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

[Oliver S. <rev...@us...>]

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
>