Confirmed issues in the Level 3 Version 1 Core Specification
This page lists all issues officially noted for any release of the the SBML Level 3 Version 1 Core specification.
Release 1 (Final)
Release 1 of the SBML Level 3 Version 1 Core specification was made available on 6 October 2010. The following are the errors and other issues discovered in the Release 1 specification after it was issued. In the following table, the ID # of each issue refers to the reference number automatically assigned to the issue in the SBML issue tracking system. The gaps in this numbering are not consequential for SBML and do not necessarily signify deleted or unresolved issues.
| ID# | Description | Page(s) and line number(s) | Date added |
|---|---|---|---|
| 3427989 | The UML diagram does not show that Trigger is derived from SBase. A line is missing to show the derivation. | p. 71 Fig. 20 | 1 Dec.'11 |
| 3424957 | The UML box for EventAssignment declares the data type of attribute variable to be SId, but in fact the correct data type is SIdRef.
| p. 71 Fig. 20 | 1 Dec.'11 |
| 3398119 | The UML box for Model misspells the data type UnitSIdRef as UnitsSIdRef. The former is the correct spelling.
| p. 30 Fig. 10 | 1 Dec.'11 |
| 3295596 | The sentence begins "The Event attribute variable ..." but the attribute is actually on EventAssignment, not Event.
| p. 76 line 16 | 30 Apr.'11 |
| 3295599 | The text refers to "MathML ci attributes", but ci is an element, not an attribute, so the text should really read "MathML ci elements".
| p. 77 lines 8, 11 | 30 Apr.'11 |
| 3523426 | The XML diagram illustrating the history structure is complete and defines what is optional and what is required, but the text under the figure is not complete and does not recapitulate what is in the diagram. The text should be expanded. | p. 92 lines 9–40 | 19 Jun.'12 |
| 3485275 | The XML fragment defines a namespace prefix size but this is incorrect; the namespace prefix should be named struct.
| p. 16 line 13 | 19 Jun.'12 |
| 3476019 | Validation rule #10311 should include the units attribute on LocalParameter along with the other SBML components listed.
| p. 144 line 10–14 | 19 Jun.'12 |
| 3485275 | The specification lacks a validation rule stating that the value of the attribute substanceUnits on a Model object should be either "mole", "item", "gram", "kilogram", "dimensionless", "avogadro", or the identifier of a UnitDefinition object based on these units. The rule should be number 20233.
| p. 150 line 13 | 19 Jun.'12 |
| 3459194 | Figure 10 has a misspelled attribute name. The attribute listOfContraints on Model should be named listOfConstraints.
| p. 30 Figure 10 | 19 Jun.'12 |
| 3293971 | The paragraph about UnitDefinition should make it explicit that new unit identifiers cannot be the same as any of the base units defined in Table 2 on p. 37. | p. 17 lines 9–11 | 19 Jun.'12 |
| 2090717 | A long-standing bug that was forgotten until recently is that the RDF subset defined in the spec does not allow the attributes rdf:ID and rdf:about. It should. This change has to be introduced as part of a Version 2 of SBML Level 3.
| p. 89 | 19 Jun.'12 |
| 3214113 | The explanation of what constitutes unique top-level elements in an annotation is insufficiently clear about whether it is the namespace or the namespace prefixes that matter. It is the namespaces that matter, not the prefixes. | p. 15–16 | 19 Jun.'12 |
| 3295573 | The use of the word 'symbol' in different parts of the specification is not always consistent. | (many) | 19 Jun.'12 |
| 3414863 | The precise extent of identifier shadowing by local parameters is unclear. The specification should give a complete list about what is shadowed. | p. 17 lines 12–16 | 19 Jun.'12 |
| 3536424 | Validation rule #20608 mentions the availability of a unit named "substance", but this does not exist in Level 3 Version 1 Core. It should be removed from the list of valid unit names.
| p. 152 lines 28 | 20 Jun.'12 |
| 3537594 | The text states that the type of attribute 'id' is UnitSIdRef, but in fact it is UnitSId. This is clear from the UML diagram.
| p. 36 lines 2 | 25 Jun.'12 |
| 3537052 | Validation rules #10311 and #20401 have overlap: both of them state that the value of the attribute id in a UnitDefinition object must conform to the syntax of the SBML type UnitSId. Rule #20401 also adds the condition that the identifier must be unique and not be identical to certain other identifiers. The overlapping condition should be removed from rule #20401; the rule should only be concerned with the topic of uniqueness of identifiers.
| p. 144 lines 10–14, p. 150 lines 35–41 | 25 Jun.'12 |
| 3538515 | The text misleadingly implies there is something special about the designated examples that use attributes boundaryCondition and constant, when in fact, all models must provide values for these attributes because the attributes are not optional.
| p. 45 lines 34–35 | 28 Jun.'12 |
| 3487945 | Section 4.6.6 is insufficiently clear about when species amounts may or may not change. Table 4 states that a species quantity never changes under some circumstances, but it is specifically the species amount that does not change; if the compartment size changes, species concentrations may change even for the conditions where the table indicates "never changes". The section would benefit from a rewrite. | p. 45 Section 4.6.6 | 3 Jul.'12 |
Release 1 Candidate (superceded by Release 1)
Release 1 Candidate of the SBML Level 3 Version 1 specification was made available on 31 December 2009. For historical interest, on a separate page you may find the issues that were found in the candidte release and later incorporated into the final Level 3 Version 1 Core release.