The issue with CAS identifiers

To a recent post by Glyn Moody (The World’s Leading Anti-Scientific Society)
[ largely quoting me so I shan’t repeat it…]

[GM] … Clearly, it’s time to kill off this pernicious closed CAS system, which is damaging science, by boycotting it entirely…

ChemSpiderMan replied:

I’ve made two comments on CAS and the Wikipedia commentary.
http://www.chemspider.com/blog/cas-discourages-using-scifinder-to-help-curate-wikipedia-structures-and-cas-numbers.html
http://www.chemspider.com/blog/enforcing-copyright-of-cas-numbers.htmlI am not ready to abandon hope that the ACS/CAS can reach a point whereby they recognize the value, both public relations wise as well as good for their business. I believe it’s easy to declare that we should just abandon CAS and their dominant position but it is not so easy. The relationship between CAS numbers and their >100 years of literature/patents is deeply entrenched in their offering. They have very skilled people dealing with their systems and, other than the protectionism we judge is prevailing, their systems are good. Sure, they can be more open but let’s try and achieve that with a common-good discussion rather than abandoning them. While it’s easy to talk about RDF solutions and OWL and, and, and, these are solutions yet to be proven. They are valiant efforts and need to be pursued but they are yet to be proven. Also, think about the politics…if PubChem IDs prevail and damage CAS’ business then CAS initial views of PubChem damaging their business will have been validated…people will be out of jobs and all hell might break loose. I say bring the right people to the table to work through the complex business issues and do it soon.
That said, I’ll acknowledge that I prefer to try and navigate the complex issues to a mutually beneficial point rather than go into attack mode preferred by others.

5:56 PM

glyn moody said…

Thanks for your thoughts.Fortunately (for me) I have the luxury of not being directly involved with any of this. I also write from the position of one who blogs extensively about these issues, and is not afraid to rush in where angels fear to tread.I accept that there is plenty of room to negotiate and to attempt to move the ACS; I wish the best of luck to those trying to do that.But I also think it can be useful (good cop, bad cop) to suggest more outrageously radical solutions – like chucking the ACS completely.
Speaking as an outsider observer, I have been frankly disgusted (as in Tunbridge Wells) by its behaviour – not just on this occasion, but previously, too. As I said in the post, science seems a quintessentially open endeavour, and for the ACS to put money over knowledge seems unforgivable.

PMR: I will try and clarify the issues, and I hope that the ACS or CAS can reply if I get them wrong…

• There is no god-given chemical informatics system – Principia Chimica. All systems of names, chemical structures, identifiers have a degree of arbitrariness. To avoid chaos we look to authorities to provide and to some extent regulate these. Authorities include IUPAC, CAS, PubChem, SwissProt, Genbank, International Union of Crystallography and hundreds more.
• These authorities influence the community by (a) respect (e.g. the International Unions and learned societies) (b) market dominance (as for Thomson ISI for citations) (c) regulation, either legal or enforced by other autorities (e.g. patents, FDA, etc.). Anything in (c) is very difficult to change. It is up to the players to argue their cases.
• There is usually no absolute right or wrong – what is the CAS number for penicillin? For many years the structure wasn’t known (Dorothy Hodgkin solved it) but there was still a name and an identifier. I do not now know whether “penicillin” has a CAS number. What is the CAS number for “glucose” – not alpha-D-glucopyanoside…? So although it is a worthy attempt to curate the “right” structure for a guiven name in many cases it is impossible – it is simply a question of authority. What is the structure of “snow”? This depends on an authority and cannot be answered without also quoting them.

The ONLY definitive statement of the relationship between CAS numbers, structures and names is from Chemical Abstracts. It is no use looking them up in catalogs as these are frequently wrong and in any case do not carry the authority.
To give an example from another authority – what is the PDB number for insulin (also solved by Dorothy Hodgkin and coworkers)? I go to the PDB site and type in “insulin” and find

Ooops! There’s more than one “insulin” – (there’s more than one “penicillin” as well). But I can browse all of them if required. If I want the one shown its accession number is 1T1K. If I send that to any bioscientist they will know what I am talking about. But if there is any disgareement about the identity of 1T1K then this page is the ONLY authority.
The problems with the current CAS identifiers are:

• There is NO public lookup of them (unlike everything in bioscience including PubChem, and PubMed).
• It is now expressly FORBIDDEN to transmit publicly the results of any lookup of this information

Traditionally a library would purchase a printed copy of Chemical Abstracts. Libraries were proud of their CAS – it could run to several metres of celluose and carbon. But then anyone with access to a library (the BL if necessary) could resolve questions like this. I doubt very much if there was a prohibition on telling people what names were associated with which CAS numbers.
In the electronic age control is easier. Note that the control will not be through copyright but by contract to subscribers. ACS can and does cut of subscribers for what they unilaterally determine are breaches of contract. The current prohibition specifically relates to contracts. Since, however, I know of no way of accessing modern CAS information other than through a contract-based system (and I’d be grateful to know if there is) I will break my instituition’s contract if I try to help create better science by clarifying information.
Chemspiderman and some Wikipedians take the view that WP should negotiate with CAS. Since WP is a democracy it will find its own way of resolving this. I take the following view:

• Wikipedia requires authoritative sources for its information.
• The assignment of a CAS number to one or more WP entries requires the authority of CAS
• CAS forbids WP to use this authority
• Therefore WP cannot include CAS numbers if it wishes to uphold its principles of authoritative sources – there are NONE available to it.

This is the logical argument for a boycott and I’d be happy to see counter arguments.
On the political front I regard CAS’s action as unacceptable for a scientific society which enjoys charitable status by virtue of its respect in the community. Charities have a responsibility to help the community – this action is diametrically opposed.