": "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=", + "JCVI_GenProp": "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=", + "SGN": "http://identifiers.org/sgn/", + "BFO": "http://purl.obolibrary.org/obo/BFO_", + "Genesys-pgr": "https://www.genesys-pgr.org/acn/search?q=", + "UniMod": "http://www.unimod.org/modifications_view.php?editid1=", + "UM-BBD_reactionID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=", + "PubChem_Substance": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=", + "EcoCyc": "http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=", + "Reactome": "http://identifiers.org/reactome/", + "InterPro": "http://identifiers.org/interpro/", + "UniRule": "http://www.uniprot.org/unirule/", + "MGCSC_GENETIC_STOCKS": "http://www.maizegdb.org/cgi-bin/displaystockrecord.cgi?id=", + "dictyBase": "http://identifiers.org/dictybase/", + "PO_GIT": "https://github.com/Planteome/plant-ontology/issues/", + "AspGD_LOCUS": "http://identifiers.org/aspgd.locus/", + "SGD": "http://identifiers.org/sgd/", + "COG_Pathway": "http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=", + "ENZYME": "http://www.expasy.ch/cgi-bin/nicezyme.pl?", + "PAMGO_MGG": "http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=", + "AgBase": "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=", + "AraCyc": "http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=", + "EcoCyc_REF": "http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=", + "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", + "HGNC": "http://identifiers.org/hgnc/", + "dictyBase_gene_name": "http://dictybase.org/gene/", + "TAIR": "http://identifiers.org/tair.locus/", + "EnsemblFungi": "http://www.ensemblgenomes.org/id/", + "Wikipedia": "http://en.wikipedia.org/wiki/", + "SUPERFAMILY": "http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF", + "SWALL": "http://ca.expasy.org/cgi-bin/sprot-search-de?S=1&T=1&SEARCH=", + "PSI-MOD": "http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:", + "FYPO": "http://purl.obolibrary.org/obo/FYPO_", + "RGD": "http://identifiers.org/rgd/", + "UM-BBD_enzymeID": "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=", + "Broad_MGG": "http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S", + "Swiss-Prot": "http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinac=", + "PMID": "http://www.ncbi.nlm.nih.gov/pubmed/", + "Xenbase": "http://identifiers.org/xenbase/", + "PR": "http://purl.obolibrary.org/obo/PR_", + "MIPS_funcat": "http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=", + "GR_REF": "http://www.gramene.org/db/literature/pub_search?ref_id=", + "MaizeGDB": "http://maizegdb.org/gene_center/gene/", + "HAMAP": "http://hamap.expasy.org/unirule/", + "SGN_ref": "http://www.sgn.cornell.edu/chado/publication.pl?pub_id=", + "TO_GIT": "https://github.com/Planteome/plant-trait-ontology/issues/", + "MeSH": "http://n2t.net/MESH:", + "GR_PROTEIN": "http://identifiers.org/gramene.protein/", + "MaizeGDB_REF": "http://maizegdb.org/data_center/reference?id=", + "GEO": "http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=", + "PO": "http://purl.obolibrary.org/obo/PO_", + "PomBase": "http://identifiers.org/pombase/", + "ENA": "http://www.ebi.ac.uk/ena/data/view/", + "PIRSF": "http://pir.georgetown.edu/cgi-bin/ipcSF?id=", + "EMBL": "http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=", + "Prosite": "http://www.expasy.ch/cgi-bin/prosite-search-ac?", + "H-invDB_cDNA": "http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=", + "EC": "http://www.expasy.org/enzyme/", + "MACSC_REF": "http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=", + "PAMGO_VMD": "http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=", + "IRGC": "https://www.genesys-pgr.org/acn/search?q=IRGC+", + "NASC_code": "http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=", + "COG_Cluster": "http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=", + "TreeGenes": "http://dendrome.ucdavis.edu/treegenes/protein/view_protein.php?id=", + "WB_REF": "http://www.wormbase.org/db/misc/paper?name=", + "TGD_LOCUS": "http://db.ciliate.org/cgi-bin/locus.pl?locus=", + "MA": "http://purl.obolibrary.org/obo/MA_", + "UniProtKB": "http://identifiers.org/uniprot/", + "MGI": "http://identifiers.org/mgi/", + "GRINDesc": "https://npgsweb.ars-grin.gov/gringlobal/descriptordetail.aspx?id=", + "DDANAT": "http://purl.obolibrary.org/obo/DDANAT_", + "RAP-DB": "http://rapdb.dna.affrc.go.jp/tools/search/run?id=on&attr=desc&attr=cgs&attr=cgn&attr=cgss&attr=cgns&attr=rgss&attr=rgns&keyword=", + "KEGG_PATHWAY": "http://identifiers.org/kegg.pathway/", + "JCVI_CMR": "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=", + "dictyBase_REF": "http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=", + "DOI": "http://dx.doi.org/", + "LIFEdb": "http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=", + "PANTHER": "http://identifiers.org/panther.family/", + "Gene3D": "http://gene3d.biochem.ucl.ac.uk/search?mode=family&sterm=", + "PATRIC": "http://patric.vbi.vt.edu/gene/overview.php?fid=", + "FB": "http://identifiers.org/flybase/", + "PAINT_REF": "http://www.pantherdb.org/panther/lookupId.jsp?id=PTHR", + "CASREF": "http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=", + "ENSEMBL": "http://identifiers.org/ensembl/", + "SMART": "http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=", + "RefSeq": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=", + "WBls": "http://purl.obolibrary.org/obo/WBls_", + "MaizeGDB_QTL": "http://www.maizegdb.org/data_center/trait?id=", + "SOY_ref": "http://www.soybase.org/sbt/search/search_results.php?category=Soybase_ID&search_term=", + "ECO": "http://purl.obolibrary.org/obo/ECO_", + "CGD_REF": "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=", + "ECK": "http://www.ecogene.org/geneInfo.php?eck_id=", + "CGD": "http://identifiers.org/cgd/", + "GR_GENE": "http://identifiers.org/gramene.gene/", + "RNAmods": "http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?", + "KEGG_ENZYME": "http://identifiers.org/kegg.enzyme/", + "CACAO": "http://gowiki.tamu.edu/wiki/index.php/", + "IUPHAR_GPCR": "http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=", + "JCVI_TIGRFAMS": "http://search.jcvi.org/search?p&q=", + "SOY_QTL": "http://soybase.org/sbt/search/search_results.php?category=QTLName&search_term=", + "DDBJ": "http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=", + "PRINTS": "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=", + "PO_REF": "http://planteome.org/po_ref/", + "IMG": "http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=", + "CL": "http://purl.obolibrary.org/obo/CL_", + "UniProtKB-SubCell": "http://www.uniprot.org/locations/", + "NIF_Subcellular": "http://www.neurolex.org/wiki/", + "GeneDB": "http://identifiers.org/genedb/", + "ApiDB_PlasmoDB": "http://www.plasmodb.org/gene/", + "RNAcentral": "http://rnacentral.org/rna/", + "CGD_LOCUS": "http://www.candidagenome.org/cgi-bin/locus.pl?locus=", + "Rfam": "http://rfam.sanger.ac.uk/family/", + "Broad_NEUROSPORA": "http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S", + "AGI_LocusCode": "http://arabidopsis.org/servlets/TairObject?type=locus&name=", + "OBO_SF2_PO": "http://sourceforge.net/p/obo/plant-ontology-po-term-requests/", + "FMA": "http://purl.obolibrary.org/obo/FMA_", + "CDD": "http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=", + "PubChem_Compound": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=", + "HGNC_gene": "http://identifiers.org/hgnc.gene/", + "PharmGKB": "http://www.pharmgkb.org/do/serve?objId=", + "VMD": "http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=", + "UniParc": "http://www.uniprot.org/uniparc/", + "MEROPS": "http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=", + "GDB": "http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:", + "SEED": "http://www.theseed.org/linkin.cgi?id=", + "SO": "http://purl.obolibrary.org/obo/SO_", + "Soy_gene": "http://www.soybase.org/sbt/search/search_results.php?category=FeatureName&search_term=", + "CORUM": "http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=", + "RHEA": "http://www.rhea-db.org/reaction.xhtml?id=", + "dbSNP": "http://identifiers.org/dbsnp/", + "MaizeGDB_Locus": "http://identifiers.org/maizegdb.locus/", + "MO": "http://mged.sourceforge.net/ontologies/MGEDontology.php#", + "PLANA_REF": "http://purl.obolibrary.org/obo/plana/references/", + "BRENDA": "http://www.brenda-enzymes.info/php/result_flat.php4?ecno=", + "ASAP": "https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=", + "CAS": "http://identifiers.org/cas/", + "H-invDB_locus": "http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=", + "UM-BBD_ruleID": "http://eawag-bbd.ethz.ch/servlets/rule.jsp?rule=", + "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITaxon_", + "ComplexPortal": "https://www.ebi.ac.uk/complexportal/complex/", + "JSTOR": "http://www.jstor.org/stable/", + "GRIMS": "https://www.genesys-pgr.org/acn/search2?q=IRGC+", + "PATO": "http://purl.obolibrary.org/obo/PATO_", + "GR_QTL": "http://identifiers.org/gramene.qtl/", + "ECOGENE": "http://www.ecogene.org/geneInfo.php?eg_id=", + "HPA_antibody": "http://www.proteinatlas.org/antibody_info.php?antibody_id=", + "VBRC": "http://vbrc.org/query.asp?web_id=VBRC:", + "EO_GIT": "https://github.com/Planteome/plant-environment-ontology/issues/", + "EchoBASE": "http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=", + "CASGEN": "http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=", + "IUPHAR_RECEPTOR": "http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=", + "IRIC": "http://oryzasnp.org/_variety.zul?irisid=", + "GenBank": "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=", + "TGD": "http://identifiers.org/tgd/", + "JCVI_EGAD": "http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=", + "PubChem_BioAssay": "http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=", + "TC": "http://www.tcdb.org/tcdb/index.php?tc=", + "SABIO-RK": "http://sabio.villa-bosch.de/reacdetails.jsp?reactid=", + "OBO_SF2_PECO": "https://sourceforge.net/p/obo/plant-environment-ontology-eo/", + "MetaCyc": "http://identifiers.org/metacyc/", + "PAMGO_GAT": "http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=", + "ModBase": "http://salilab.org/modbase/searchbyid?databaseID=", + "OMIM": "http://omim.org/entry/", + "GR_MUT": "http://www.gramene.org/db/genes/search_gene?acc=", + "HPA": "http://www.proteinatlas.org/tissue_profile.php?antibody_id=", + "IntAct": "http://identifiers.org/intact/", + "ProDom": "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=", + "GRIN": "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=", + "WBPhenotype": "http://purl.obolibrary.org/obo/WBPhenotype_", + "BioCyc": "http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=", + "ENSEMBL_GeneID": "http://www.ensembl.org/id/", + "PIR": "http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=", + "UniProtKB-KW": "http://www.uniprot.org/keywords/", + "Planteome_gene": "https://www.google.com/search?q=", + "AspGD": "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=", + "JCVI_Medtr": "http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=", + "EuPathDB": "http://eupathdb.org/gene/", + "PMCID": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=" + } +} \ No newline at end of file diff --git a/python/json_export.py b/python/json_export.py index adf5244..7317878 100644 --- a/python/json_export.py +++ b/python/json_export.py @@ -2,8 +2,6 @@ import json from pathlib import Path import os -from ontobio.rdfgen.assoc_rdfgen import prefix_context -#from prefixcommons.curie_util import contract_uri from curies import Converter, Record from pyshexc.parser_impl import generate_shexj @@ -18,12 +16,27 @@ OUT_JSON = os.path.join('../shapes/json/shex_dump.json') -converter = Converter.from_prefix_map(prefix_context) +ROOT_ENTITY = "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity" + + +def get_converter(): + with open('go_context.json') as file: + go_context = json.load(file) + prefix_context = go_context['@context'] + + converter = Converter.from_prefix_map(prefix_context) + + return converter + +converter = get_converter() def get_suffix(uri): + suffix = converter.compress(uri) + print(suffix if suffix else uri) + return suffix if suffix else uri @@ -65,7 +78,9 @@ def gen_terms_metadata(self): def _load_root_subject_expr(self, expr: Optional[Union[shapeExprLabel, shapeExpr]]) -> str: if expr is not None and len(expr)>0 and isinstance(expr[0], str): - return self.get_shape_name(expr[0]) + if ROOT_ENTITY == expr[0]: + return '' + return self.get_shape_name(expr[0]) return None @@ -145,7 +160,7 @@ def parse(self): if shape_name is None: continue - print('Parsing Shape: ' + shape['id']) + #print('Parsing Shape: ' + shape['id']) shexps = shape.shapeExprs or [] diff --git a/python/shex_json_linkml.py b/python/shex_json_linkml.py index 9cc6e6e..4fa37cc 100644 --- a/python/shex_json_linkml.py +++ b/python/shex_json_linkml.py @@ -72,8 +72,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.subject, URIorCURIE): self.subject = URIorCURIE(self.subject) - if self._is_empty(self.root_subject): - self.MissingRequiredField("root_subject") if not isinstance(self.root_subject, URIorCURIE): self.root_subject = URIorCURIE(self.root_subject) diff --git a/shapes/json/shex_dump.json b/shapes/json/shex_dump.json index 658d0a0..93a5e3d 100644 --- a/shapes/json/shex_dump.json +++ b/shapes/json/shex_dump.json @@ -2,7 +2,7 @@ "goshapes": [ { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -14,7 +14,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431", "CARO:0000000", @@ -29,7 +29,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431", "CARO:0000000", @@ -43,7 +43,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431" ], @@ -55,7 +55,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431" ], @@ -67,7 +67,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -79,7 +79,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:33695", "GO:0032991" @@ -92,7 +92,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -104,7 +104,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -116,7 +116,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "GO:0003674", @@ -130,7 +130,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "GO:0003674", @@ -144,7 +144,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "GO:0003674", @@ -158,7 +158,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -170,7 +170,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -182,7 +182,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -194,7 +194,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000", "NCBITaxon:1" @@ -207,7 +207,7 @@ }, { "subject": "GO:0008150", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0044848", "UBERON:0000105", @@ -504,7 +504,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:33695", "GO:0032991" @@ -513,11 +513,11 @@ "is_required": false, "context": "", "predicate": "RO:0002333", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -529,7 +529,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674" ], @@ -537,11 +537,11 @@ "is_required": false, "context": "", "predicate": "BFO:0000051", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -553,7 +553,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431", "GO:0032991" @@ -566,7 +566,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431", "GO:0032991" @@ -579,7 +579,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431", "GO:0032991" @@ -592,7 +592,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431", "GO:0032991" @@ -605,7 +605,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -614,11 +614,11 @@ "is_required": false, "context": "", "predicate": "RO:0002413", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -631,7 +631,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -644,7 +644,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -657,7 +657,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -670,7 +670,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -683,7 +683,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -696,7 +696,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -705,11 +705,11 @@ "is_required": false, "context": "", "predicate": "RO:0012012", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -718,11 +718,11 @@ "is_required": false, "context": "", "predicate": "RO:0002407", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -731,11 +731,11 @@ "is_required": false, "context": "", "predicate": "RO:0002409", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -744,11 +744,11 @@ "is_required": false, "context": "", "predicate": "RO:0012009", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent" @@ -757,11 +757,11 @@ "is_required": false, "context": "", "predicate": "RO:0012010", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431" ], @@ -769,11 +769,11 @@ "is_required": false, "context": "", "predicate": "RO:0012000", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431" ], @@ -781,11 +781,11 @@ "is_required": false, "context": "", "predicate": "RO:0012001", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:24431" ], @@ -793,11 +793,11 @@ "is_required": false, "context": "", "predicate": "RO:0012002", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674", "http://purl.obolibrary.org/obo/go/shapes/MolecularEvent", @@ -807,11 +807,11 @@ "is_required": false, "context": "", "predicate": "RO:0002418", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -819,11 +819,11 @@ "is_required": false, "context": "", "predicate": "RO:0004046", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150" ], @@ -831,11 +831,11 @@ "is_required": false, "context": "", "predicate": "RO:0004047", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "GO:0003674", @@ -849,7 +849,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "GO:0003674", @@ -863,7 +863,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "GO:0003674", @@ -877,7 +877,7 @@ }, { "subject": "GO:0003674", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0044848", "UBERON:0000105", @@ -955,7 +955,7 @@ }, { "subject": "CARO:0000000", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -967,7 +967,7 @@ }, { "subject": "CARO:0000000", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CHEBI:33695", "GO:0032991" @@ -980,7 +980,7 @@ }, { "subject": "CL:0000000", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -992,7 +992,7 @@ }, { "subject": "GO:0005575", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -1004,7 +1004,7 @@ }, { "subject": "GO:0005575", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -1016,7 +1016,7 @@ }, { "subject": "GO:0005575", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -1028,7 +1028,7 @@ }, { "subject": "GO:0005575", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "UBERON:0000105", @@ -1042,7 +1042,7 @@ }, { "subject": "GO:0005575", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "UBERON:0000105", @@ -1056,7 +1056,7 @@ }, { "subject": "GO:0032991", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000" ], @@ -1064,11 +1064,11 @@ "is_required": false, "context": "", "predicate": "RO:0001025", - "exclude_from_extensions": false + "exclude_from_extensions": true }, { "subject": "GO:0032991", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "CARO:0000000", "http://purl.obolibrary.org/obo/go/shapes/RootCellularComponent" @@ -1077,24 +1077,47 @@ "is_required": false, "context": "", "predicate": "RO:0002432", + "exclude_from_extensions": true + }, + { + "subject": "GO:0032991", + "root_subject": "", + "object": [ + "CARO:0000000" + ], + "is_multivalued": false, + "is_required": false, + "context": "", + "predicate": "BFO:0000050", "exclude_from_extensions": false }, { "subject": "GO:0032991", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ - "CHEBI:33695", - "GO:0032991" + "CARO:0000000" ], "is_multivalued": true, "is_required": false, "context": "", - "predicate": "BFO:0000051", + "predicate": "RO:0002220", + "exclude_from_extensions": false + }, + { + "subject": "GO:0032991", + "root_subject": "", + "object": [ + "CARO:0000000" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "RO:0002131", "exclude_from_extensions": false }, { "subject": "GO:0032991", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "UBERON:0000105", @@ -1108,7 +1131,7 @@ }, { "subject": "GO:0032991", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0008150", "UBERON:0000105", @@ -1120,9 +1143,22 @@ "predicate": "RO:0002491", "exclude_from_extensions": false }, + { + "subject": "GO:0032991", + "root_subject": "", + "object": [ + "CHEBI:33695", + "GO:0032991" + ], + "is_multivalued": true, + "is_required": false, + "context": "", + "predicate": "BFO:0000051", + "exclude_from_extensions": true + }, { "subject": "CHEBI:24431", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674" ], @@ -1134,7 +1170,7 @@ }, { "subject": "CHEBI:24431", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674" ], @@ -1146,7 +1182,7 @@ }, { "subject": "CHEBI:24431", - "root_subject": "http://purl.obolibrary.org/obo/go/shapes/GoCamEntity", + "root_subject": "", "object": [ "GO:0003674" ], diff --git a/shapes/json/shex_full.json b/shapes/json/shex_full.json index 65af115..c64b4a9 100644 --- a/shapes/json/shex_full.json +++ b/shapes/json/shex_full.json @@ -2384,7 +2384,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2398,7 +2408,17 @@ "predicate": "http://purl.obolibrary.org/obo/BFO_0000051", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/MolecularFunction", "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2470,7 +2490,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2561,7 +2591,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2574,7 +2614,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2587,7 +2637,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2600,7 +2660,17 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2613,28 +2683,68 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0012000", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0012001", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0012002", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/ChemicalEntity", "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2648,21 +2758,51 @@ ] }, "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0004046", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", "predicate": "http://purl.obolibrary.org/obo/RO_0004047", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/BiologicalProcess", "min": 0, - "max": -1 + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -2723,6 +2863,118 @@ ] }, "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, { "type": "Annotation", "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", @@ -3418,7 +3670,17 @@ "predicate": "http://purl.obolibrary.org/obo/RO_0001025", "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", "min": 0, - "max": 1 + "max": 1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] }, { "type": "TripleConstraint", @@ -3431,18 +3693,36 @@ ] }, "min": 0, + "max": 1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/BFO_0000050", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", + "min": 0, "max": 1 }, { "type": "TripleConstraint", - "predicate": "http://purl.obolibrary.org/obo/BFO_0000051", - "valueExpr": { - "type": "ShapeOr", - "shapeExprs": [ - "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule", - "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" - ] - }, + "predicate": "http://purl.obolibrary.org/obo/RO_0002220", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", + "min": 0, + "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/RO_0002131", + "valueExpr": "http://purl.obolibrary.org/obo/go/shapes/AnatomicalEntity", "min": 0, "max": -1 }, @@ -3473,10 +3753,57 @@ }, "min": 0, "max": -1 + }, + { + "type": "TripleConstraint", + "predicate": "http://purl.obolibrary.org/obo/BFO_0000051", + "valueExpr": { + "type": "ShapeOr", + "shapeExprs": [ + "http://purl.obolibrary.org/obo/go/shapes/InformationBiomacromolecule", + "http://purl.obolibrary.org/obo/go/shapes/ProteinContainingComplex" + ] + }, + "min": 0, + "max": -1, + "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + } + ] } ] }, "annotations": [ + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, + { + "type": "Annotation", + "predicate": "http://purl.obolibrary.org/obo/go/shapes/exclude_from_extensions", + "object": { + "value": "true", + "type": "http://www.w3.org/2001/XMLSchema#boolean" + } + }, { "type": "Annotation", "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", diff --git a/shapes/json/terms_metadata.json b/shapes/json/terms_metadata.json index bbeb58a..aec9fbc 100644 --- a/shapes/json/terms_metadata.json +++ b/shapes/json/terms_metadata.json @@ -23,29 +23,29 @@ "definition": "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.", "comment": "A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.", "synonyms": [ - "macromolecular complex", - "macromolecule complex", - "protein containing complex" + "macromolecular complex@", + "@macromolecule complex@", + "@protein containing complex" ] }, { "id": "GO:0005575", "label": "cellular_component", - "definition": "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).", - "comment": "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", + "definition": "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).", + "comment": "Note that, in addition to forming the root of the cellular component ontology, this term is recommended for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "synonyms": [ - "cell or subcellular entity", - "cellular component" + "cell or subcellular entity@", + "@cellular component" ] }, { "id": "GO:0008150", "label": "biological_process", - "definition": "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.", + "definition": "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.", "comment": "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.", "synonyms": [ - "biological process", - "physiological process" + "physiological process@", + "@biological process" ] }, { @@ -72,14 +72,14 @@ "definition": "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.", "comment": "", "synonyms": [ - "anatomical structure organization", - "morphogenesis" + "anatomical structure organization@", + "@morphogenesis" ] }, { "id": "GO:0030154", "label": "cell differentiation", - "definition": "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.", + "definition": "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.", "comment": "", "synonyms": [ "" @@ -97,7 +97,7 @@ { "id": "GO:0045165", "label": "cell fate commitment", - "definition": "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.", + "definition": "The cellular developmental process by which a cell establishes the intrinsic character of a cell or tissue region irreversibly committing it to a particular fate.", "comment": "Note that this term was 'cell fate determination' but the term name was changed to better match its existing definition and the child term 'cell fate determination; GO:0001709' was also created.", "synonyms": [ "" @@ -106,7 +106,7 @@ { "id": "GO:0001709", "label": "cell fate determination", - "definition": "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.", + "definition": "The cellular developmental process involved in cell fate commitment that occurs after cell fate specification, in which a cell is irreversibly committed to a cellular developmental fate which is heritable on cell division.", "comment": "", "synonyms": [ "" @@ -115,7 +115,7 @@ { "id": "GO:0001708", "label": "cell fate specification", - "definition": "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.", + "definition": "The cellular developmental process involved in cell fate commitment in which the cell is designated to follow a developmental path, unless they receive extrinsic cues that direct an alternative fate.", "comment": "", "synonyms": [ "" @@ -127,18 +127,18 @@ "definition": "The aggregation, arrangement and bonding together of a cellular component.", "comment": "", "synonyms": [ - "cell structure assembly", - "cellular component assembly at cellular level" + "cell structure assembly@", + "@cellular component assembly at cellular level" ] }, { "id": "GO:0022411", "label": "cellular component disassembly", "definition": "A cellular process that results in the breakdown of a cellular component.", - "comment": "", + "comment": "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.", "synonyms": [ - "cell structure disassembly", - "cellular component disassembly at cellular level" + "cell structure disassembly@", + "@cellular component disassembly at cellular level" ] }, { @@ -147,11 +147,11 @@ "definition": "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.", "comment": "", "synonyms": [ - "cell organisation", - "cellular component organisation at cellular level", - "cellular component organisation in other organism", - "cellular component organization at cellular level", - "cellular component organization in other organism" + "cell organisation@", + "@cellular component organisation at cellular level@", + "@cellular component organisation in other organism@", + "@cellular component organization at cellular level@", + "@cellular component organization in other organism" ] }, { @@ -178,9 +178,9 @@ "definition": "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.", "comment": "", "synonyms": [ - "establishment and maintenance of localization", - "establishment and maintenance of position", - "localisation" + "establishment and maintenance of localization@", + "@establishment and maintenance of position@", + "@localisation" ] }, { @@ -198,7 +198,7 @@ "definition": "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex.", "comment": "", "synonyms": [ - "" + "protein-containing complex remodelling" ] }, { @@ -231,8 +231,8 @@ { "id": "GO:0003674", "label": "molecular_function", - "definition": "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", - "comment": "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.", + "definition": "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.", + "comment": "This is the same as GO molecular function", "synonyms": [ "molecular function" ] @@ -274,16 +274,16 @@ ] }, { - "id": "CL:0000003", - "label": "native cell", - "definition": "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).", - "comment": "", + "id": "CL:0000000", + "label": "cell", + "definition": "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", + "comment": "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).", "synonyms": [ "" ] }, { - "id": "NCBITaxon:1", + "id": "taxon:1", "label": "root", "definition": "", "comment": "", @@ -315,8 +315,8 @@ "definition": "A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.", "comment": "", "synonyms": [ - "etapa de desarrollo de estructura vegetal (Spanish, exact)", - "plant growth and development stage (exact)" + "etapa de desarrollo de estructura vegetal (Spanish, exact)@", + "@plant growth and development stage (exact)" ] }, { @@ -465,7 +465,7 @@ }, { "id": "RO:0002413", - "label": "directly provides input for", + "label": "provides input for", "definition": "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", "comment": "", "synonyms": [ @@ -481,6 +481,60 @@ "" ] }, + { + "id": "RO:0012000", + "label": "has small molecule regulator", + "definition": "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012001", + "label": "has small molecule activator", + "definition": "a relation between a process and a continuant, in which the process is activated by the small molecule continuant", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012002", + "label": "has small molecule inhibitor", + "definition": "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012004", + "label": "is small molecule regulator of", + "definition": "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012005", + "label": "is small molecule activator of", + "definition": "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process", + "comment": "", + "synonyms": [ + "" + ] + }, + { + "id": "RO:0012006", + "label": "is small molecule inhibitor of", + "definition": "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process", + "comment": "", + "synonyms": [ + "" + ] + }, { "id": "RO:0001025", "label": "located in", @@ -520,7 +574,7 @@ { "id": "RO:0002211", "label": "regulates", - "definition": "process(P1) regulates process(P2) iff:\u00a0P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.", + "definition": "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.", "comment": "", "synonyms": [ "" @@ -564,8 +618,8 @@ }, { "id": "RO:0002406", - "label": "directly activates", - "definition": "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q", + "label": "obsolete directly activates", + "definition": "", "comment": "This term was obsoleted because it has the same meaning as 'directly positively regulates'.", "synonyms": [ "" @@ -582,8 +636,8 @@ }, { "id": "RO:0002407", - "label": "indirectly activates", - "definition": "p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.", + "label": "indirectly positively regulates", + "definition": "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.", "comment": "", "synonyms": [ "" @@ -591,7 +645,7 @@ }, { "id": "RO:0002409", - "label": "indirectly inhibits", + "label": "indirectly negatively regulates", "definition": "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.", "comment": "", "synonyms": [ @@ -619,7 +673,7 @@ { "id": "RO:0002418", "label": "causally upstream of or within", - "definition": "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.", + "definition": "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.", "comment": "", "synonyms": [ "" @@ -646,7 +700,7 @@ { "id": "RO:0002411", "label": "causally upstream of", - "definition": "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain", + "definition": "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.", "comment": "", "synonyms": [ "" @@ -656,7 +710,7 @@ "id": "RO:0002305", "label": "causally upstream of, negative effect", "definition": "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", - "comment": "holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y", + "comment": "", "synonyms": [ "" ]