Known issues in the specification of SBML Level 2 Version 3 Release 1

The SBML Level 2 Version 3 Release 1 specification was made available on 16 June 2007. The following are the errors and other issues discovered in the specification document 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 online 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 and line number(s) Date added
1742495 Incorrect MathML in the example of Sec. 7.10. The example contained the MathML expression <apply><cn>0</cn></apply>, which is invalid. The <cn>0</cn> should not be inside <apply>. p. 118 lines 66–69; p. 119 lines 17–19 (not noted)
1745160 Validation rule 10204 is incorrect. Validation rule 10204 incorrectly stated that the definitionURL is only allowed on MathML csymbol elements, whereas in fact it must be allowed on semantics as well. In the section on SBO, the examples already use the attribute on semantics. The validation rule needs to be modified, as does the text in Sec. 3.4.1 and the MathML subset schema; see also issue #1801776 below. p. 140 lines 20–21 (not noted)
1760157 Incorrect statement about id on Event. The text stated that attribute id was required on an Event instance, but this was not true and disagreed with the UML diagram, in which the field is actually optional. p. 78, lines 2–3 (not noted)
1761663 Incorrect description of event action. The text stated that “When the event fires, the value of the model component identified by variable is changed by the EventAssignment to the value computed by the math element”. This was incorrect: the change takes place when the event assignment is executed. p. 80 lines 19–20 (not noted)
1772814 Bad typo in example. The example on page 17 had xmlns:"URL". The : character should actually be =. p. 17 line 31 (not noted)
1785279 Inconsistency in example of Sec. 7.7. The text description said the volume of the compartment was equal to 1, but the SBML disagreed. Moreover, the text description was so confusing that people misinterpreted it. p. 114 line 61 (not noted)
1785712 Error in rate equation example. The rate expressions examples on p.72 incorrectly had negative signs. The negatives are added later and should not have appeared where they did. p. 72, lines 37, 39 (not noted)
1787185 Out of order words. The text of validation rule 21103 contained words out of order. p. 150 line 33 (not noted)
1792674 Attribute encoding must be allowed on MathML elements annotation and annotation-xml. The encoding element was incorrectly disallowed from these MathML elements, both in validation rule 10203 and in Sec. 3.4.1. It must be allowed for annotation and annotation-xml as well. The SBML MathML subset XML Schema allowed encoding, so the text and validation rule were at odds with the schema definition. p. 140 line 27 (not noted)
1796300 Error in stoichiometry of example formulas in Sec. 4.13.6. The last example in that section, involving grams as units, had expressions such as 1000 * mA, when in fact they should have divided by molecular mass. p. 75 lines 19–20 (not noted)
1797728 Species’ constant attribute is “false” by default. A sentence in the text description incorrectly stated that the default of Species’ constant attribute is “true”. p. 49 line 11 (not noted)
1797729 Confusing language about species size. The passage on p. 49 had language that referred to a species’ size, but it would be less confusing to talk about the species’ quantity rather than its size. Compartments have size, but species don’t. p. 49 line 11 (not noted)
1800685 Clarification needed about shadowing of parameters. The implications of local parameters shadowing global identifiers of any kind was not stated explicitly enough and could too easily be missed by readers. Sec. 3.3.1 and p. 70 lines 17–19 (not noted)
1801776 MathML schema must change, allow definitionURL on semantics. The MathML subset schema does not allow the definitionURL attribute on the <semantics> element, but must in order to address issue #1745160 above. p. 138 line 54 (not noted)
SBML Level 2 Version 3 Release 1