Collected Errata to the SBML Level 2 Version 3 Specification
Errata in Release 1 (corrected in Release 2)
Release 2 of the SBML Level 2 Version 3 specification was made available on 26 September 2007. The following are the errors and other issues corrected or changed in Release 2 relative to Release 1. 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.
|Page(s) and line number(s) in documents|
|ID #||Description||Release 2||Release 1|
Incorrect MathML in the example of Sec. 7.10.
The example contained the MathML expression
||p. 119 lines 2 and 20||p. 118 lines 6669; p. 119 lines 1719||1745160||
Validation rule 10204 is incorrect.
10204 incorrectly stated that the
p. 140 line 31;
p. 21 line 31
|p. 140 lines 2021||1760157||
Incorrect statement about
||p. 77, line 19||p. 78, lines 23||1761663||
Incorrect description of event action.
stated that "When the event fires, the value of the model component
||p. 80 line 21||p. 80 lines 1920||1772814||
Bad typo in
||p. 17 line 31||p. 17 line 31||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 58 to p. 115 line 2||p. 114 line 61||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 line 44; p. 73 line 2||p. 72, lines 37, 39||1787185||Out of order words. The text of validation rule 21103 contained words out of order.||p. 150 line 33||p. 150 line 33||1792674||
||p. 21 line 30; p. 140 line 28||p. 140 line 27||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. 76 lines 2526||p. 75 lines 1920||1797728||
||p. 49 line 11||p. 49 line 11||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||p. 49 line 11||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.||p. 19 line 24; p. 70 lines 1924||Sec. 3.3.1 and p. 70 lines 1719||1801776||
MathML schema must change, allow
||p. 138 line 54||p. 138 line 54|