Some (probably not original) thoughts about originality

A number of things have prompted me to be thinking about what makes a piece of writing “original” in a web based world where we might draft things in the open, get informal public peer review, where un-refereed conference posters can be published online, and pre-print servers of submitted versions of papers are increasingly widely used. I’m in the process of correcting an invited paper that derives mostly from a set of blog posts and had to revise another piece because it was too much like a blog post but what got me thinking most was a discussion on the PLoS ONE Academic Editors forum about the originality requirements for PLoS ONE.

In particular the question arose of papers that have been previously peer reviewed and published, but in journals that are not indexed or that very few people have access to. Many of us have one or two papers in journals that are essentially inaccessible, local society journals or just journals that were never online, and never widely enough distributed for anyone to find. I have a paper in Complex Systems (volume 17, issue 4 since you ask) that is not indexed in Pubmed, only available in a preprint archive and has effectively no citations. Probably because it isn’t in an index and no-one has ever found it.  But it describes a nice piece of work that we went through hell to publish because we hoped someone might find it useful.

Now everyone agreed, and this is what the PLoS ONE submission policy says quite clearly, that such a paper cannot be submitted for publication. This is essentially a restatement of the Ingelfinger Rule. But being the contrary person I am I started wondering why. For a commercial publisher with a subscripton business model it is clear that you don’t want to take on content that you can’t exert a copyright over, but for a non-profit with a mission to bring science to wider audience does this really make sense? If the science is currently unaccessible and is of appropriate quality for a given journal and the authors are willing to pay the costs to bring it to a wider public, why is this not allowed?

The reason usually given is that if something is “already published” then we don’t need another version. But if something is effectively inaccessible is that not true. Are preprints, conference proceedings, even privately circulated copies, not “already published”. There is also still a strong sense that there needs to be a “version of record”, that there is a potential for confusion with different versions. There is a need for better practice in the citation of different versions of work but this is a problem we already have. Again a version in an obscure place is unlikely to cause confusion. Another reason is that refereeing is a scarce resource that needs to be protected. This points to our failure to publish and re-use referee’s reports within the current system, to actually realise the value that we (claim to) ascribe to them. But again, if the author is willing to pay for this, why should they not be allowed to?

However, in my view, at the core to the rejection of “republication” is an objection to the idea that people might manage to get double credit for a single publication. In a world where the numbers matter people do game the system to maximise the number of papers they have. Credit where credit’s due is a good principle and people feel, rightly, uneasy with people getting more credit for the same work published in the same form. I think there are three answers to this, one social, one technical, and one…well lets just call it heretical.

Firstly placing two versions of a manuscript on the same CV is simply bad practice. Physicists don’t list both the ArXiv and journal versions of papers on their publication lists. In most disciplines, where conference papers are not peer reviewed, they are listed separate to formally published peer reviewed papers in CVs. We have strong social norms around “double counting”. These differ from discipline to discipline as to whether work presented at conferences can be published as a journal paper, whether pre-prints are widely accepted, and how control needs to be exerted over media releases but while there may be differences over what constitutes “the same paper” there are storng social norms that you only publish the same thing once.  These social norms are at the root of the objection to re-publication.

Secondly the technical identification of duplicate available versions, either deliberately by the authors to avoid potential confusion, or in an investigative roleto identify potential misconduct, is now trivial. A quick search can rapidly identify duplicate versions of papers. I note paranthetically that it would be even easier with a fully open access corpus but where there is either misconduct, or the potential for confusion, tools like Turnitin and Google will sort it out for you pretty quickly.

Finally though, for me the strongest answer to the concern over “double credit” is that this is a deep indication we have the whole issue backwards. Are we really more concerned about someone having an extra paper on their CV than we are about getting the science into the hands of as many people as possible? This seems to me a strong indication that we value the role of the paper as a virtual notch on the bedpost over its role in communicating results. We should never forget that STM publishing is a multibillion dollar industry supported primarily through public subsidy. There are cheaper ways to provide people with CV points if that is all we care about.

This is a place where the author (or funder) pays model really comes it in its own. If an author feels strongly enough that a paper will get to a wider audience in a new journal, if they feel strongly enough that it will benefit from that journal’s peer review process, and they are prepared to pay a fee for that publication, why should they be prevented from doing so? If that publication does bring that science to a wider audience, is not a public service publisher discharging their mission through that publication?

Now I’m not going to recommend this as a change in policy to PLoS. It’s far too radical and would probably raise more problems in terms of public relations than it would solve in terms of science communication. But I do want to question the motivations that lie at the bottom of this traditional prohibition. As I have said before and will probably say over and over (and over) again. We are spending public money here. We need to be clear about what it is we are buying, whether it is primarily for career measurement or communication, and whether we are getting the best possible value for money. If we don’t ask the question, then in my view we don’t deserve the funding.

Who’s got the bottle?

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.

What to use as a the primary key for chemicals?

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.

D2O bottle label