ModelPolisher
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draeger-lab
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
Running the docker container as non-root consistently produces ```May 13, 2020 6:47:47 AM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode --- WARNING: Could not lock User prefs. Unix error code 2.``` ```May 13, 2020 6:47:47...
@Midnighter requests at https://github.com/SBRG/bigg_models/issues/368: Many models in BiGG are currently annotated with a taxonomic identifier and a reference to the model itself, for example, as shown below. ```xml ``` On...
Request a new SBO term to be used for confidence scores.
As @matthiaskoenig mentioned during GSoC, it would be nice to restructure ModelPolisher so it can directly annotate model parts without the necessity to parse the complete model. This would also...
It would be very useful to have annotations for KEGG subsystems and genes assigned by the ModelPolisher. This would save a lot of time and work during model curation. To...
Per the [specification 3.1](https://raw.githubusercontent.com/combine-org/combine-specifications/main/specifications/files/sbml.level-3.version-1.core.release-3.pdf) (and 3.2 for that matter) the ID attribute is mandatory on both entities. I.e. if an ID is missing, the SBML is not valid. In an...
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...
Hi, I would like to add pathway information in the polished models. The issue #97 says that this feature is implemented in the branch 2.1. However, when I run "docker...
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...
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ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.