Schmoho
Schmoho
I just went through Biomodels, BiGG and some models of our group to find identifiers.org URLs that are not using valid namespaces. Labeled as "feature" because this aims to repair...
Why is this result "failed"? ```json "test_metabolite_sbo_presence": { "data": [], "duration": 0.0049783941358327866, "format_type": "count", "message": "A total of 0 metabolites (0.00%) lack annotation with any type of SBO term:", "metric":...
Occurs on this model: https://www.ebi.ac.uk/biomodels/MODEL2310020001 This model contains a number of `fbc:geneProduct` elements with names like `G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain`. MP removes the strings "LPAREN" and "RPAREN" only on the id of the...
The issue can be observed on this model: https://www.ebi.ac.uk/biomodels/MODEL1604280030 After application of the polisher the cobrapy validator gives this `SBML_ERROR`: > "E0 (Error): MathML consistency (core, L40425); A `ci` element...
Unlike expected, the render specification seems to specify the `GlobalRenderInformation` class to use a `renderInformation` tag, possibly because it derives from the `RenderInformation` tag. (Section 3.5.3) https://raw.githubusercontent.com/combine-org/combine-specifications/main/specifications/files/sbml.level-3.version-1.render.version-1.release-1.pdf However, after application...
We actually have a test for this specific behaviour: https://github.com/draeger-lab/ModelPolisher/blob/113b46764b2df15a0333e6a1244fa1215cee7c39/lib/src/test/java/de/uni_halle/informatik/biodata/mp/fixing/fbc/ListOfObjectivesFixerTest.java#L99C1-L117C6 Evaluation of cobrapy validator results for the Biomodels dataset however revealed this yields a COBRA_WARNING. This behaviour can be seen...
This occurs on model https://www.ebi.ac.uk/biomodels/BIOMD0000000807 The error is very serious since it changes the mathematical interpretation of the model. This method https://github.com/draeger-lab/ModelPolisher/blob/113b46764b2df15a0333e6a1244fa1215cee7c39/lib/src/main/java/de/uni_halle/informatik/biodata/mp/polishing/SpeciesPolisher.java#L84-L103 has two errors: 1. It interprets the species...
Can be observed on model https://www.ebi.ac.uk/biomodels/MODEL2308220001 where this annotation exists: ```xml [...] ``` (chemspider and hmdb annotations) MP truncates this, so the whitespace is gone. cobrapy does not recognize the...
We are currently supporting SBML 3.1 in our code, but this is never handled explicitly. Proper support for 3.2 and 2.X versions suggests we restructure the code s.t. fixing/polishing/annotation modules...
I am trying to access the actual underlying data point of a selection. If this is possible at all, I was not able to see how from the [documentation](https://vega.github.io/vega/docs/signals/). The...