Synonym Functionality Broken?

Hi,

I recently re-ran some of my software that queries the ZINC database's synonym feature and got a response that there was no data available. (There was data available previously.)

Some examples:

Vitamin B12
ZINC01545892
Isobromindione
Temsirolimus

Other names that are missing from synonym:
Deoxyelephantopin, Gamma Aminobutyric acid, Glycyrrhizin, Glycyrrhizinate, INCB024360

Any help is appreciated! If there is a master synonym database or flat-file, that would be helpful too.

Thanks,

Aaron

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Hi John,

Thanks for getting back to me. It now makes sense that there was an upgrade to ZINC that changed the available set of compounds and what is included under /synonym/. Looking up substances by substance ID should be done via the /substance/... URL not through the /synonym/ interface as I had done in some edge cases -- this is something I can accommodate in my client code.

One more question:

When there are more than one physical representations of a given ZincID -- what is the best way to reference these?

For Biotin (3830316), there are two links:
http://zinc11.docking.org/fget.pl?l=0&z=56796488&f=m
http://zinc11.docking.org/fget.pl?l=0&z=56797422&f=m

I presume that the field z=56796488 and z=56797422 indicate the different representations. Would these codes potentially be appropriate was to refer to these in a publication -- are they "stable"?

Thanks again,

Aaron

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Hi Aaron

Thanks for your questions and your interest in ZINC.

Vitamin 12 is disqualified from being in ZINC 12 not only because of its size (circa 1300 g/mol, which is 40% larger than we generally allow), but also because it is a metalloenzyme.

http://zinc.docking.org/substance/1545892 was present when I went looking for it. Please try again.

Isobromindione needs a trailing star thus ( Isobromindione*) to match to http://zinc.docking.org/substance/400. This is due to limited curation in our dictionary, which we are working on.

Temsirolimus is 1030 g/mol, thus will not be loaded in ZINC in the near future. ZINC 12 is limited to really 800 g/mol. ZINC 15 will go to 999 g/mol, but Temsirolimus will still be excluded.

The synonym feature is meant to be useful, but we do not have the manpower to curate it further. Suggest you use wikipedia, chembl or drugbank, then get the smiles and search that way in ZINC. (you can also search with the chembl code in ZINC)

Thanks for the suggestion to make a synonym dictionary available. We will certainly consider it. There are already many good synonym dictionaries (e.g. via ChEMBL), and we do not have the resources to compete in this area.

John

-- sent from my iZINC

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