The component update boundary values for selected This component allow to add or update annotations or notes for the elements of the model, such as metabolites, reactions, or genes. Component updates notes and annotations separately. So to update both two instances of the component have to be added to the workflow: one with notes table and one with annotations.
Elements of the model connected to table rows by column selected ID in the configuration dialog. In the case that value in the ID column do not match any element of selected type in the model, that row will be omitted and no error or exception will be raised.
Annotations and Notes helps to provide the meaning for the elements of the model by connecting them with external databases, ontologies and dictionaries. Notes are stored in human readable form, while annotations are supposed to be in machine readable form. Within the model annotations are represended as a reference to https://identifiers.org/. Column name of the annotation ideally should correspond to one resource listed in https://registry.identifiers.org/registry and values in the column should correspond to the format of the selected resource identifier. MEMOTE (Lieven et al., 2020, DOI:10.1038/s41587-020-0446-y) checks the consistency of annotations for the following set of databases.
For metabolites:
- pubchem.compound
- kegg.compound
- seed.compound
- inchikey
- inchi
- chebi
- hmdb
- reactome
- metanetx.chemical
- bigg.metabolite
- biocyc
For reactions:
- rhea
- kegg.reaction
- seed.reaction
- metanetx.reaction
- bigg.reaction
- reactome
- ec-code
- brenda
- biocyc
For genes:
- refseq
- uniprot
- ecogene
- kegg.gene
- ncbigi
- ncbigene
- ncbiprotein
- ccds
- hprd
- asap
In the case that multiple values for the same annotation type are provided, they will be concatenated in one string separated by **Separator** symbol. By default `|` is used as a separator.
- Type: Pythonmodelcobrapy Model object from other FBA components.
- Type: Tableannotationstable of annotation to add.