Re: [cml/ccml-discuss] Identifiers in CML

[Peter Murray-R. <pm...@ca...>]

Wonderful.

Egon wants to hand on the baton of CML so I'll put you in touch with others
quite shortly. I'd say do whatever seems reasonable and not too complex...


Happy to see extensions in principle - suggest what you want to do...

On Mon, Nov 17, 2014 at 3:12 PM, Oliver Stueker <
rev...@us...> wrote:

> Thanks Peter,
>
> My goal is to add SMILES and InChI identifiers to the molecule elements in
> CML/CompChem documents.
> The CompChem convention states that <molecule> elements should conform to
> the molecular convention.
> In the  Molecular convention there is a list of allowed child elements, of
> which <property>, <label> and a bit far-fetched <name> come the closest to
> describe an identifier.
>
> I can easily just invent something but I prefer to follow an already
> defined standard or involve with defining and accepted standard.
>
> In the cmllite-validator-code repo I found this CML/CompChem file [1]
> which defines:
>
> <cml>
>
>   <module role="joblist">    <identifier convention="chemid:EmpiricalFormula" value="CCl2O2"/>    <identifier convention="chemid:InChI" value="InChI=1/CCl2O2/c2-1(4)5-3"/>    <identifier convention="chemid:CanonicalSmiles" value="ClOC(=O)Cl"/>    <identifier convention="chemid:IsomericSmiles" value="C(=O)(Cl)OCl"/>    <module role="job" title="job1">
>
>       <!-- ... -->
>
>     </module>
>
>   </module>
>
> </cml>
>
>
> However on http://www.xml-cml.org/convention/ there is no chemid
> convention nor an <identifier> element in any convention.
>
> What do you think of adding <identifier> to the allowed elements of
> <molecule> in the molecular convention and starting a chemid dictionary?
>
>
> In fact I'm currently also working on expanding the CompChem dictionary.
> I've (privately) forked the repo on bitbucket.org/cml/dictionary-compchem
> and will propose a pull request at a suitable time.
> I could do the same for the molecular convention.
>
> Best,
>  Oliver
>
> [1]
> https://bitbucket.org/cml/cmllite-validator-code/src/2eaa18f959bb0324268bf75be8a904d4c9e07944/src/test/resources/org/xmlcml/www/convention/cmlcomp/valid/two-jobs.cml?at=default
>
> On Mon, Nov 17, 2014 at 3:32 PM, Peter Murray-Rust <pm...@ca...>
> wrote:
>
>> Copying Egon,
>>
>> We did have an <identifier> label which allowed this, but you can also
>> use <label> and add a "class" attribute.
>>
>> The key approach of CML now is that communities should create conventions
>> that work for them. As these become established then conventions can become
>> normalised. trying to constrains too rigidly requires a lot of software are
>> consistent discipline.
>>
>> If different communities end up with slightly different approaches it's
>> not normally hard to convert or merge.
>>
>> P.
>>
>>
>> On Mon, Nov 17, 2014 at 8:43 AM, Oliver Stueker <
>> rev...@us...> wrote:
>>
>>> Dear CML Community,
>>>
>>>
>>> ​is there an (official) standard or best practice on how to include one
>>> or more identifiers (SMILES, InChI, etc.) in a CML document following the
>>> molecular convention?
>>>
>>> Maybe as <label> or <property> children of the <molecule> ?
>>>
>>>
>>> I couldn't find anything in the convention or the cml dictionaries.
>>>
>>>
>>> Best,
>>> Oliver ​
>>>
>>>
>>> ​​
>>> ​
>>> --
>>> Oliver Stueker, Dr. rer. nat.
>>> Postdoctoral Fellow, Poirier Lab
>>> Department of Chemistry, Memorial University
>>> Room C3052  -  phone: +1 (709) 864-8752
>>>
>>>
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>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>
>


-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069