And other big words I learnt from mathematicians…

The observant amongst you will have realised that the title of my previous post pushing a boat out into the area of semantics and RDF implied there was more to come. Those of you who followed the reaction [comments in original post, 1, 2, 3] will also be aware that there are much smarter and more knowledgeable people out there thinking about these problems. Nonetheless, in the spirit of thinking aloud I want to explore these ideas a little further because they underpin the way I think about the LaBLog and its organization. As with the last post this comes with the health warning that I don’t really know what I’m talking about. Read more »

Posted: April 8th, 2008 under FuGE, data formats, data model, format, indexing, ontologies, semantics, tagging.
Comments: 3

Lots of helpful comments from people on my question about what to use as a good identifier of chemicals? I thought it might be useful to re-phrase what it was that I wanted because I think some of the comments, while important discussion points don’t really impinge directly on my current issue.

I have in mind a special type of page on our LaBLog system that will easily allow the generation of a post that describes a new bottle of material that comes into the lab. From a user perspective you want to enter the minimum amount of necessary information, probably a name, a company, perhaps a lot number and/or catalogue number to enable reordering. From the system perspective you want to try and grab as many different ways of describing the material as possible, including where appropriate SMILES, InChi, CML, or whatever. My question was, how do I provide a simple key that will enable the system to go off and find (if possible) these other identifiers. This isn’t really a database per se but a collection of descriptors on a page (although we would like to pull the data out and into a proper database at a later stage). CAS numbers are great because they are written on most bottles and are a well curated system. However I thought that the only way of converting from CAS to anything else was to go through a CAS service. Therefore I thought PubChem CID’s (or SID’s) might be a good way to do this.

So from my perspective a lot of the technical issues with substances versus chemicals versus structures aren’t so important. All I want is to, on a best efforts basis, pull down as many other descriptors as possible to expose in the post. For some things (e.g. yeast extract) the issues of substances versus compounds (not to mention supplier) get right out of hand (I am slightly bemused that it has a CAS number, and there are multiple SID’s in PubChem). Certainly it ain’t going to have an InChi. But if you try and get nothing it doesn’t really matter. Also we are dealing here with common materials. If as Dan Zaharevitz points out, we were dealing with compounds from synthetic chemists we would get into serious trouble, but in this case I think we could rely on our collaborating chemists to get InChi’s/SMILES/CML correct and use those directly. In the ideal Open Notebook Science world we would simply point to their lab books anyway.

So the fundamental issue for me; is there something written on the bottle of material that we can use as a convenient search key to pull down as many other descriptors as we can?

Now I am with Antony Williams on this, if CAS got its act together and made their numbers an open standard then that would be the best solution. It is curated and all pervasive as an identifier. Both Antony and Rich Apodaca have pointed out that I was wrong to say that CAS numbers aren’t in PubChem (and Rich pointed to two useful posts [1], [2] on how to get into PubChem using CAS numbers). So actually, my problem is probably solved by an application of Rich’s instructions on hacking PubChem (even if it turns out we have to download the entire database). The issue here is whether they will stay there or whether they may in the end get pulled.

I do think that for my purposes that PubChem CID’s and SID’s will do the job in this specific case. However as has been pointed out there are issues with reliability and curation. So I will accept that it is probably too early to start suggesting that suppliers label their bottles with PubChem IDs. This may happen anyway (Aldrich seem to have them in the catalogue at least; haven’t been able to check a bottle yet) in the longer term and I guess we have to wait and see what happens.

Peter Murray-Rust has also updated with a series of posts [1], [2], [3] around the issues of chemical substance identity, CAS, Wikipedia et al. Peter Suber has aggregated many of the related posts together. And Glyn Moody has called us to the barricades.

Posted: March 10th, 2008 under LaBLog, PubChem, indexing.
Comments: 4

We are in the process of rolling out the LaBLog system to the new bioscience laboratory within ISIS at the Rutherford Appleton Laboratory. Because this is a new lab we have a real opportunity to embed the system in the way we run the laboratory and the way we practise our science. One of the things we definitely want to do is to use it to maintain a catalogue of all our stocks of chemicals. This is important to us because we are a user laboratory and expect people to come in on a regular basis to do their experiments. This in turn means we need to keep track of everything they bring in to the lab and any safety implications. Thus we want to use our system to log in every bottle of material that comes into the lab.

Now following on from my post about feeds it is clear that we also want to provide a good range of searchable indexes for people to be able to tell what we are using. So we would ideally want to expose InChi, InChiKey, SMILES, CML perhaps, PubChem Ids etc. These can all be converted one to the other using web services so we don’t need to type all of them in manually. All that is required is a nice logging screen where we can drop in one type of index key, the size of the bottle, supplier, lot numbers, perhaps a link to safety data. The real question is what is the index key that is easiest to input? For those of you in or near a laboratory I suggest an exercise. Go and pick up the nearest bottle of commodity stuff from a commercial supplier (i.e. not oligos or peptides). What is written on it? What is a nice short identifier that can consistently be found on pretty much any bottle of chemicals? For those unlucky people who don’t have a laboratory at their fingertips I have provided a clue below.

The Chemical Abstracts Service number is the one identifier that can reasonably reliably be found on most commercially supplied substances. Yet, as described by Peter Murray-Rust and Antony Williams recently you can’t look these up without paying for them. And indeed by recording them for your own purposes (say in a database of the compounds we have in the laboratory) we may be violating the terms of the license.

So what to do? Well we can adopt another standard or standards. Jean-Claude Bradley argued in a comment on my recent post that InChiKey is the way to go, but for this specific purpose (logging materials in) this may be too much to type in many cases (certainly SMILES, InChi and CML would be). You can’t expect people to draw in the structure each time a compound comes in, particularly if we get into arguments about which precise salt of cAMP we are using today. What is required is a simple, relatively short number. This is what makes the CAS number so appealling; it is short, easily typed in, and printed on most bottles.

So, along with Peter I think the answer is to use PubChem CID numbers. PubChem doesn’t use CAS numbers and CAS actively lobbied the US government to limit the scope of PubChem. PubChem CIDs are relatively short, and there are a range of web services from which other descriptions can be retrieved (see e.g. PubChem Power User Gateway). The only thing that is missing is the addition of CID’s on bottles. If we can get wide enough agreement on this I think the answer is to start writing to the suppliers. It’s not great effort on their part to add CIDs (or if there is something better, some other index) to the bottles I would have thought and it provides a lot of extra value for them. PubChem can provide links through to up to date safety data (without the potential legal issues that maintaining a database of MSDS forms with CAS numbers creates), it provides free access to a supplier index through which customers can find them, and it could also save them a small fortune in CAS license fees.

There is another side to this, which is that if there is a wholesale shift (or even the threat of a shift) away from CAS as the only provider of chemical indexing, then perhaps the ACS will wake up and realise that not only is this protectionism bad for chemistry, but it is bad for their business. The database of CAS numbers has no real value in its own right. It is only useful as a pointer to other information. If the ACS were to make the use and indexing of CAS numbers free then it would be driving traffic to its own value added services. The ACS needs to move into the 21st (or perhaps the 20th) century in terms of both its attitudes and business models. We often criticise the former, but without shifts in the latter there is a real risk of critical damage to an organisation that still has the potential to make a big contribution to the chemical sciences. If the major chemical suppliers were to start printing PubChem CID’s on their bottles it might start to persuade the powers that be within the ACS that things need to change.

So, to finish; do people agree that CID is a good standard index to aggregate around? If so we should start writing to the major chemical manufacturers, perhaps through open letters in the general literature (obviously not JACS), to suggest that they include these on their packaging. I’m up for drafting something if people are prepared to sign up to it.

Posted: March 8th, 2008 under PubChem, indexing.
Comments: 9