More thoughts on Microsoft funding

Bill Hooker has expanded his views on funding from Microsoft and I’ll also comment on Peter Sefton’s comment…

Peters Murray-Rust and Sefton on “science and selfishness”

Peter Murray-Rust (welcome back to blogging!) has replied to Glyn Moody’s post about semantic plugins being developed by Science Commons in collaboration with the Evil Empire, which I discussed in my last post. Peter MR takes the view, with which I concur, that it’s more important to get scientists using semantic markup than to take an ideological stand against Microsoft
[PMR …]
Another, to my mind even more important, point was raised by Peter Sefton in a comment on Peter MR’s entry:

I will have to talk about this at greater length but I think the issue is not working with Microsoft it’s working in an interoperable way. The plugins coming out of MS Research now might be made by well meaning people but unless they encode their results in something that can interop with other word processors (the main one is OOo Writer) then the effect is to prolong the monopoly. There is a not so subtle trick going on here – MS are opening up the word processing format with one hand while building addons like the Ontology stuff and the NLM work which depend on Word 2007 to work with the other hand. I have raised this with Jim Downing and I hope you can get a real interop on Chem4Word.

(Peter S, btw, blogs here and works on a little thing called The Integrated Content Enviroment (ICE), which looks to me like a good candidate for an ideal Electronic Lab Notebook…)
There’s a difference between the plugins being Open Source and the plugins being useful to the F/OSS community. If collaborators hold Microsoft to real interoperability, the “Evil Empire” concerns largely go away, because the project can simply fork to support any applications other than Word.

Thanks Bill and Peter. To amplify some of the points.

  • Our Addins are Open Source. We spent a great deal of time in negotiating the contract to make sure that all parties agreed. The Addins can be used without Word2007 (though some of the functionality such as “Open in Word” may then be no-ops.)  In principle anyone with a .NET environment can use and modify the Addin.
  • We are working hard to make sure they are interoperable (that’s why we are working with Peter Sefton.)  Complete interoperabilityis  probably impossible at present but we have achieved a lot. Joe Townsend in SPECTRa-T has shown that it is possible to extract large amounts of semantic information from chemistry *.doc without requiring the functionality of Word. (A major problem is the binary legacy application files that chemists use – and this is where the real rough edges come).
  • We are striving to make the add-in and the files it creates useful to the F/OSS community. The problem there is not Microsoft but the antiquated views of the chemical community. This is epitomized in the phrase “our software doesn’t read/write CML because no customers have asked for it”. We expect the reaction of many to be “Oh, it only reads and writes CML so it’s no use. When you add SDFiles and SMILES  [PMR: well-known legacy destroyers of semantics and creators of ambiguity and corruption] then we might take a look at it.” But I am religious on that. If the community wants to go 10 years backwards I am not going to help them. If they really want it we have written all the converters and yes, they are Open Source. In this battle Microsoft is an ally.
  • I used the phrase “rough edges” in referring to using Open Office – I was writing in the context of creating documents with embedded semantic chemistry.
  • Are we helping to cement MS’s monopoly? Possibly, possibly not. We are arguing and creating semantic operability. Our XML can be used by ICE and other Open systems. It will be harder to create a DOCX/CML file from a third-party system that can be read by Word. I believe it’s possible but hairy. My belief is that by promoting tha value of interoperable semantics then monopolies will start to disappear…

… just as Open Access will destroy the publishing monopolies.

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