Emek:
Problem : There are several separate things that often occur in pathway databases, which is used to mark things that are outside the biochemical paradigm. They are invariably ( any counter examples ?) used as input and or output. Examples include, physical factors such as photon ( DNA damage, circassian clock) , pH (golgi transport regulation), temperature ( heat-shock response), changes in cell structure and shape ( plasticity, contraction), cellular phenotype(differentiation, apoptosis, cell division), physiological phenotype ( metastasis, diabetes). Currently the only "hack" to represent these things is to put them in as entities.
BioPAX documentation: Entity :Any concept that we will refer to as a discrete biological unit when describing pathways. This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. Synonyms for this class include 'thing', 'object' and 'bioentity'. As the most abstract class in the ontology, instances of the entity class should be created rarely, if ever.
Physical Entity: An entity that has a physical structure. This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. Physical entities are frequent building blocks of interactions. As a highly abstract class in the ontology, instances of the physicalEntity class should be created rarely, if ever.
So I would call these guys entities, definitely not physical entities. I would even argue that they are disjoint from interactions, pathways and physical entities. So they sound like a new subclass(es) of entity to me. I think modeling these are out of our scope but it is perfectly legal to , but one can see the benefits if say these guys were associated with OMIM or GO unification xrefs.
So far CST and Panther are two datasources that definetely has these type of data. Others?
Mathias: photon: subclass of physical entity pH, temperature: qualities of physical entities (subclass of entity) changes in cell structure shape, plasticity, contraction: processes (subclass of entity, superclass of interaction etc.)
I am not really sure what exactly you are meaning with 'phenotypes'. In my understanding, this would be represented as some kind of 'annotation'.
Carl: NCI's pathway interaction database has such things. They act as conditions on concrete interactions and as abstract causes/effects of physical entities.