Issues with information in synonym table

[matthiaskoenig]

I worked a bit with the bigg database in the last few days. I found some issues in the synonym table with most of them easy to fix (see an attached log of all issues in the bigg synonym table). This is a duplicate (but more comprehensive) of #340, #331, #275, #260

A full set of the required fixes here (WARNING can be fixed, ERROR no solution possible right now) bigg-v1.5-mapping.log This includes:

• adding reactome prefixes
• kegg glycans belong in kegg.glycan
• some rhea, sabiork, kegg.reaction have incorrect #1 or #2 endings, probably some software or curation bug somewhere
• creating correct ec-code codes (things like 1.2.1 -> 1.2.1.-)
• there seem to be some duplicates in the ec codes (?!)

In addition some namespaces are incorrect in the data_source table

    ns_replacements = {
        "mnx.chemical": "metanetx.chemical",
        "ec": "ec-code",
        "REBASE": "rebase",
        "sabiork": "sabiork.reaction", # check
    }

with corresponding update of the url prefixes required.

Best Matthias