regenerated derived artefacts

biolinkmodel/datamodel.py

@@ -475,7 +475,25 @@ def __repr__(self):
 
 class ChemicalSubstance(MolecularEntity):
     """
-    may be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
+    May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
+    """
+    def __init__(self,
+                 id=None,
+                 label=None,
+                 in_taxon=None):
+        self.id=id
+        self.label=label
+        self.in_taxon=in_taxon
+
+    def __str__(self):
+        return "id={} label={} in_taxon={} ".format(self.id,self.label,self.in_taxon)
+    def __repr__(self):
+        return self.__str__()
+
+
+class Drug(ChemicalSubstance):
+    """
+    A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
     """
     def __init__(self,
                  id=None,
@@ -623,6 +641,22 @@ def __repr__(self):
         return self.__str__()
 
 
+class Device(NamedThing):
+    """
+    A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
+    """
+    def __init__(self,
+                 id=None,
+                 label=None):
+        self.id=id
+        self.label=label
+
+    def __str__(self):
+        return "id={} label={} ".format(self.id,self.label)
+    def __repr__(self):
+        return self.__str__()
+
+
 class GenomicEntity(MolecularEntity):
     """
     an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
@@ -769,7 +803,43 @@ def __repr__(self):
 
 class Protein(GeneProduct):
     """
-    None
+    A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
+    """
+    def __init__(self,
+                 id=None,
+                 label=None,
+                 in_taxon=None):
+        self.id=id
+        self.label=label
+        self.in_taxon=in_taxon
+
+    def __str__(self):
+        return "id={} label={} in_taxon={} ".format(self.id,self.label,self.in_taxon)
+    def __repr__(self):
+        return self.__str__()
+
+
+class GeneProductIsoform(GeneProduct):
+    """
+    This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.
+    """
+    def __init__(self,
+                 id=None,
+                 label=None,
+                 in_taxon=None):
+        self.id=id
+        self.label=label
+        self.in_taxon=in_taxon
+
+    def __str__(self):
+        return "id={} label={} in_taxon={} ".format(self.id,self.label,self.in_taxon)
+    def __repr__(self):
+        return self.__str__()
+
+
+class ProteinIsoform(Protein):
+    """
+    Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/
     """
     def __init__(self,
                  id=None,
@@ -803,6 +873,24 @@ def __repr__(self):
         return self.__str__()
 
 
+class RnaProductIsoform(RnaProduct):
+    """
+    Represents a protein that is a specific isoform of the canonical or reference RNA
+    """
+    def __init__(self,
+                 id=None,
+                 label=None,
+                 in_taxon=None):
+        self.id=id
+        self.label=label
+        self.in_taxon=in_taxon
+
+    def __str__(self):
+        return "id={} label={} in_taxon={} ".format(self.id,self.label,self.in_taxon)
+    def __repr__(self):
+        return self.__str__()
+
+
 class NoncodingRnaProduct(RnaProduct):
     """
     None
@@ -2495,10 +2583,52 @@ def __repr__(self):
         return self.__str__()
 
 
-class MolecularActivity(Occurrent):
+class MolecularActivity(BiologicalEntity):
     """
     An execution of a molecular function
     """
+    def __init__(self,
+                 id=None,
+                 label=None):
+        self.id=id
+        self.label=label
+
+    def __str__(self):
+        return "id={} label={} ".format(self.id,self.label)
+    def __repr__(self):
+        return self.__str__()
+
+
+class ActivityAndBehavior(Occurrent):
+    """
+    Activity or behavior of any independent integral living, organization or mechanical actor in the world
+    """
+    def __init__(self):
+        pass
+
+    def __str__(self):
+        return "".format()
+    def __repr__(self):
+        return self.__str__()
+
+
+class Procedure(Occurrent):
+    """
+    A series of actions conducted in a certain order or manner
+    """
+    def __init__(self):
+        pass
+
+    def __str__(self):
+        return "".format()
+    def __repr__(self):
+        return self.__str__()
+
+
+class Phenomenon(Occurrent):
+    """
+    a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
+    """
     def __init__(self):
         pass
 
@@ -2540,6 +2670,22 @@ def __repr__(self):
         return self.__str__()
 
 
+class Physiology(BiologicalProcess):
+    """
+    None
+    """
+    def __init__(self,
+                 id=None,
+                 label=None):
+        self.id=id
+        self.label=label
+
+    def __str__(self):
+        return "id={} label={} ".format(self.id,self.label)
+    def __repr__(self):
+        return self.__str__()
+
+
 class CellularComponent(AnatomicalEntity):
     """
     A location in or around a cell

biolinkmodel/schema.py

@@ -282,13 +282,22 @@ def make_object(self, data):
 
 class ChemicalSubstanceSchema(MolecularEntitySchema):
     """
-    may be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
+    May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
     """
 
     @post_load
     def make_object(self, data):
         ChemicalSubstance(**data)
 
+class DrugSchema(ChemicalSubstanceSchema):
+    """
+    A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
+    """
+
+    @post_load
+    def make_object(self, data):
+        Drug(**data)
+
 class AttributeSchema(Schema):
     """
     A property or characteristic of an entity
@@ -372,6 +381,15 @@ class ClinicalInterventionSchema(ClinicalEntitySchema):
     def make_object(self, data):
         ClinicalIntervention(**data)
 
+class DeviceSchema(NamedThingSchema):
+    """
+    A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
+    """
+
+    @post_load
+    def make_object(self, data):
+        Device(**data)
+
 class GenomicEntitySchema(MolecularEntitySchema):
     """
     an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
@@ -446,13 +464,34 @@ def make_object(self, data):
 
 class ProteinSchema(GeneProductSchema):
     """
-    None
+    A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
     """
 
     @post_load
     def make_object(self, data):
         Protein(**data)
 
+class GeneProductIsoformSchema(GeneProductSchema):
+    """
+    This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.
+    """
+
+    @post_load
+    def make_object(self, data):
+        GeneProductIsoform(**data)
+
+class ProteinIsoformSchema(ProteinSchema):
+    """
+    Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/
+    """
+    id = fields.Str()
+    label = fields.Str()
+    in_taxon = fields.Str()
+
+    @post_load
+    def make_object(self, data):
+        ProteinIsoform(**data)
+
 class RnaProductSchema(GeneProductSchema):
     """
     None
@@ -462,6 +501,18 @@ class RnaProductSchema(GeneProductSchema):
     def make_object(self, data):
         RnaProduct(**data)
 
+class RnaProductIsoformSchema(RnaProductSchema):
+    """
+    Represents a protein that is a specific isoform of the canonical or reference RNA
+    """
+    id = fields.Str()
+    label = fields.Str()
+    in_taxon = fields.Str()
+
+    @post_load
+    def make_object(self, data):
+        RnaProductIsoform(**data)
+
 class NoncodingRnaProductSchema(RnaProductSchema):
     """
     None
@@ -1164,7 +1215,7 @@ class OccurrentSchema(Schema):
     def make_object(self, data):
         Occurrent(**data)
 
-class MolecularActivitySchema(OccurrentSchema):
+class MolecularActivitySchema(BiologicalEntitySchema):
     """
     An execution of a molecular function
     """
@@ -1173,6 +1224,33 @@ class MolecularActivitySchema(OccurrentSchema):
     def make_object(self, data):
         MolecularActivity(**data)
 
+class ActivityAndBehaviorSchema(OccurrentSchema):
+    """
+    Activity or behavior of any independent integral living, organization or mechanical actor in the world
+    """
+
+    @post_load
+    def make_object(self, data):
+        ActivityAndBehavior(**data)
+
+class ProcedureSchema(OccurrentSchema):
+    """
+    A series of actions conducted in a certain order or manner
+    """
+
+    @post_load
+    def make_object(self, data):
+        Procedure(**data)
+
+class PhenomenonSchema(OccurrentSchema):
+    """
+    a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
+    """
+
+    @post_load
+    def make_object(self, data):
+        Phenomenon(**data)
+
 class BiologicalProcessSchema(BiologicalEntitySchema):
     """
     One or more causally connected executions of molecular functions
@@ -1191,6 +1269,15 @@ class PathwaySchema(BiologicalProcessSchema):
     def make_object(self, data):
         Pathway(**data)
 
+class PhysiologySchema(BiologicalProcessSchema):
+    """
+    None
+    """
+
+    @post_load
+    def make_object(self, data):
+        Physiology(**data)
+
 class CellularComponentSchema(AnatomicalEntitySchema):
     """
     A location in or around a cell

contrib/monarch/golr-views/chemical_substance-config.yaml

@@ -1,4 +1,4 @@
-description: may be a chemical entity or a formulation with a chemical entity as active
+description: May be a chemical entity or a formulation with a chemical entity as active
   ingredient, or a complex material with multiple chemical entities as part
 display_name: chemical substance
 document_category: chemical substance

contrib/monarch/golr-views/molecular_activity-config.yaml

@@ -1,7 +1,15 @@
 description: An execution of a molecular function
 display_name: molecular activity
 document_category: molecular activity
-fields: []
+fields:
+- description: null
+  display_name: id
+  id: id
+  property: []
+- description: A human-readable name for a thing
+  display_name: label
+  id: label
+  property: []
 id: molecular activity
 schema_generating: true
 weight: 20

contrib/monarch/golr-views/protein-config.yaml

@@ -1,4 +1,5 @@
-description: null
+description: A gene product that is composed of a chain of amino acid sequences and
+  is produced by ribosome-mediated translation of mRNA
 display_name: protein
 document_category: protein
 fields:

docs/AnatomicalEntity.md

@@ -10,6 +10,9 @@ A subcellular location, cell type or gross anatomical part
 URI: [http://bioentity.io/vocab/AnatomicalEntity](http://bioentity.io/vocab/AnatomicalEntity)
 ## Mappings
 
+ * [UMLSSG:ANAT](http://purl.obolibrary.org/obo/UMLSSG_ANAT)
+ * [SIO:010046](http://purl.obolibrary.org/obo/SIO_010046)
+ * [WD:Q4936952](http://purl.obolibrary.org/obo/WD_Q4936952)
  * [UBERON:0001062](http://purl.obolibrary.org/obo/UBERON_0001062)
 
 ## Inheritance