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Collected Errata to the SBML Level 3 Version 1 Core Specification

Image:Updated.gif 6 October 2010.

Release 1 Candidate of the SBML Level 3 Version 1 specification was made available on 31 December 2009. The following are the errors and other issues discovered in the Release 1 Candidate 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
2964794 The specification¬†fails to stipulate whether the delay csymbol can be used within a FunctionDefinition object, yet it¬†explicitly disallows time and avogadro. In the interest of consistency and simplicity, the csymbol for delay is also disallowed. p. 34 lines 19–20 7 Apr. '10
2980574 The definition of an SBML species in this paragraph states that they "(b) participate in reactions ...", which may leave the impression that they must participate in reactions. The wording will be changed to "(b) may participate in reactions ..." p. 43 line 3 19 Apr. '10
2930524 The capitalization of SBase is inconsistent in Figure 8 as compared to elsewhere in the specification: it should be SBase, not Sbase. p. 13 Fig. 8 19 Apr. '10
3012506 In the SBML of example 7.8, the <compartment> elements should each have a value for the attribute spatialDimensions. Without it, the compartments will not inherit the volume units declared on the enclosing <model> element, and thus they will have no units declared. p. 113 lines 38, 39 12 Sep.'10
3012484 The number "2" in the function definition of "f" has an attached unit declaration, and it is the unit "conc". However, this is incorrect. The unit of "2" in this example should actually be "dimensionless". p. 116 line 31 12 Sep.'10
2993291 The text on this line states that the identifier of a UnitDefinition object "must not contain a value from Table 2". The text should be changed to "must not be equal to one of the reserved base unit names listed in Table 2". p. 36 line 7 12 Sep.'10
2993285 Table 1 is referenced incorrectly as "Figure 1" on this line. (Figure 1 is in fact a completely different figure and present on page 5). p. 21 line 9 12 Sep.'10
2993284 The text within the Unit UML box for the kind attribute states "Restricted to values in Table 1", while the legend text for that figure says that the reserved words are in Table 2. The figure is wrong, the legend is right; the table is Table 2. p. 36 12 Sep.'10
2991130 Rule 21131 is incorrectly listed as a new rule; in fact, the number existed in Level 2, and had a different meaning. This particular rule should be renumbered to 21132. p. 150 line 36 12 Sep.'10
2991120 Rule 20413 states "The ListOfUnits container object in a UnitDefinition object is optional, but if present, it must not be empty." It is listed as a new validation rule, but in fact, this rule did partly exist in Level 2 versions 2–4 as rule 20409. p. 145 lines 5–6 12 Sep.'10
3012489 The units of "k1" in the example of Appendix B should be changed to "per time" instead of "per concentration per time". This also entails defining a new unit for "per time" in the example. p. 154 line 49 12 Sep.'10
2980587 The word "global" should be inserted before the word "Parameter". p. 53 line 34 12 Sep.'10
3001488 There is a validation rule missing for the case where a compartment has no value for either attribute units or spatialDimensions. In that case, the compartment's unit of size is undefined. The correction needs a new validation rule, 20518. p. 146 15 Sep.'10
3071318 An SBML community vote has resulted in the addition of a way to put priorities on events that trigger simultaneously. This has lead to the addition of a new subobject to Event called Priority. Section 4.12 19 Sep.'10
3071319 An SBML community vote has resulted in the addition of a way to specify the value that should be assumed for an event's trigger prior to t=0. This has lead to the addition of a new attribute, initialValue, on Trigger. Section 4.12 19 Sep.'10
3071322 An SBML community vote has resulted in the addition of a way to indicate whether events can be disabled after being triggered but before they are executed. This has lead to the addition of a new attribute, persistent, on Trigger. Section 4.12 19 Sep.'10
2993312 Allyson Lyster reported over 40 editorial, consistency and clarity issues in the document. This lead to numerous small edits all over the document. (many) 19 Sep.'10
3071274 Validation rules 20507, 20508, and 20509 incorrectly referred to unit identifiers "volume", "area", and "length", which do not exist in SBML Level 3 Core. p. 145 lines 28–39 26 Sep.'10
3076195 The specification lacked an explicit statement that AlgebraicRule objects must not be used to determine the values of reaction rate expressions. (Equivalent statements existed for other kinds of rules, but not for algebraic rules.) This needs to be stated explicitly in the section for AlgebraicRule Section 4.9.2 6 Oct.'10
3073084 The set of validation rules involving Compartment objects and its attributes missed the case where both size and spatialDimensions are undefined. New validation rule 20518 is needed to state that if both attributes are undefined, the unit associated with the compartment's size is undefined. p. 152 6 Oct.'10
3072228 Nowhere did the specification mention that implementations should use identical values of Avogadro's constant for both the base unit mole and the added unit and csymbol for Avogadro. This needs to be stated explicitly. Section 4.4.2 6 Oct.'10

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