groups
A list of
Member_t objects.
In the SBML Level 3 Groups package, the membership of a group is defined by placing Member_t objects within a ListOfMembers_t object contained within a Group_t object. A ListOfMembers_t object is optional, but, if present, it must contain at least one Member_t object. In common with other ListOf___ classes in SBML, ListOfMembers_t is derived from SBase_t. However, an uncommon feature of ListOfMembers_t is that it has optional "id" and "name" attributes that can be used in a manner discussed below.
A ListOfMembers_t must have one or more Member_t children. Since ListOfMembers_t is derived from SBase_t, it inherits the "sboTerm" and "metaid" attributes, as well as the optional children Notes and Annotation. Unlike most lists of objects in SBML, however, the "sboTerm" attribute and the Notes and Annotation children are taken here to apply directly to every SBML element referenced by each child Member_t of this ListOfMembers_t, if that referenced element has no such definition. Thus, if a referenced element has no defined "sboTerm" attribute or child Notes or Annotation objects, that element should be considered to now have the "sboTerm", child Notes, or child Annotation of the ListOfMembers_t.
If multiple ListOfMembers_t have child Member_t elements that reference the same SBML element, and more than one ListOfMembers_t or Member_t has a value for an sboTerm attribute, Notes, or Annotation element, those Member_t elements should be consistent with each other: the "sboTerm" attributes should either be identical, or one should inherit from the other; Notes should say the same or similar things; and Annotation elements should not conflict. Interpreters may choose to resolve any such conflicts arbitrarily.
An uncommon feature about ListOfMembers_t is that, if it is referenced by a Member_t of a different Group_t, the children of the referenced ListOfMembers_t are also considered to be members of the referencing group. In this way, groups may be nested semantically to create larger groups out of subgroups.
Semantics of group memberships
- If a Member_t object within a Group_t object's ListOfMembers_t references another Group_t object, it is the referenced Group_t itself that is considered to be a member of the parent Group_t, not the corresponding referenced model component(s). This is true regardless of whether those components themselves happen to point to other components using some mechanism defined by another SBML Level 3 package (as happens, for example, in the SBML Level 3 Hierarchical Model Composition package and its use of SBaseRef_t). However, if instead a Member_t object references a ListOfMembers_t object (using the "id" attribute permitted on ListOfMembers_t objects), it is the components of that ListOfMembers_t that are considered to be part of the parent Group_t. In other words: if in some Group_t G, a Member_t M references another Group_t, that Group_t is the member of G; if M references a ListOfMembers_t, it is the entities referenced by the Member_t objects within the ListOfMembers_t that are the members of G and not the ListOfMembers_t object itself.
The implication of this is that any rule that applies to members of a group (such the meaning of the "kind" attribute, or the restrictions on the application of "sboTerm" attributes on a ListOfMembers_t) applies to the child group when referenced by the Group_t "id", and to the members of the child group when referenced by the ListOfMembers_t "id". In an example situation where a parent group includes two Species_t plus a Group_t which itself contains three other Species_t, if the parent group's ListOfMembers_t is given an "sboTerm" attribute value, that SBO_t term applies to the two species and the group, not to the three child species members of the second group. (Note also that in such a case, the parent group's "kind" attribute value would almost certainly be "collection" or "partonomy", and not "classification", as two species and a group are very unlikely to be classified as the same thing.) In contrast, in the situation where a parent group includes two Species_t plus a ListOfMembers_t which contains three other Species_t, the parent group's ListOfMembers_t "sboTerm" would apply to the five Species_t, and could be more reasonably marked as a "classification".
In a future version of this SBML Level 3 Groups specification, it may be possible to perform set operations on groups, but for now, this type of union is the only set operation that is possible.
Groups are not permitted to be circular: no Member_t may reference itself, its parent ListOfMembers_t, nor its parent Group_t. If a Member_t references a Group_t, the same restrictions apply to that subgroup's children: they may not reference the Member_t, its parent ListOfMembers_t, nor its parent Group_t, and if any of those children reference a Group_t, the same restrictions apply to them, etc.
If a Member_t has a "idRef" or "metaIdRef" attribute which references an object from a namespace that is not understood by the interpreter of the SBML model, that Member_t must be ignored. The referenced object will not be understood by the interpreter, and therefore has no need to become a member of the group. If an interpreter cannot tell whether a referenced object does not exist or if exists in an unparsed namespace, it may choose to produce a warning.
- See also
- Group_t
-
Member_t
-
ListOfGroups_t
