Merge branch 'master' of https://github.com/SynBioDex/Owlet

.github/workflows/python-tests.yml

@@ -29,6 +29,8 @@ jobs:
             python-version: 3.x
     steps:
     - uses: actions/checkout@v2
+      with:
+        submodules: true
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "tyto/ontologies/sbol-owl3"]
+	path = tyto/ontologies/sbol-owl3
+	url = https://github.com/SynBioDex/sbol-owl3.git
+[submodule "tyto/ontologies/sbol-owl"]
+	path = tyto/ontologies/sbol-owl
+	url = https://github.com/dissys/sbol-owl.git

README.md

@@ -1,7 +1,7 @@
 ![gh-action badge](https://github.com/SynBioDex/tyto/workflows/CI/badge.svg)
 ![readthedocs badge](https://readthedocs.org/projects/tyto/badge/)
 
-![Tyto deroepstorffi](./tyto.png "Andaman masked owl")
+<img src="tyto.png" height="300" />
 
 # Tyto
 **Take Your Terms from Ontologies (Tyto)** is a lightweight Python tool that makes the semantic web more user-friendly and accessible.
@@ -33,9 +33,13 @@ Since these ontology lookup services host hundreds of ontologies, Tyto does not
 'http://www.biomodels.net/kisao/KISAO#KISAO_0000029'
 ```
 
+### Documentation
+
+[Documentation on Readthedocs](https://tyto.readthedocs.io/en/latest/index.html)
+
 ### Inference and reasoning
 
-Additionally Tyto supports reasoning and inference over ontology terms.  For example, the following evaluates to `True` because the Sequence Ontolgoy categorizes an `inducible_promoter` as a specialized type of `promoter`. 
+Additionally Tyto supports reasoning and inference over ontology terms.  For example, the following evaluates to `True` because the Sequence Ontology categorizes an `inducible_promoter` as a specialized type of `promoter`. 
 ```
 >>> tyto.SO.inducible_promoter.is_a(tyto.SO.promoter)
 True
@@ -51,7 +55,7 @@ term1.get_children()
 
 ## About our mascot
 
-_Tyto_ is the genus of birds to which owls belong, alluding to the Web Ontology Language (OWL) in which most ontologies are encoded. Tyto's logo is derived from the ``Owl of Minerva''~\cite{owlofminerva} which is licensed under CC BY-SA 4.0.
+_Tyto_ is the genus of birds to which owls belong, alluding to the Web Ontology Language (OWL) in which most ontologies are encoded. Tyto's logo is derived from the "Owl of Minerva" which is licensed under CC BY-SA 4.0.
 
 ## Acknowledgments
 

setup.py

@@ -31,7 +31,9 @@
       packages=find_packages(),
       package_data={'tyto': ['ontologies/*.owl',
                               'ontologies/*.rdf',
-                              'ontologies/*.ttl']},
+                              'ontologies/*.ttl',
+                              'ontologies/sbol-owl3/sbolowl3.rdf',
+                              'ontologies/sbol-owl/sbol.rdf']},
       include_package_data=True,
       install_requires=[
             'rdflib>=5.0',

test/test_ontology.py

@@ -160,6 +160,18 @@ def test_SBO(self):
         uri = 'https://identifiers.org/SBO:0000241'
         self.assertEqual(SBO.get_term_by_uri(uri), 'functional entity')
 
+class TestSBOL(unittest.TestCase):
+
+    def test_sbol2(self):
+        self.assertEqual(SBOL2.inline, 'http://sbols.org/v2#inline')
+        self.assertEqual(SBOL2.reverseComplement, 'http://sbols.org/v2#reverseComplement')
+        self.assertEqual(SBOL2.ComponentDefinition, 'http://sbols.org/v2#ComponentDefinition')
+
+    def test_sbol3(self):
+        self.assertEqual(SBOL3.inline, 'http://sbols.org/v3#inline')
+        self.assertEqual(SBOL3.reverseComplement, 'http://sbols.org/v3#reverseComplement')
+        self.assertEqual(SBOL3.Component, 'http://sbols.org/v3#Component')
+
 
 if __name__ == '__main__':
     unittest.main()

tyto/__init__.py

@@ -5,3 +5,6 @@
 from .ncit import NCIT
 from .om import OM
 from .ncbi_taxon import NCBITaxon
+from .sbol2 import SBOL2
+from .sbol3 import SBOL3
+from .edam import EDAM

tyto/edam.py

@@ -0,0 +1,7 @@
+from .tyto import Ontology, Ontobee, installation_path, multi_replace
+
+
+EDAM = Ontology(endpoints=[Ontobee],
+                uri='http://edamontology.org/EDAM.owl')
+"""EDAM (EMBRACE Data and Methods) is an ontology of common bioinformatics operations, topics, types of data including identifiers, and formats. EDAM comprises common concepts (shared within the bioinformatics community) that apply to semantic annotation of resources."""
+

tyto/sbol2.py

@@ -0,0 +1,7 @@
+from .tyto import Ontology, installation_path
+
+
+SBOL2 = Ontology(path=installation_path('ontologies/sbol-owl/sbol.rdf'),
+                 uri='http://sbols.org/v2')
+
+

tyto/sbol3.py

@@ -0,0 +1,6 @@
+from .tyto import Ontology, installation_path
+
+
+SBOL3 = Ontology(path=installation_path('ontologies/sbol-owl3/sbolowl3.rdf'),
+                uri='http://sbols.org/v3')
+