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Re: Question about standardization

From: Bijan Parsia <bparsia@cs.manchester.ac.uk>
Date: Sun, 17 May 2009 21:56:44 +0100
Cc: public-semweb-lifesci@w3.org
Message-Id: <0FC1F925-8620-4D88-83AB-36AC64244B10@cs.manchester.ac.uk>
To: "Michael Hucka" <mhucka@caltech.edu>
On 17 May 2009, at 20:07, Michael Hucka wrote:
> 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.
> * 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.,

That doesn't address development or patent issues, of course. But it's  
a good first step and a good first step toward standardization.

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.

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:

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:

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  

An XG is also a good way to "test out" the process and the group.

Received on Sunday, 17 May 2009 20:57:20 UTC

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