petermr's blog

NOTE: even if you are not a chemist, this should be worth reading…
Rich Apodaca evangelises the value of JRuby as a simple way of glueing together the Java offerings in our Open toolkit. Here he shows how easy it is to use Opsin for converting chemical names to structures. It’s worth reading in full if you are a chemical hacker (but I’ll omit the code here…) . After that I make some comments on OPSIN. Note that OPSIN is commonly distributed with the OSCAR3 package and the names are sometimes confused; OPSIN is a standalone tool for name2structure.

JRuby for Cheminformatics: Parsing IUPAC Nomenclature with OPSIN

Recent articles have discussed the use of JRuby for cheminformatics. We’ve seen how to parse SMILES strings, and read or write InChIs. In this article, we’ll see how easy it is to parse IUPAC nomenclature from JRuby using Peter Corbett’s OPSIN library.

Installation

After installing JRuby, simply download the OPSIN jarfile and copy it to your JRuby lib directory. You’re done.

A Simple Library

We can write a simple library to convert an IUPAC name into a CML document:
[details snipped; see JRuby for Cheminformatics: Parsing IUPAC Nomenclature with OPSIN]
This simple Ruby library has parsed the name ‘4-iodobenzoic acid’ and has returned a string containing the CML representation for the molecule. If we had wanted the read_name method to return a traversable XML object model, we could have enabled that as well.

Conclusions

One of the objections raised whenever the issue of “new” programming languages comes up, regardless of their merit, is the age-old refrain “Yeah, but where’s the software?” With JRuby, we bypass this question altogether. We can leverage the full scope of the massive Java development effort over the last ten years, which includes several excellent cheminformatics libraries. With virtually no effort, we have a working cheminformatics platform based on a widely-used, versatile and dynamic object-oriented scripting language. Future articles will discuss extensions to this platform and some applications.

PMR: Absolutely true. I don’t do a lot of glueware so I don’t use these languages, but my colleagues do.
OPSIN… I am sure Peter Corbett will add more, but the roots of OPSIN are about 5 years ago when we started the OSCAR work. OSCAR started as the Experimental Data Checker sponsored by the Royal Society of Chemistry, and after the first year it became clear that much of the data checking could not happen unless we knew the chemical structure. You can’t check that a compound has the right NMR spectrum if you don’t know how the atoms are connected.
Current chemical publishing and publishers destroy huge amounts of useful chemical information.
(Reread this sentence if you don’t believe it).
If you doubt it, visit the RSC’s Project Prospect (which is based on our collaboration over OSCAR). Find an example paper. (Most of the papers are closed, but there are a few open examples (e.g.) so you can see how it works). By default you will see a normal HTML page. However if you switch on the prospect enhancements, and select “Show Compounds” you should see the compounds highlighted

PMR: now I haven’t a clue what cycloproparadicicol is. I don’t even know how to pronounce it as it’s a made-up name. It’s not very interesting, in fact, as there are only 4 references in Pubmed and all to synthetic studies. It’s not interesting enough to be in Pubchem.
What Project Prospect does is to add this information in the paper. Click the link and you get a box like this which tells you what the molecule actually is:

PMR: The irony is that the author knew all this when the paper was submitted but that there is no way of conveying it to the publisher. Publishers have no mechanism for authors to submit semantic info. And apart from these first starts at the RSC none of them have shown the slightest public interest during the last 10 years since e-publications became routine.
A simple analogy. When a food manufacturer gets wheat they throw out all the brown stuff that is good for you are produce white bread. It’s worse for you, the eater, but easier for them to produce. PDF is similar to white bread. Pretty but horrible and bad for your semantics. So Prospect is adding back the goodness that the publishing process takes out.
The problem is therefore that when robots read papers they don’t know the connection tables (e.g. the “SMILES” or “InChI” representation of the molecules above). So the only way to get the structure (in most cases) is to try to interpret the name. “4-iodo-benzoic-acid” is relatively easy to work out; cycloproparadicicol is impossible without a lookup table and there isn’t one. (I expect CAS has the structure but it will cost you 6 USD for each lookup).
If authors added InChIs and SMILES to their papers, much of the problems would be solved. The world would save thousands of person-years work. So why, over 10 years, haven’t we started doing it?
Mainly cock-up – I have only seen 1-2 publishers who have the slightest idea what is going on in Web 2.0 for example. Nature is one. But a small amount of deliberate opposition. I’ll let you see where that idea leads.
Until a brighter day dawns, with semantic papers, we’ll need InChI to get around the appaling lack of products that the current chemical publishers provide.

In One Day I’ll Have Lunch with Egon Willighagen Too… Chemspiderman wrote

1. David Wild Says:
   October 11th, 2007 at 1:41 pm eSo does anyone have any ideas on how we can pursuade ACS to change? I’m not sure the usual forms of protest would work. We can obviously resign our memberships, but that will have no sizeable impact and will just make ACS conference attendance more expensive. We could refuse to publish in ACS journals or to attend ACS conferences but that would also likely have minimal impact (unless we boycotted JCIM en masse) and could hurt our careers. More positively, we could try to raise awareness in the chemistry community of the benefits of open access in our own respective spheres, and encourage chemists to send letters to ACS leadership expressing their concern and desire for open access.

PMR: I am not a US citizen, do not work in US academia and am not a member of ACS so you may ask why I am responding. Partly because of that – I can claim a certain measure of detachment and non-involvement. To reiterate – I have been invited to many ACS meetings, know many of the staff and have been invited to talk to the ACS publishing staff (on technical matters) and at that level the ACS is what you would expect – hardworking staff, large and impersonal bureaucracy, conservative but wishing to be aware of the likely future.
But the last 2-3 years have seen concerns about the integrity of the ACS – integrity of purpose and integrity of practice. I am not taking some the hearsay as fact, but the very existence of these widespread allegations would require a responsible scientific society to be immediately and seriously concerned. The allegations of Paul Thacker ( “This explains a lot”) and ACS insider ( A sad day for ACS) are independent and – if true – very serious.
The ACS is not a national society, it is effectively an international one. In crystallography world governance (and a considerable amount of leadership) is provided by the International Union of Crystallography (IUCr) . Chemistry is much more diffuse and while there is the International Union of Pure and Applied Chemistry (IUPAC) it has much less effective governance it exerts much less effective governance over the world community of chemists. (They have recently done me the honour of electing me as a fellow). However, ultimately, it is the international body to which all national chemical bodies (should) belong and could, I imagine, decide that any member society was behaving inappropriately. For example many young scientists (including some who work with me) would see the ACS national meetings as the appropriate place to announce their work rather than IUPAC.

Being a de facto international society has responsibilities, not least of which is to give leadership within the chemical community and also in the wider world. For example our planet is in danger, and chemistry is a necessary (if not sufficient) discipline in saving it. An international society must give truthful, balanced, verifiable, and independent advice to the world. If there is any hint that it is hiding information, pursuing the interests of a lobby, or failing to meet accepted standards of evidence it is unfit to lead us.
The ACS is unique in its make-up and to understand it I am going to explore 3-4 areas.
(a) Non-profit journal and serial publisher. As Alma Swan has made clear commercial publishers have a responsibility to their shareholders to make as much money as possible, subject only to legality and general human morality (e.g. non-exploitation of humans, even if legal). To do this a commercial publisher may employ a salesforce which is rewarded for its efforts by bonuses. This has been a problem when selling to a library community which has clung onto the old-style notion of a publisher as providing a service to the community for money.
Those days are gone. The problem is that it necessarily rubs off onto the society sector, which see their “rivals” getting richer and skewing the market. So there is a natural tendency to emulate successful practices. However this can immediately start going against the interest of the community (e.g. by creating journals which are unnecessary but which could raise revenue).
There is clearly an element of this in ACS journal publishing. The ACS (rightly) has a distinguished history and has a near-monopoly position in parts of academic chemistry. Promotion can depend on how many JACS papers someone has published. There can be a tendency to exploit this monopoly and I would regard it as unethical (I have no evidence it happens) if a college had to purchase journals from a given society to get certification from that society for their courses.
I do not know whether other societies suffer the same pressures from the pseudo-commercial world – it could be useful to know if it were a general phenomenon. In the current case, however, I would hope that the ACS has an ethics committee to monitor potential abuses in this area.
(b) Chemical Abstracts Service. This is a division of the ACS and that makes it effectively unique among learned societies. CAS is ca. 100 years old and has done a magnificent job of extracting chemical data from the literature. It employs over 1000 staff and I estimate its turnover to be ca 500-1000 million USD/year. This is similar to the GDP of a very small country. Although CAS is a division of the ACS there is a large degree of devolution and it is commonly seen as quasi-independent. I do not believe figures are published but it gives the air of being profitable and has earned a near monopoly position both in academia and chemical industry. In particular CAS is seen by the pharmaceutical industry as being the gold standard for chemical information both in numbers of compounds and quality. Being a monopoly allows CAS to set its own prices and many academic departments find the annual fees extremely difficult to raise. CAS is still a must-have, but it is increasingly not seen as a service to the chemical community but a highly priced commercial product.
There are many smaller colleges who cannot afford CAS products and I would question whether it is in the spirit of a learned society to disadvantage many chemists throughout the world.
In 2004-5, however, CAS felt threatened by the NIH’s Pubchem project (from WP):

Since the inception of National Center for Biotechnology Information‘s open access PubChem chemical compound database initiative, ACS has actively lobbied NCBI and its supervising agencies to stop the database development effort. ACS markets its own subscription- and pay-based Chemical Abstracts Service. In a May 23, 2005, press-release, the ACS stated:

The ACS believes strongly that the Federal Government should not seek to become a taxpayer supported publisher. By collecting, organizing, and disseminating small molecule information whose creation it has not funded and which duplicates CAS services, NIH has started ominously, down the path to unfettered scientific publishing…

PMR: At this stage Pubchem had ca. 11 staff, compared ton the ACS’s 1000+. However this marks the time at which ACS became publicly active in lobbying against Open Data and Open Access. If my memory still works it was slightly earlier that ACS made it clear that it would not support Open Access – it ran a meeting to which I and others were invited and where both sides of the questions were presented. At that stage, however, the OA issue appeared to be the normal conservative position of any large publisher and no different – say – from Wiley or Royal Society of Chemistry. Pubchem changed all that.
The Pubchem argument was very public and could be summarised as: “ACS sees Pubchem as a threat to CAS (not publications); The way to prevent it is to lobby state and central government; to make our arguments more convincing we label NIH as socialist.”
The biologists were incensed, as were several provosts, ARL etc. However the chemical community was completely unaware and uninterested. Probably no more than 5-10 mainstream chemists made a public fuss including Henry Rzepa, Steve Heller and me. We managed to get it highlighted in Nature and several other organs and ultimately won the day (though the ACS deludedly regards themselves as having won).
I will write later about why I think CAS’s days are more limited than they suspect.
I suspect that it was the Pubchem affair that triggered the current ACS management into its current campaign. Once having railed against the NIH and lobbied government, it becomes easier to spend the society’s money on lobbyists, lawyers and the rest.
I do not know the current ACS management but whatever else they seem to have completely lost sight of what a learned society is about. They have spent money on absurd legal cases (suing Google over the word “Scholar”) and wasting money on Dezenhall. Even if these were reasonable things to do (and for a learned society they are not), the management now exudes a mixture of arrogance, loss of reality, and self-centeredness.
None of these should be seen in a learned society. We desperately need an ACS.
I hope to write more on the issue of truth and integrity and will return to what Paul Thacker alleges.