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Re: Question about standardization

From: Michael Hucka <mhucka@caltech.edu>
Date: Sun, 17 May 2009 12:07:42 -0700
Message-ID: <18960.24702.86148.123270@frantic.local>
To: Bijan Parsia <bparsia@cs.manchester.ac.uk>
Cc: public-semweb-lifesci@w3.org
Hi Bijan, and others,

The following are some replies to parts of multiple separate
messages, all put here in one place to (hopefully) make
reading easier:

  bparsia> MIchael, there's no question in my mind that
  bparsia> HCLSIG is a perfectly find venue to discuss SBML
  bparsia> and do HCLSIG style things elated to it.

Excellent; good news.

  bparsia> That's distinct from the question whether HCLSIG
  bparsia> can produce a recommendation based on SBML. It
  bparsia> can't without a charter change because it (almost
  bparsia> certainly) can't produce recommendations.

  (and in a separate message:)

  bparsia> If you really want (and need) to produce a
  bparsia> *standard*, that is, a specification of a
  bparsia> language that has the formal endorsement of the
  bparsia> W3C, then HCLSIG is merely a place to start
  bparsia> building consensus for the chartering of such a
  bparsia> group.

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.

  bparsia> [...] if you have interop already and buy-in from
  bparsia> key players, then all that's left is publicity
  bparsia> (or badge collecting). These can be worthwhile,
  bparsia> but they come at considerable cost, not just for
  bparsia> you, but for the W3C.
  bparsia> [...] 
  bparsia> what goals do you have for standardization?  Are
  bparsia> there implementations that don't comply? Are
  bparsia> there vendors who can't sell their SBML tool to
  bparsia> govt agencies due to the procurement requirement
  bparsia> to use "recognized standards" thus they are
  bparsia> forced to use older, inadequate standards? Or is
  bparsia> there a user base that likely *would* use (and
  bparsia> benefit) from it but just need to know they are
  bparsia> working "with a standard"? Or are there patent
  bparsia> implications you are trying to work around?

These are good questions.  I may not have all the right
answers, but here are a few reasons from my own perspective
and experience; other people in the SBML community might
have other (possibly better) reasons that I'm not thinking
of right now.  If it becomes necessary, I can conduct a
survey of the SBML community and collect a more complete
set.

* 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.  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.  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.  My sense is
  that trying to have a neutral standards organization
  (e.g., W3C) do it, would be acceptable to individuals and
  institutions.  In addition, and perhaps even more
  importantly, the W3C has developed agreeable and
  time-tested usage terms, patent policies, etc.  If we
  tried to develop our own, we might never be able to reach
  agreement among all the institutions where contributors
  were employed at one time or another.  In summary, it
  seems to me that moving SBML to the W3C would neutralize
  questions of "ownership", and allow SBML to leverage
  various procedural and legal structures that the W3C has
  developed.

* 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.  A colleague said to me the
  following recently:

    "I keep hearing and reading comments that there is no
    standard and (more recently) that SBML and [X]/[Y]
    are equivalent and none dominant (my own opinion is that
    SBML is used a lot more than [X] and in turn even
    more than [Y])."

  (I haven't asked the colleague if I can share that quote,
  so I must keep their identity confidential, but please
  rest assured it is a reputable and prominent person in
  this field.  My colleague also named specific efforts,
  but I edited the above to use [X] and [Y] because I feel
  great hesitation in disclosing the specific projects
  mentioned -- I'm not looking for a confrontation here.)
  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.
  
* 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.

* 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.

I hope these give some reasons for being interested in
pursuing this in the W3C.  

(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.

Thanks again,
MH

Footnotes
---------
[1] http://sbml.org/Events/Workshops/The_7th_SBML_Forum_Meeting
Received on Sunday, 17 May 2009 19:08:23 GMT

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