1. What does ChemSpider want to be?
Is it a resource for researching experimental data, if so what are the critera for accepting data? Should every record be a compound you can isolate and store in a pot? Or do you also include experimentally observed (but un-isolable) reactive intermediates? At the complete other end of the spectrum is the idea of ChemSpider as a hub for connecting out to information on chemical structures, where the only real rule is that all links and data in a record are consistent with the stated InChI. The advantage of being closer to the latter case is that you can (in theory at least) generate/search more specific subsets of the data from this sort of database.

2. Would the information on virtual compounds be widely used?
If the data is used widely by lots of researchers from differing backgrounds then there is justification for incorporating it. But if the principle users of the virtual compounds are likely to be a small group of companies or specific research groups, who’s main interest is in screening libraries of virtual compounds, a separate database that is suited to their needs would seem to be a much better idea. Why would they want to get the data from ChemSpider rather than the source library?

I would also suggest that unless there is a change of attitude in the science community and disclosure of unsuccessful reactions becomes more commonplace, almost all records for virtual compounds are likely to be ‘orphans’ in the sense that there will be nothing to link them to (other than information on other virtual libraries that hold the same structure).

I don’t know what the answer to question 2 is, but I would say that in my previous life as a bench-based synthetic chemist, I was only ever interested either synthetic procedures or analytical data, and I would have wanted searching of virtual compounds to be something I opted into (rather than being the default).

I suppose the short answer is I personally think virtual compounds are fine so long as the data is being used, is not a significant drain on resources (in terms of curation and hardware). Above all, it must be clear when records relate to virtual compounds, and this creates a restriction that it must be possible to incorporate virtual compounds in a way that is not a hindrance to people who specifically want to search for real compounds, but aids researchers who are interested in virtual compounds.

Dave

Some companies might offer a synthesis on request, strictly speaking are those compounds virtual, because you can not pick them up. Anyhow, after a certain time such compounds are accessible, so I see no problems with such a scenario.

Finally, nonetheless, molecule spam should get clearly avoided, e.g. by “report this compound as spam or impossible”, which could be an interesting RSS feed to follow, especially if people have to provide argumentations why certain compounds are not accessible

In my opinion, as soon as there is some secondary information available about a compound – independent of whether it is classified virtual or real it is worthwhile to store it into a database. By secondary information I mean any information that is not accessible from the chemical structure itself. Might be as little as an URL to a (trustworthy) source. Or might be what Egon said: it is confirmed that the compound is “virtual”, i.e. can not be synthesized.

It is a trivial matter to generate, say, acyclic alkane isomers, but what is the lightest alkane which has yet to be isolated or synthesized? Herein lies the distinction between chemical information and mathematics. The “virtual chemists” should stay exactly that – virtual, not real.

The concerns about “validity” of virtual compounds
can be easily dismissed, nomen est omen, they are
of course not “real existing” compounds, but all
virtual. Are they “valid” compounds, hell yeah,
not sure if cursing is allowed here, of course
they are.

In case of selection of compounds, its easy
to set a filter, “natural product” or
existing organic compound or “virtual
compound” which can be changed once fully synthesized.
So that is none of the users concern, but
rather a small technical issue for RSC.

If Chemspider (similar to PubChem, which actually
has a different mandate) decides to drop
virtual compounds, other databases will come up,
if virtual compound databases are needed.

The existence of ZINC (http://docking.org/?q=node/131)
or the GDB-13 database (unibe.ch) which currently
covers around 1 billion compounds downloadable for free
http://www.dcb-server.unibe.ch/groups/reymond/gdb/home.html
speaks volumes.

Just because people never heard about data driven science,
or don’t have imaginations what to do with such virtual
compounds doesn’t make it automatically “junk chemistry”.
I am well aware of your quotation marks

This is a good example where scientific p2p technology
would work, instead of a single host, people upload and
download part of such a database via peer-to-peer networks.
Or maybe Sigma-Aldrich, which just recently bought
ChemNavigator with its 83 million compound database,
will be the new kid on the block, similar to Chemspider
some months/years ago. Once isomer generators and
combinatorial algorithms and their filters will be
fast enough to work in real-time, there’s no need to
put such virtual compounds in a database anyway.

But such large databases of virtual compounds
must be downloadable in bulk for HT drug screening,
as datasets for cheminformatics or other purposes.
It does not really make sense to scroll online
through 1 to 10 compounds a at time.

As you have said, semantic annotation of
new chemistry publications is much more important.
I wouldn’t care that much about the old stuff, that is
very well covered in Beilstein and CAS Scifinder.

That said, if Chemspider can store one or two billion
compounds with full download capability – keep it.
If not – drop it.

Cheers
Tobias