#280 CHEBI:51730 MDL molfile is a query, not a structure

[Egon Willighagen]

Mark Rijnbeek filed a bug report about the CDK MDLV2000Reader not parsing bond types 4-8 as found in the ChEBI entry:

http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51730

The MDL molfile specification (version "November 2007") reserves bond orders 4-8 as *query* bond types, to be used in search queries.

I guess it is reasonable that a functional group in ChEBI is represented as query, but I was wondering how I should see from the MDL SD file if the entry is an actual chemical structure or another entity like a functional group query specification? Or do I need to browse the ChEBI ontology for that and see that it ultimately is marked as like organic group?

[pmatos]

Very late response to this, sorry.

A group is normally represented by an asterisk in the atom block as per IUPAC specification. It also has the name bla-bla group and yes its linked within the ontology.
P