The primary issue is that many of the vendors/depositors are so used to dealing with SDF files that our mutual systems have to deal with problematic submissions. AND, they get passed on from system to system. Right now I want people to post a comment when they see issues with organometallics or ANY structures and then we can deal with them. Unfortunately, on the long list of issues to work on, this is not top, but it is in the top third. I’ve only had 2 comments regarding poor organometallic representations and I think I a more concerned about it than the majority of users. Of course, inorganic and organmetallic chemists would want to shoot us for the poor representations and I acknowledge it, thank them and have to keep working on what we can.

I don’t think there IS a good system out there dealing with organometallics other than maybe CrystalEye and that does use CML as part of the underlying technology so that makes sense. Jim Downing and I are in email exchange at present about using the atom feeds so maybe we can figure out how to get the value out of that.

Now, one thing I did discover is that some complexation (coordination) bonds are correctly represented in PubChem’s ASN.1 format (both plain text and XML, binary probably too, but is so difficult to read)… However, I spotted at least some MDL molfile versions (SD files, in case of search results), where these complexation were represented as single, covalent bonds. That will surely mess up your chemoinformatics.

Therefore, I can surely understand the desire to submit as CML, which has more power in expressing chemistry than MDL molfiles. Particularly important for organometallics… Alternatively, I guess one can submit to PubChem in the ASN.1 format too?