I worked for a publicly funded body. Whilst there I designed and developed a number of epidemiological surveillance applications.

I have left the organisation but since then I have noticed that some of my ex-coworkers have started to publish papers based on the data collected by the systems that I designed without crediting myself in the publication (in at least two cases directly referring to my system in the paper).

Since the publications wouldn't be possible without the systems I developed would I have any remit to ask for credit and/or authorship? How is this viewed any different from a co-worker using someone's lab results without credit for their own publication?

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    Sorry if I sound mean here. Were you the only person who designed and developed the system? To the best of your knowledge, has the system been modified since you left? If yes, to what extent? I am playing devil here in case they refute your claim for the credit.
    – Nobody
    Jan 14 '14 at 13:11
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    Technically they are not publishing papers about the systems, but about the data collected by the systems. Potentially, since these systems are in Github, anyone could use them, get some data and publish the results. I doubt whether the real contribution is the software or the data but in principle they are two different things to be published separately. E.g. people developing a DB system may publish some papers about the DB system, while people using the DB system will probably just mention they use it (in case it is relevant, and often it isn't).
    – Trylks
    Jan 14 '14 at 13:45
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    Just add a positive spin, why not just write this up and publish it? Then you can send the reference back to the coworker and hint that from this point and on, they are welcome to cite this method paper when mentioning the system. Jan 14 '14 at 14:41
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    Have you tried talking with the authors about it? It is difficult to say whether or not you have contributed significantly enough to the particular work in those papers to have earned coauthorship ... but it sounds to me like you have ... that it's not just off-the-shelf software you developed. I know that if I were using such software developed by a colleague for a paper, I would talk with them and give them the opportunity to help out with the paper and solidify a coauthorship. At the very least, even minor contributions to dedicated software would earn an Acknowledgement in my book.
    – badroit
    Jan 14 '14 at 18:10
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    I can say that it's common for the people working at an organization in the technical fields to not get credit for their contributions. I'm not sure if this exactly applies, but often such staff is looked at as essentially a technical support or IT worker, even if the programming and methodology is original. If in fact your system is novel or original, then there is nothing excluding you from writing your own research paper and submitting it for publication. BTW - I'm assuming that the researchers published in peer reviewed academic journals and not white papers?
    – Twitch
    Jan 15 '14 at 8:27

As per the comments on your question, I think this is really context specific and the role of an author can vary quite subtly from area to area. I'll try give a general answer to the general question first, and then look at the specfics of your case afterwards.

How to handle not being credited for research software development in papers?

The first question is whether or not you should be credited for the software you developed in the paper. The answer is predicated on what precisely the contribution of the paper is and what the contribution of the software is.

If, for example, (part of) the core contribution of the paper is describing optimisations and techniques that you invented and applied in the software, then I think it is more than fair that you should be credited as a co-author.

If, for example, the core contribution relates to a methodology for doing X where your software was specifically designed for that methodology, then you should probably be credited as a co-author or, at the very least, mentioned in the acknowledgements.

If the core contribution of the paper is not directly related to the software itself but the software is used to some ends, then you should probably not be credited on the paper (otherwise Linus Torvalds would have millions of publications). But if the software system was described in another paper and played a significant/specialised role in the current paper, you could expect a citation.

Since the publications wouldn't be possible without the systems I developed would I have any remit to ask for credit and/or authorship?

I think your reasoning is a little flawed here. Making a research paper possible does not entitle you to co-authorship (as a simple counter-example, if paper A builds upon the results of paper B such that paper A would not be possible without paper B, the authors of paper B should not expect co-authorship on paper A). Providing part of the core contribution of the paper—the reason why it was accepted in the first place—entitles you to co-authorship.

I noticed something crucial in your comments that you didn't clarify in your question:

"Since xxxx our system has collated data on x cases and found that.."

The authors should absolutely not be claiming credit for a system they did not design or build. This is clearly wrong. (And it also indirectly suggests that part of the contribution is indeed the system and the authors are trying to claim credit for it.)

Since you know the authors, you should talk with them, show them the relevant quotes in the papers and tell them that you are not happy with them claiming the system as their own. Tell them that if they wish to continue claiming the system in future then you should be a co-author on the paper.

If you wish to escalate, you can contact the editor(s) of the journal(s) involved and tell them your story. The editor(s) might agree to let you publish a letter referring to the specific paper and outlining your case. This should be considered the "nuclear" option.

EDIT: Not in answer to the question, but this quote in the transcript of Hamming's address "You and Your Research" (well worth a read for anyone in research) reminded me of this question:

I also did a second thing. When I loaned what little programming power we had to help in the early days of computing, I said, "We are not getting the recognition for our programmers that they deserve. When you publish a paper you will thank that programmer or you aren't getting any more help from me. That programmer is going to be thanked by name; she's worked hard." I waited a couple of years. I then went through a year of BSTJ articles and counted what fraction thanked some programmer. I took it into the boss and said, "That's the central role computing is playing in Bell Labs; if the BSTJ is important, that's how important computing is." He had to give in.

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    Nice answer :) As for the systems in question they are a mix of software and databases - the databases were generated from a mix of legacy data that was in flat files (it had to be validated, parsed and linked to other data before being imported for further processing). I would probably estimated that around 50% of the data on the legacy system was generated by myself the rest being entered by external stakeholders from around the country (before being processed and linked to other data in the system). I'll have to recheck the papers for how the authors have referred to the system(s).
    – Pasted
    Jan 17 '14 at 10:16
  • @Pasted : from what you're describing, I'm not sure if you should be recognized for your work with the data, the software or both ... either way, it's important to distinguish between that indirect contribution vs. a direct contribution to the paper. You can have an indirect contribution without even agreeing with the work; if you were a co-author, you'd be effectively signing off on all of the work done.
    – Joe
    Jan 17 '14 at 13:51
  • @Joe : From what i gather from at least one of the papers, which analyses the data in the system, the paper itself wouldn't be possible without the system. It's not as if the data is available anywhere else or that the processing of the data is trivial. I would think that a lab assistant who say sequenced a series of genomes, the sequence data from which was then used in a paper, should be recognised in the authorship. I feel that my work on the system and integrated data should be treated in the same way.
    – Pasted
    Jan 17 '14 at 14:31
  • @Pasted, I think the key point is really whether or not they are taking credit for your work, by claiming that the system is theirs or that they collected and curated the database, etc. Otherwise I'm afraid it will come down to your opinion vs. theirs and you won't have much to gain from that.
    – badroit
    Jan 17 '14 at 19:27

The style guidelines used for citations in the paper usually include guidelines for the citation of software. In most cases, the question is not so much who was responsible for writing the software as how can other researchers acquire the software (theoretically to reproduce the results). As others have mentioned, though, if they are discussing algorithms that you introduced into the software as if they were their own work, there may be a significant problem.

Finally, there is the question of the conditions (contractual and otherwise) under which the software was developed and whether that software is somehow unique, or just automates tasks that are otherwise tedious. The vast majority of the software I have written belongs to the people that paid for it to be written and the majority of the credit I have received has been in my salary and my resume, and the occasional thank you from a co-worker that wasn't followed up with a "...now can you change this?".

  • Ah yes the "thanks but could you move this image 1 pixel to the right"! I do agree with some of your points however I would say that often in a research environment the people who write and maintain the software / databases used by others in the group are themselves looking to work towards a research career (and often have equivalent qualifications). Software development in these organisations (at least in the UK) doesn't pay a fraction of the renumeration available in the private sector and often access to the software after you leave is restricted (due to Patient Identifiable Information).
    – Pasted
    Jan 17 '14 at 10:07
  • +1 for the useful link ... but I think you're being naïve in thinking that the salary means the software doesn't need to be credited; if the software is recognized as a vital component to research, it's easier to justify continued funding for it ... and thus you continue to get paid. (just like recognizing someone's contributions to science as a whole helps them get funding later via grants, etc.)
    – Joe
    Jan 17 '14 at 13:55

It's probably too late to deal with this after the fact, but much of the discussions that have occurred over the last few years regarding proper scholarly credit for data also apply to software. In 2012, I presented a poster at the American Astronomical Society on Recommendations for Data & Software Citation in Solar Physics that is broadly applicable to any research data or software.

The one tricky part is that many journals will consider something simply posted on a website is often considered grey literature rather than 'Published'. For this reason, it's useful to get a DOI assigned to it, as you effectively make the citation look like any other cited work. If you're not attached to an institution that can mint DOIs, a possible work-around would be to post something to FigShare and they'll assign one.

  • Thanks for the link to the poster looks useful. I'll have to read up on the DOI part.
    – Pasted
    Jan 17 '14 at 10:10
  • Just to update the DOI reply with some developments with Guthub biostars.org/p/100669
    – Pasted
    May 15 '14 at 9:31
  • @Pasted : um ... that links to something talking about bulk discounts for accounts ... you probably want to refer people to : guides.github.com/activities/citable-code
    – Joe
    May 15 '14 at 18:26
  • Ah yup sorry the biostars forum post included links to the citable code URL (or at least it did last time I checked :P)
    – Pasted
    May 16 '14 at 13:55

The key here is that it is a publicly funded effort. Any intellectual property belongs to the public. Just as if you developed that system for a corporation let say at work. The product is owned by the company. They paid you to develop it.

In your example you do not own the system it was developed with public dollars. Even if you were volunteering the works you created belong to the organization.

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    Ownership of the system isn't really the issue - it is authors of papers either describing the system or using the outputs from the system and not crediting the actual system developers. However just to take your point to it's logical conclusion - if public ownership meant that anyone in a publicly funded effort, say the Human Genome Project could not be attributed credit then I doubt that such projects would ever be undertaken. For most people in research, citations in papers are as important as renumeration.
    – Pasted
    Jan 22 '14 at 12:33

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