- From: Susie Stephens <susie.stephens@gmail.com>
- Date: Sun, 17 May 2009 20:45:08 -0400
- To: Michael Hucka <mhucka@caltech.edu>
- Cc: public-semweb-lifesci@w3.org, Bijan Parsia <bparsia@cs.manchester.ac.uk>
- Message-ID: <fcc499200905171745i25bcf140j5e4a528dd02a365a@mail.gmail.com>
Hi Mike, It's good to hear from you. Would you be interested in having a call to discuss the various options? Cheers, Susie On Sun, May 17, 2009 at 4:56 PM, Bijan Parsia <bparsia@cs.manchester.ac.uk>wrote: > On 17 May 2009, at 20:07, Michael Hucka wrote: > [snip] > >> OK, I understand now. I'm happy to start here, then. >> >> mhucka> Indeed. Standardization of SBML has been discussed >> mhucka> over many years in the SBML community, >> bparsia> >> bparsia> Pointers? >> >> Probably the earliest mention with a record online is a >> presentation I did in at an SBML workshop in 2003, titled >> "Organizing the SBML Standardization Process" [1]. After >> that, it was generally discussed verbally at subsequent >> workshops. I can't immediately find a specific presentation >> about it after the one in 2003. Around 2005 +/- a year, it >> was decided (again during verbal discussions at an SBML >> Forum meeting) that it wasn't a pressing issue and that >> resources were better put to other things, so the matter was >> put on the back burner. >> > > So there's a change now? Seems so from what you write below. > [snip] > >> * I was recently contacted by a software group at a large >> international company, asking about licensing terms for >> using SBML. Currently, there are no explicit terms; SBML >> is open, and the SBML editors and contributors always >> considered no one to be the owner of SBML. This turned >> out to be problematic for the company: no terms of use, no >> copyright, no patent terms, etc., meant they didn't know >> what was permitted and what wasn't, and they pointed out >> that if no one owns SBML, then no one can grant rights to >> using SBML either. >> > > This is a standard and excellent reason to go the standardization route at > an organization (like the W3C or, I believe, OASIS or OMG) that has an IP > policy. > > Although in the end the company's >> lawyers went ahead and green-lighted the project, it >> brought to light the weakness of SBML's current scheme >> (and it made me wonder how many other commercial >> developers might have turned away without asking). Now, >> an obvious approach would be to add copyrights and license >> terms ourselves to the current specifications. >> > > You should do that anyway (and need to in order to proceed with e.g., a > member submission), but patent concerns are hard to handle without an org > like the W3C. > > The SBML >> Editors actually started trying to do that a couple of >> weeks ago, and we quickly ran into the question of who >> would hold the rights. SBML has involved many people over >> the years; attempting to establish copyrights among >> ourselves seems to lead to either every institution having >> to be listed, or someone taking it alone. The former >> seems impossible; the latter seems unfair. >> > > You need to clear copyright on the text. A reasonable story is that only > the people who contributed physical text are copyright owners (you can > liberalize that a little). The key is to get all of them to ceded copyright > to *someone*. > > My sense is >> that trying to have a neutral standards organization >> (e.g., W3C) do it, would be acceptable to individuals and >> institutions. >> > > A good way to do this, short term, is via a member submission which > requires a license to the W3C, e.g., > http://www.w3.org/Submission/2008/04/ > > That doesn't address development or patent issues, of course. But it's a > good first step and a good first step toward standardization. > [snip] > > This is an excellent reason, in my book. > > * SBML has so far been endorsed by a very large user base, >> in terms of actual, functioning software that uses SBML, >> and published models expressed in SBML, and people who >> recognize and use SBML in their work. Nevertheless, >> several other languages have been proposed over the years, >> and new ones continue to appear. To people working in >> this field, I think there is no question of what is the >> closest to being a "standard". However, to people who are >> coming at it from the outside (for example, trying to >> figure out what they should use in their own modeling, or >> what to implement in their software, or what to encourage >> in journal publication guidelines), there is apparently >> not the same level of clarity. >> > [snip] > > Competing, near-equivalent proposals muddying the waters...another > excellent reason. > > However, recognize that people who have been developing these other > proposals have an interest in either *their* language being standardized, > or, at least, some say at the table. This means a "lightweight" > standardization process is less likely. This is a reason to do it at > someplace like the W3C, but it might be a good idea to start thinking less > about standardizing SBML per se and more about standardizing a "Biological > Modeling Language" to which SBML is one (but a major! input). > > Of course, if all the rivals are fine with it, then no problem :) > > I believe this confusion is increasingly hurting the >> biological modeling field -- it doesn't help >> interoperability and it doesn't help commercial developers >> sell products, which are two important things that we need >> in order for the field to grow and mature. For the past >> several years, I personally didn't worry much about >> getting standards-body approval because I thought if we >> pressed ahead with SBML and made it work for as many >> people as we could, eventually the rest would sort itself >> out. I now think this was naive, and that SBML needs more >> than that. Getting the imprimatur of a well-respected >> body such as the W3C would settle the issue, and let >> competition move on to new topics, further helping the >> field to mature and move forward. Otherwise, I think >> we'll continue to be in this situation where everyone >> claims theirs is a standard. >> > > Pitch a wide tent, if you can. If you can unify proposals *before* > standardization, do so. The more buy in from the more disparate parties, the > better. > > One way to do this other than HCLS (at the W3C) is to start an Incubator > Group: > http://www.w3.org/2005/Incubator/ > > An XG is like a very lightweight WG which, again, cannot produce > recommendations, but it can produce a report that sometimes is fast tracked > toward standardization. The clearest example of this is the POWDER wg which > came out of the Web Content Label XG: > http://www.w3.org/2007/02/powder_charter > > I would *personally* say that an XG is a better idea than trying for a task > force within HCLS. In some sense, it's all W3C so who cares. But an XG is > focused and is in a better position to pull in people who really only care > about working on the biological modeling language and might feel overwhelmed > by everything that HCLS is doing. (That's not to say that HCLS wouldn't have > a role.) > > XGs are pretty easy to get going. You just need 3 w3c members to request to > start one. > > * There are indeed varying degrees of conformance among the >> software packages currently supporting SBML. Developing a >> "stronger", more precise technical specification would, I >> think, help improve that. Hopefully, having a "true" >> standard to work towards would also serve as an incentive >> for commercial efforts to produce fully conformant >> implementations. Again, this would help interoperability >> and the field in general. >> > > So, it sounds like to me that there are technical issues as well as the > afore mentioned social/political issues. This really suggests to me an XG. > > * The SBML process is home-grown and still relatively >> informal. It has served well enough so far, for mostly >> academic open-source developers and researchers, and a few >> commercial closed-source developers. But it only works as >> long as there are not too many people involved, and the >> people play nicely. The latter hasn't always happened, >> but we've been lucky so far in that the most disruptive >> people have tended either to lose interest or leave. >> Looking ahead a few years, when (hopefully) SBML will >> involve a lot more people, I'm concerned that this process >> will not be sufficient. I don't feel we are capable by >> ourselves of developing a process that's sufficient to the >> task, and besides, it doesn't seem to make sense to try, >> when other groups have already gone through the pain and >> achieved hard-won, working solutions. The W3C's process >> appears stronger and better suited to larger undertakings >> by parties that may have a lot of different agendas. This >> seems better, for the sake of SBML in the future. (The >> process is also a lot heavier, as you pointed out. This >> is an important consideration. The pros and cons still >> need to be debated.) In summary, I think it would benefit >> the SBML community to partner with HCLSIG/W3C to work >> toward a more scalable process. >> > > Sounds reasonable. > > (In another message:) >> >> bparsia> HCLSIG cannot, itself, standardize SBML under the >> bparsia> current charter. HCLSIG can, of course, do a lot >> bparsia> of things that make standardization of SBML more >> bparsia> likely. One thing it to publicize it, evangelize >> bparsia> it, and gather evidence of consensus behind >> bparsia> it. Not only can it do these things for various >> bparsia> technologies, it's arguably part of its purpose. >> >> Yes, it seems to me HCLSIG is a good starting point for this >> effort. At the very least, it should help clarify what will >> be needed in the long run, and whether it's worth it. >> > > > Yeah, but I'd also consider an XG if you're serious about moving forward. > > An XG is also a good way to "test out" the process and the group. > > Cheers, > Bijan. > >
Received on Monday, 18 May 2009 00:45:49 UTC