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 |
| 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. 119 lines 2 and 20 | p. 118 lines 66–69; p. 119 lines 17–19 | 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 line 31; p. 21 line 31 |
p. 140 lines 20–21 | 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. 77, line 19 | p. 78, lines 2–3 | 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 line 21 | p. 80 lines 19–20 | 1772814 |
Bad typo in xmlns:"URL". The ":" character
should actually be "=".
|
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 |
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. 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 25–26 | p. 75 lines 19–20 | 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 | 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 19–24 | Sec. 3.3.1 and p. 70 lines 17–19 | 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 | p. 138 line 54 |