15.0.0 MINERVA Release

22 June 2020

New features:

  • Import and export of GPML (Graphical Pathway Markup Language) is implemented.

  • The logs provided for the validation of the data model (during project’s upload) are structured now. The logs contain information about entry’s severity (warning, error) and its type (parsing issue, annotation conflict, other).

  • API allows to merge files (check API documentation).

  • Export to SBGNML/SBML/GPML format provides popup with the list of warnings occurred in the translation process.

  • Support for colours rendering in SBGNML is added.

Feature removal:

  • Old connection to CTD is removed and replaced with new Data-API interface that closely check license compliance.

  • Old connection to DrugBank is removed and replaced with new Data-API interface that closely check license compliance.

  • Particular custom fields (e.g. ‘TransparencyZoomLevelVisibility’, ‘SemanticZoomLevelTransparency’) are not exported to CellDesigner file.

  • Truncation/association/dissociation anchor points are represented as a dot in new uploaded maps. Previously the anchor point was displayed as & symbol.

  • All reactant/product anchors points are represented as a dot in all newly uploaded maps. Previously the anchor point was displayed as & symbol.

  • The reactions are displayed on the top of the elements in case of upload the files in formats without Z-index parameter.

  • When uploading advanced project (with submaps) there is no possibility to change the submaps names.

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Small improvement:

  • The compartments in SBML with no layout file are more scattered (the offset between the borders of the compartments is bigger).

  • During the export of map result, and if the size of the result exceeds 1MB, the content is compressed and returned as a zip file.

  • The confirmation warning is displayed before removing ‘general view’ overlays.

  • CellDesigner text area objects have BorderColor property defined.

  • The list of the submaps in the left panel is sorted alphabetically.

  • The notification about new releases of MINERVA is added in the Administrator panel.

  • The font Awesome upgraded to 5.1 (new icon styles).

  • In the User View the top bar contains new buttons - login/logout button and access to Administrator panel button.

  • Autocomplete for chemical searches is enabled.

  • When typing a drug’s name in the search box, the list of the autocomplete drugs is limited to the drugs that target species on the map.

  • The uri qualifiers bqmodel:isDerivedFrom, bqbiol:occursIn, bqbiol:hasProperty and bqbiol:isPropertyOf are handled in the annotations.

  • 3DMET, Chemical Component Dictionary, ChemIDplus, EcoGene, Evidence Code Ontology, FlyBase, GeneDB, Intact, KEGG Drug, KEGG Glycan, KNApSAcK, LIPID MAPS, LipidBank, NCBI Protein, PATO, RGD, SPIKE, SWISS-model, TTD Drug and ZFIN BioEntity annotations are supported.

  • Small CSS improvement in the INFO tab in left panel (i.e. text adjustment).

  • Import/export of a unit of the information, obtained from SBGN source, to SBML is supported.

  • The rounded rectangle is used to visualise Simple Chemicals in SBGN-like view according to the newest SBGN specification.

  • If removing of a project is confirmed, the system enforce waiting until the remove status is confirmed and displays status ‘Project removing(0%)’.

  • Data not compliant with database constraints (e.g. too long species identifiers) will be automatically adjusted instead of crashing a project upload.

  • Reaction lines in SBML files without layout are set outside of the species. Previously, these were in the center of the species.

  • The order of tables in Administrator panel, sorted by user, is preserved among sessions.

  • Simple molecules in SBGN compliant view are drawn as ellipses not circles.

  • Uploaded map is automatically cached.

  • MolArt updated to version 1.5.0: new feature - show unobserved structure regions in the sequence view.

  • The list of genomes is automatically refreshed during genome upload in Administrator panel.

  • Items in the context menu in User View (e.g. open in MolArt, Add comment) are reorganised.

  • CellDesigner files from version 2.5 should be parseable.

  • Plugins in Administrator panel can be revalidated to update plugin’s details (name, version).

  • The default plugins can be defined in Administrator panel. These plugins are loaded with opening of any map.

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  • The pathways are visualised in API image converter.

  • The conversion of a file containing BOM in the header did not work.

  • Upload of SBGN files did not process unicode characters properly when server was running with encoding different than UTF-8.

  • The proper colour is parsed from CellDesigner species marked as ‘brief’ (e.g. complex viewed compact).

  • The kinetic equation in a reaction that referenced to complex (instead of a target species) crashed CellDesigner file upload.

  • The kinetic equation in SBML that used speciesReference id crashed project upload.

  • The layout reaction with a duplicated reaction element crashed SBML upload.

  • The conversion from SBML to CellDesigner escaped “<” twice.

  • Currently, Select annotation dialog width is at least 840px.

  • The modifiers joined by operator were exported to SBML without the line corresponding to the operator.

  • Currently, when importing from SBGNML, the first state variable that does not match modification residue is translated to the structural state.

  • The exported SBML was not compliant with the standard if the element’s name was empty.

  • During advanced map upload, if the zipped file contained invalid data overlays, the project upload was successful but the map could not be opened. Currently, the upload finishes with failure and corresponding warning.

  • The cardinality in SBGN-like view is drawn in separate unit.

  • Notes from SBML are parsed along with all html tags.

  • Converter API appends conversion warnings to the generated output notes.

  • Newt uses incorrect attributes when exporting render information that might not be parsed by MINERVA.

  • The catalysis reaction to phenotype was not parsed from SBGN file.

  • AntisenseRna shape is inferred from SBGN when antisenseRna text is present in glyph label.

  • Export to SBGN sometimes crashed due to the concurrency issues.

  • CellDesigner models, where start and end point of the reaction were the same, were not handled properly.

  • CellDesigner file containing more than one author was not parsed properly.

  • SBGN reaction with no reactants crashed map upload.

  • Import from SBGN assigned invalid names to species that did not have label defined. Currently, the name is left empty.

  • Drawing a protein in SBGN-like style did not handle properly the dimension of the species for multimers greater than 2.

  • The dimension of the modifications is preserved if the file is exported to SBGNML-PD.

  • Drawing of the structural state in SBGN-like style used Ellipse instead of RoundedRectangle, what was not SBGN-compliant.

  • The structural states of the proteins are imported properly from SBGNML-PD.

  • The position of the structural state is preserved on the upload of CellDesigner file.

  • Import from CellDesigner rounded alias dimension to integer.

  • The compartments limited by corner (left-top corner compartment, etc.) are parsed properly from CellDesigner files.

  • Export to CellDesigner elements names with a new line character is properly handled.

  • Layout of the exported Reactome pathways is fixed if Reactome exporter violates SBGN specification.

  • Unknown catalysis boolean gate modifiers in CellDesigner are visualised with dashed line across all included modifiers.

  • Particular problematic notes do not crash CellDesigner upload.

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