Sync dev branch

CHANGELOG.md

@@ -0,0 +1,12 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+
+## 2026-01-26
+
+- [x] updated the package dependencies to resolve install errors coming from older packages
+- [x] updated the ontology references in `ontologies.csv`

pyproject.toml

@@ -1,18 +1,18 @@
 [project]
 name = "text2term"
-version = "4.5.0"
+version = "4.6.0"
 description = "A tool for mapping free-text descriptions of entities to ontology terms"
 readme = "README.md"
 requires-python = ">=3.9"
 license = "MIT"
 keywords = ["ontology", "metadata", "text mining", "metadata curation", "ontology mapping"]
 
 authors = [
-    { name="Rafael Goncalves", email="goncalves@stanford.edu" },
+    { name="Rafael Goncalves", email="rsgoncalves@gmx.com" },
     { name="Jason Payne", email="paynejason@gmail.com" }
 ]
 maintainers = [
-    { name="Rafael Goncalves", email="goncalves@stanford.edu" }
+    { name="Rafael Goncalves", email="rsgoncalves@gmx.com" }
 ]
 
 classifiers = [
@@ -25,25 +25,20 @@ classifiers = [
 ]
 
 dependencies = [
-    "owlready2~=0.47",
-    "argparse~=1.4.0",
-    "pandas~=2.2.3",
-    "numpy~=1.26.4",
-    "gensim~=4.3.2",
-    "scipy~=1.12.0",
-    "scikit-learn~=1.6.1",
-    "setuptools~=80.8.0",
-    "requests~=2.32.3",
-    "tqdm~=4.67.1",
-    "sparse-dot-topn~=1.1.3",
-    "bioregistry~=0.11.10",
-    "nltk~=3.9.1",
-    "rapidfuzz~=3.12.2",
-    "shortuuid~=1.0.11",
+    "bioregistry>=0.11.10",
+    "nltk>=3.9.1",
+    "owlready2>=0.47",
+    "pandas>=2.2.3",
+    "rapidfuzz>=3.12.2",
+    "requests>=2.32.3",
+    "scikit-learn>=1.6.1",
+    "shortuuid>=1.0.11",
+    "sparse-dot-topn>=1.1.3",
+    "tqdm>=4.67.1",
 ]
 
 [project.optional-dependencies]
-dev = ["pytest==8.1.1"]
+dev = ["pytest>=8.1.1"]
 
 [tool.setuptools]
 packages = ["text2term"]
@@ -53,7 +48,7 @@ include-package-data = true
 omit = ["*/__main__.py"]
 
 [build-system]
-requires = ["setuptools>=80.8", "wheel"]
+requires = ["setuptools>=61"]
 build-backend = "setuptools.build_meta"
 
 [project.urls]

test/test_input.txt

@@ -1,2 +1,2 @@
-asthma
-acute bronchitis
+cheese pizza
+fish pizza

test/test_input_with_tags.txt

@@ -1,4 +1,4 @@
-asthma;:;disease
-acute bronchitis;:;important,tags
-hypertension NOS;:;disease
-colon disease
+cheese pizza;:;pizza
+fish pizza;:;seafood,topping
+pizza NOS;:;unspecified
+mystery topping

test/test_ontology.owl

@@ -1,101 +1,73 @@
 <?xml version="1.0"?>
-<rdf:RDF xmlns="http://www.semanticweb.org/rafaelsg/ontologies/2025/5/untitled-ontology-18/"
-     xml:base="http://www.semanticweb.org/rafaelsg/ontologies/2025/5/untitled-ontology-18/"
-     xmlns:dc="http://purl.org/dc/elements/1.1/"
+<rdf:RDF xmlns="https://text2term.ontology/test/"
+     xml:base="https://text2term.ontology/test/"
      xmlns:owl="http://www.w3.org/2002/07/owl#"
      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:xml="http://www.w3.org/XML/1998/namespace"
      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:skos="http://www.w3.org/2004/02/skos/core#"
-     xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
      xmlns:Thesaurus="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#">
-    <owl:Ontology rdf:about="https://text2term.ontology/test">
-        <owl:imports rdf:resource="https://raw.githubusercontent.com/owlcs/pizza-ontology/refs/heads/master/pizza.owl"/>
-    </owl:Ontology>
-
 
-
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Annotation properties
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
-
-
-
-
-    <!-- http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90 -->
+    <owl:Ontology rdf:about="https://text2term.ontology/test/"/>
 
     <owl:AnnotationProperty rdf:about="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P90"/>
-
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
-
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym"/>
-
-
-
-    <!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->
-
     <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>
-
-
-
-    <!-- http://www.w3.org/2004/02/skos/core#definition -->
-
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
     <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
-
 
+    <owl:ObjectProperty rdf:about="https://text2term.ontology/test/hasTopping">
+        <rdfs:label>contains topping</rdfs:label>
+    </owl:ObjectProperty>
 
-    <!-- 
-    ///////////////////////////////////////////////////////////////////////////////////////
-    //
-    // Classes
-    //
-    ///////////////////////////////////////////////////////////////////////////////////////
-     -->
+    <owl:ObjectProperty rdf:about="https://text2term.ontology/test/hasLocation">
+        <rdfs:label>location</rdfs:label>
+    </owl:ObjectProperty>
 
-
+    <owl:Class rdf:about="https://text2term.ontology/test/Pizza">
+        <rdfs:label>Pizza</rdfs:label>
+        <skos:definition>A dish made with dough and toppings</skos:definition>
+    </owl:Class>
 
+    <owl:Class rdf:about="https://text2term.ontology/test/IceCream">
+        <rdfs:label>Ice Cream</rdfs:label>
+        <owl:disjointWith rdf:resource="https://text2term.ontology/test/Pizza"/>
+    </owl:Class>
 
-    <!-- https://text2term.ontology/test/FishyPizza -->
+    <owl:Class rdf:about="https://text2term.ontology/test/CheesePizza">
+        <rdfs:subClassOf rdf:resource="https://text2term.ontology/test/Pizza"/>
+        <rdfs:label>Cheese Pizza</rdfs:label>
+        <oboInOwl:hasExactSynonym>Plain Pizza</oboInOwl:hasExactSynonym>
+    </owl:Class>
 
     <owl:Class rdf:about="https://text2term.ontology/test/FishyPizza">
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="https://raw.githubusercontent.com/owlcs/pizza-ontology/refs/heads/master/pizza.owl#Pizza"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="https://raw.githubusercontent.com/owlcs/pizza-ontology/refs/heads/master/pizza.owl#hasTopping"/>
-                        <owl:someValuesFrom rdf:resource="https://raw.githubusercontent.com/owlcs/pizza-ontology/refs/heads/master/pizza.owl#FishTopping"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="https://text2term.ontology/test/Pizza"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="https://text2term.ontology/test/hasTopping"/>
+                <owl:someValuesFrom rdf:resource="https://text2term.ontology/test/FishTopping"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
         <Thesaurus:P90>pizza with fish</Thesaurus:P90>
         <oboInOwl:hasBroadSynonym>Seafood Pizza</oboInOwl:hasBroadSynonym>
         <oboInOwl:hasRelatedSynonym>Fish Pizza</oboInOwl:hasRelatedSynonym>
         <rdfs:label>Pizza that contains fish</rdfs:label>
         <skos:definition>A pizza that contains a fish ingredient</skos:definition>
     </owl:Class>
-
 
+    <owl:Class rdf:about="https://text2term.ontology/test/FishTopping">
+        <rdfs:label>Fish Topping</rdfs:label>
+    </owl:Class>
 
-    <!-- https://text2term.ontology/test/VanillaIceCream -->
+    <owl:Class rdf:about="https://text2term.ontology/test/TomatoTopping">
+        <rdfs:label>Tomato Topping</rdfs:label>
+    </owl:Class>
 
     <owl:Class rdf:about="https://text2term.ontology/test/VanillaIceCream">
-        <rdfs:subClassOf rdf:resource="https://raw.githubusercontent.com/owlcs/pizza-ontology/refs/heads/master/pizza.owl#IceCream"/>
+        <rdfs:subClassOf rdf:resource="https://text2term.ontology/test/IceCream"/>
         <rdfs:label>Vanilla Ice Cream</rdfs:label>
         <owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
     </owl:Class>
 </rdf:RDF>
-
-
-
-<!-- Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi -->
-