sparc methods first pass at definition for sparc:Site

ttl/sparc-methods.ttl

@@ -520,6 +520,12 @@ sparc:Scaffold a owl:Class ;
     definition: "A resource that provides a three dimensional coordinate system for an organ or other anatomical entity." ;
     rdfs:subClassOf sparc:Resource .
 
+sparc:Site a owl:Class ;
+    rdfs:label "site" ;
+    definition: "A location on a specimen. More generally a location on any participant in a process." ;
+    editorNote: "A site may be defined by a variety of criteria, but those criteria usually reduce to a notion of relative closeness, that is, a centroid and a distance metric to centroids that define other sites. For example a site could be defined as the location of an anatomical entity in an intact specimen, or as locations closer to one electrode array than another. See the definitions for atom:Border and atom:Centroid for further discussion.",
+        "As used in the SDS the definition of site may appear to depart from the BFO definition that sites are immaterial. One way to interpret sparc:Site is as a union of bfo site and bfo fiat object part. Another would be that sparc:Site is more like a bfo spatial region, in that sparc:Site might also be though of as a place with all the fuzzyness that the notion of place entails. A related question is whether it is possible to come up with real bounds in either the material or immaterial case for the entities that sparc:Site is expected to be used to describe (consider \"in the trashcan\" vs \"the intact left vagus nerve\"). The primary relation of interest in defining sparc:Site is that a site has some location that is distinct from some other site, the exact nature of the sites are not of concern. Said another way, we are not really interested in physical things that mark sites, rather in the distinctness that being marked in different ways gives them. Examples include an electrode, a nerve cuff, a utah array, laminar probes, the place marked by a stitch made in a dissected nerve, a cell in an in vitro brain slice, the left vagus nerve when it is still intact in the body, etc." .
+
 sparc:Specimen a owl:Class ;
     definition: "Any atomic participant in a scientific protocol, includes both subjects and samples. The use of specimen for subjects is based on the notion of a type specimen e.g. Carl Linnaus is the type specimen for homo spaiens sapiens." ;
     rdfs:subClassOf sparc:Participant .
@@ -597,4 +603,4 @@ TEMPRAW: a ilxtr:Namespace ;
     editorNote: "any predicate or type that has TEMPRAW as a prefix should be excluded" ;
     ilxtr:curationInternal true .
 
-### Serialized using the ttlser deterministic serializer v1.2.0
+### Serialized using the ttlser deterministic serializer v1.2.1