Merge pull request #115 from SED-ML/create-dae-solver

Create new 'DAE Solver' category; put IDA-like things in it.

Author: luciansmith

.github/workflows/BioPortal-submission.json

@@ -1,9 +1,9 @@
 {
   "ontology": "https://data.bioontology.org/ontologies/KISAO",
-  "pullLocation": "https://raw.githubusercontent.com/SED-ML/KiSAO/2.32/kisao.owl",
+  "pullLocation": "https://raw.githubusercontent.com/SED-ML/KiSAO/2.34/kisao.owl",
   "hasOntologyLanguage": "OWL",
   "description": "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs.",
-  "version": "2.32",
+  "version": "2.34",
   "released": "2023-05-24T02:54:00-00:00",
   "status": "production",
   "homepage": "http://biomodels.net/kisao/",

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## 2.34 (OWL 2)
+- Added organizational 'DAE solver' (`KISAO_0000699`) for collecting solvers that can solve DAE problems.
+- Removed 'has characteristic' some 'differential-algebraic equation problem' from KINSOL and from 'method for solving a system of linear equations'.
+- The characteristics 'differential-algebraic equation problem' and ''ordinary differential equation problem' are no longer disjoint (and in fact the former are a complete subset of the latter).
+
+## 2.33 (OWL 2)
+- Reorganized the steady state algorithms: moved flux balance and steady state to 'general steady state method' (`KISAO_0000630`), and others to the 'steady state root-finding method' (`KISAO_0000407`)
+
 ## 2.32 (OWL 2)
 - Added algorithm concepts for eQuilibrator.
 - Added organizational 'ODE solver' (`KISAO_0000694`) for noting in SED-ML that some solver should be used, but which is not important.

kisao.owl

@@ -19,7 +19,7 @@
         <rdfs:comment xml:lang="en">Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes)</rdfs:comment>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
-        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.33</owl:versionInfo>
+        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>
         <skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
     </owl:Ontology>
 

kisao_full.owl

@@ -1 +1 @@
-__version__ = '2.33'
+__version__ = '2.34'

libkisao/python/kisao/_version.py

@@ -35,10 +35,11 @@
 
 ID_HAS_CHARACTERISTIC_RELATIONSHIP = 'KISAO_0000245'  # has characteristic
 
-ID_ODE_PROBLEM_CHARACTERISTIC = 'KISAO_0000374'  # ordinary differential equation problem
 ID_SDE_PROBLEM_CHARACTERISTIC = 'KISAO_0000371'  # stochastic differential equation problem
-ID_STEADYSTATE_PROBLEM_CHARACTERISTIC = 'KISAO_0000696'  # steady state root-finding problem
 ID_PDE_PROBLEM_CHARACTERISTIC = 'KISAO_0000372'  # partial differential equation problem
+ID_DAE_PROBLEM_CHARACTERISTIC = 'KISAO_0000373'  # differential algebraic equation problem
+ID_ODE_PROBLEM_CHARACTERISTIC = 'KISAO_0000374'  # ordinary differential equation problem
+ID_STEADYSTATE_PROBLEM_CHARACTERISTIC = 'KISAO_0000696'  # steady state root-finding problem
 ID_EXACT_SOLUTION_CHARACTERISTIC = 'KISAO_0000236'  # exact solution
 ID_APPROXIMATE_SOLUTION_CHARACTERISTIC = 'KISAO_0000237'  # approximate solution
 

libkisao/python/kisao/data_model.py

@@ -13,6 +13,7 @@
                          ID_SDE_PROBLEM_CHARACTERISTIC,
                          ID_STEADYSTATE_PROBLEM_CHARACTERISTIC,
                          ID_PDE_PROBLEM_CHARACTERISTIC,
+                         ID_DAE_PROBLEM_CHARACTERISTIC,
                          ID_EXACT_SOLUTION_CHARACTERISTIC,
                          ID_APPROXIMATE_SOLUTION_CHARACTERISTIC,
                          ID_ALGORITHM,
@@ -45,6 +46,7 @@
     'get_rule_based_algorithms',
     'get_sde_algorithms',
     'get_pde_algorithms',
+    'get_dae_algorithms',
     'get_flux_balance_algorithms',
     'get_logical_simulation_algorithms',
     'get_logical_stable_state_search_algorithms',
@@ -140,6 +142,18 @@ def get_ode_algorithms():
     return get_terms_with_characteristics([ID_ALGORITHM], [ID_ODE_PROBLEM_CHARACTERISTIC])
 
 
+@ functools.lru_cache(maxsize=None)
+def get_dae_algorithms():
+    """ Get the terms for DAE integration algorithms::
+
+        'modelling simulation algorithm' and 'has characteristic' some 'differential algebraic equation problem'
+
+    Returns:
+        :obj:`set` of :obj:`pronto.Term`: terms
+    """
+    return get_terms_with_characteristics([ID_ALGORITHM], [ID_DAE_PROBLEM_CHARACTERISTIC])
+
+
 @ functools.lru_cache(maxsize=None)
 def get_gillespie_like_algorithms(exact=True, approximate=False):
     """ Get the terms for algorithms that execute similar simulations to Gillespie's

libkisao/python/kisao/utils.py

@@ -73,6 +73,8 @@ def test_ode_algorithms(self):
         self.assertIn(kisao.get_term('KISAO_0000086'), terms)  # Fehlberg method
         self.assertIn(kisao.get_term('KISAO_0000088'), terms)  # LSODA
         self.assertIn(kisao.get_term('KISAO_0000560'), terms)  # LSODA/LSODAR hybrid method
+        self.assertIn(kisao.get_term('KISAO_0000355'), terms)  # DASPK
+        self.assertIn(kisao.get_term('KISAO_0000283'), terms)  # IDA
 
         self.assertNotIn(kisao.get_term('KISAO_0000499'), terms)  # DFBA
 
@@ -145,14 +147,31 @@ def test_sde_algorithms(self):
         self.assertEqual(sdes.intersection(odes), set())
         self.assertEqual(sdes.intersection(pdes), set())
 
+    def test_dae_algorithms(self):
+        kisao = Kisao()
+        daes = utils.get_dae_algorithms()
+        odes = utils.get_ode_algorithms()
+
+        self.assertNotIn(kisao.get_term('KISAO_0000019'), daes)  # CVODE
+        self.assertNotIn(kisao.get_term('KISAO_0000030'), daes)  # Euler forward
+        self.assertIn(kisao.get_term('KISAO_0000355'), daes)     # DASPK
+        self.assertIn(kisao.get_term('KISAO_0000283'), daes)     # IDA
+
+        self.assertNotIn(kisao.get_term('KISAO_0000499'), daes)  # DFBA
+
+        self.assertEqual(daes.intersection(odes), daes)  # subset of ODE algorithms
+        self.assertEqual(daes.intersection(utils.get_gillespie_like_algorithms(
+            exact=True, approximate=False)), set())  # disjoint from Gillespie-like terms
+        self.assertEqual(daes.intersection(utils.get_gillespie_like_algorithms(
+            exact=False, approximate=True)), set())  # disjoint from Gillespie-like terms
+
     def test_steadystate_algorithms(self):
         kisao = Kisao()
         terms = utils.get_steadystate_algorithms()
 
         self.assertIn(kisao.get_term('KISAO_0000407'), terms)  # steady state root-finding algorithm
         self.assertIn(kisao.get_term('KISAO_0000568'), terms)  # NLEQ1
         self.assertIn(kisao.get_term('KISAO_0000569'), terms)  # NLEQ2
-        self.assertIn(kisao.get_term('KISAO_0000355'), terms)  # DASPK
         self.assertIn(kisao.get_term('KISAO_0000413'), terms)  # Exact Newton Method
 
         self.assertNotIn(kisao.get_term('KISAO_0000499'), terms)  # DFBA

libkisao/python/tests/test_utils.py

@@ -0,0 +1,10 @@
+# What needs to be updated when making a new release
+
+Put new version into:
+* libkisao/python/kisao/_version.py
+* kisao.owl (i.e. <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>)
+* kisao_full.owl (i.e. <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.34</owl:versionInfo>)
+* .github/workflows/BioPortal-submission.json
+
+Summarize changes in:
+* CHANGELOG.md