bioregistry 0.13.8__tar.gz → 0.13.9__tar.gz

{bioregistry-0.13.8 → bioregistry-0.13.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.8
+Version: 0.13.9
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.8 → bioregistry-0.13.9}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.8"
+version = "0.13.9"
 description = "Integrated registry of biological databases and nomenclatures"
 readme = "README.md"
 authors = [
@@ -254,7 +254,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.13.8"
+current_version = "0.13.9"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

bioregistry-0.13.9/src/bioregistry/curation/add_sweet.py

@@ -0,0 +1,146 @@
+"""Add SWEET ontologies."""
+
+from typing import cast
+
+import click
+import pystow
+
+import bioregistry
+
+MODULE = pystow.module("bioregistry", "sweet")
+
+ALL_PREFIXES_URL = "https://github.com/ESIPFed/sweet/raw/refs/heads/master/sweetPrefixes.ttl"
+
+MANUAL = {
+    "sosto": "Acute",
+    "sostri": "Catastrophic",
+    "sostsp": "Big",
+    "sorel": "hasPhenomena",
+    "sorelch": "atomicMass",
+    "sorelh": "hasAttribute",
+    "soreaer": "AbyssopelagicZone",
+    "sorelcl": "hasAverageAnnualPrecipitation",
+    "sorelm": "averageOver",
+    "sorelph": "colderThan",
+    "sorelsc": "causedBy",
+    "sorelt": "dayOfYear",
+    "sorelsp": "adjacentTo",
+    "sorepsd": "Counterclockwise",
+    "sorelpr": "fillValue",
+    "sostss": "Continental",
+    "sostrt": "Accurate",
+    "sostsl": "CaK",
+    "sosttf": "Annual",
+    "sosttg": "0MYA",
+    "sostv": "Clear",
+}
+
+
+@click.command()
+def main() -> None:
+    """Add SWEET ontologies."""
+    graph = MODULE.ensure_rdf(url=ALL_PREFIXES_URL)
+    sparql = """
+        SELECT ?prefix ?namespace
+        WHERE {
+            ?x sh:prefix ?prefix;
+               sh:namespace ?namespace .
+        }
+    """
+    for sweet_internal_prefix, uri_prefix in graph.query(sparql):  # type:ignore
+        sweet_internal_prefix = str(sweet_internal_prefix)
+        uri_prefix = str(uri_prefix)
+
+        if sweet_internal_prefix in {"soall", "sweet"}:
+            continue  # this is the combine one, not its own prefix
+
+        sweet_internal_key = uri_prefix.removeprefix("http://sweetontology.net/").rstrip("/")
+        if not sweet_internal_key:
+            raise ValueError(f"no internal key found for {sweet_internal_prefix}")
+
+        download_rdf = (
+            f"https://github.com/ESIPFed/sweet/raw/refs/heads/master/src/{sweet_internal_key}.ttl"
+        )
+        inner_graph = MODULE.ensure_rdf(url=download_rdf)
+
+        ontology_name_query = """
+            SELECT ?name
+            WHERE { owl:Ontology ^rdf:type/rdfs:label ?name }
+            LIMIT 1
+        """
+        name = str(next(iter(inner_graph.query(ontology_name_query)))[0])  # type:ignore
+        name_short = name.removeprefix("SWEET Ontology ")
+
+        example_query = f"""
+            SELECT ?term
+            WHERE {{
+                ?term rdf:type owl:Class;
+                      rdfs:label ?name ;
+                FILTER STRSTARTS(str(?term), "{uri_prefix}")
+            }}
+            LIMIT 1
+        """
+        example_records = list(inner_graph.query(example_query))
+        if example_records:
+            example_uri = cast(str, example_records[0][0])  # type:ignore[index]
+            example = example_uri.removeprefix(uri_prefix)
+        elif sweet_internal_prefix in MANUAL:
+            example = MANUAL[sweet_internal_prefix]
+        else:
+            raise ValueError(
+                f"[{sweet_internal_prefix}] missing example in {name_short} ({uri_prefix})"
+            )
+
+        if not sweet_internal_prefix.startswith("so"):
+            raise ValueError
+
+        nsl = name_short.lower()
+        if nsl.startswith("human "):
+            keywords = [nsl.removeprefix("human ")]
+        elif nsl.startswith("material "):
+            keywords = ["materials", nsl.removeprefix("material ")]
+        elif nsl.startswith("phenomena "):
+            keywords = ["phenomena", nsl.removeprefix("phenomena ")]
+        elif nsl.startswith("property relationships "):
+            keywords = [nsl.removeprefix("property relationships ")]
+        elif nsl.startswith("property "):
+            keywords = [nsl.removeprefix("property ")]
+        elif nsl.startswith("process "):
+            keywords = [nsl.removeprefix("process ")]
+        elif nsl.startswith("realm land "):
+            keywords = [nsl.removeprefix("realm land") + "land"]
+        elif nsl.startswith("realm "):
+            keywords = ["realm", nsl.removeprefix("realm ")]
+        elif nsl.startswith("representation "):
+            keywords = [nsl.removeprefix("realm ")]
+        elif nsl.startswith("state "):
+            keywords = [nsl.removeprefix("realm ")]
+        elif nsl.startswith("relationships "):
+            keywords = [nsl.removeprefix("relationships ")]
+        else:
+            keywords = [nsl.lower()]
+
+        prefix = f"sweet.{sweet_internal_prefix.removeprefix('so')}"
+        resource = bioregistry.Resource(
+            prefix=prefix,
+            synonyms=[sweet_internal_prefix],
+            name=name,
+            keywords=sorted(keywords),
+            homepage=str(uri_prefix),
+            uri_format=f"{uri_prefix}$1",
+            description=f"The Semantic Web for Earth and Environmental Terminology (SWEET) ontology for {name_short}",
+            example=example,
+            download_rdf=download_rdf,
+            part_of="sweet",
+            license="CC0-1.0",
+            repository="https://github.com/ESIPFed/sweet",
+            contributor=bioregistry.Author.get_charlie(),
+            github_request_issue=1772,
+        )
+        bioregistry.add_resource(resource)
+
+    bioregistry.manager.write_registry()
+
+
+if __name__ == "__main__":
+    main()