On Feb 19, 2010, at 9:06 AM, Peter Murray-Rust wrote:
> I take a completely different view here. There were several early
> implementations of CML done without my knowledge or the simple courtesy of
> contacting me/Henry. There are programs supplied by commercial companies
> which "save as CML" and the CML is not conformant. One company simply wrapped
> a load of completely random XML in <cml>... </cml> wrappers. Then people try
> to read this and it fails and they blame CML. So right to modify a spec
> without consultation and in any way I believe is harmful.
And your copyright on the CML specification makes no difference here, since
this format was not at all based on the spec.
That's why I conjecture the relevant legal protection here is trademark, not
copyright.
Which has the disadvantage of costing £200 for 10 years (and £100 for each
following 10 years), while copyright is free, but it gives you the control you
want, doesn't it? Is it worth 20 quid per year for you?
(International fees are likely different, but not an order of magnitude
different. Do note that Open Source has a long history of owning and protecting
trademarks - see the Linux trademark for an example.)
> CML was developed specifically for the process of creating a machine-readable
> specification that could enforce validation (as far as I am aware it's the
> only one in chemistry).
NCBI's ASN.1-based structure formats also enforce validation.
Both of them provide only partial validation and not a full validation against
the chemistry model. Quoting from
cdk-1.2.4.1/org/openscience/cdk/io/cml/data/cml25b1.xsd
The references cannot (yet) cannot be schema- or schematron-validated.
since, I assume, it would be hard to say that two atoms are connected by at
most a single bond.
> It's worth thinking about Openness in MDL-molfile has evolved. It certainly
> was not even public let alon Open when it was first deployed (I ran a meeting
> in 1983 where this was a significant issue).
And that was resolved at least 20 years ago, in part I assume because of
historical efforts like SMD to develop an open format which could replace the
MDL formats. Why bring up old issues?
Is not the solution simply rewriting the connection table format definition,
using a copyright statement you and Blue Obelisk agrees with? This seems to be
acceptable for OpenSMILES - why not an OpenCT?
> However as far as I know there are no Open methods for it to evolve. It's
> copyright Symyx (and probably trademarked) and Symyx have the legal right to
> forbid any mofication of the spec. As far as I know neither MDL or Symyx has
> made any offical statement about the public modification of MDL-mol. AFAIK
> they are disinteredly benevolent but it's still their spec, not ours. So I
> regard MDL as de facto openly accessible and implementable but not modifiable.
AFAIK, CML is your spec, not mine. What's your complaint concerning "ours" vs.
"theirs" - that you don't any control over the MDL file format?
At this point so many tools depend on the spec, that if MDL would change the
spec (V3000, for example?) then those tools would BREAK. There is no good
reason for MDL to change thing. They have a very strong interest to keep it
public and compatible, and should not be "disinterested."
Andrew
[email protected]
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