Re: [sbml-annot] SBML Level 3 Annotation package proposal

[Nick J. <ju...@eb...>]

should we set up a doodle poll for this? or will someone keep track?

Nicolas Le nove`re wrote:
> On 17/01/11 18:27, Neil Swainston wrote:
> 
>> You'll note that Nick Juty's suggestions for new predicates has been
>> added as a table towards the end of the document. Where there are
>> multiple candidates, I've highlighted my personal preference in bold,
>> but obviously this is all open for discussion. Please let me know your
>> preference (if you have one).
> 
> Since the discussion is not in the spec anymore, let's move it here plus 
> biomodels-net-discuss.
> 
> The "accepted" ones
> ===================
> bqmodel:is
> bqmodel:identity
> 
> bqmodel:isDescribedBy
> bqmodel:description
> 
> bqbiol:hasPart
> bqbiol:part
> 
> bqbiol:hasProperty
> bqbiol:property
> 
> bqbiol:hasVersion
> bqbiol:version
> 
> bqbiol:is
> bqbiol:identity
> 
> bqbiol:isDescribedBy
> bqbiol:description
> 
> bqbiol:isHomologTo
> bqbiol:homolog
> 
> bqbiol:isEncodedBy
> bqbiol:encoder
> 
> bqbiol:encodes
> bqbiol:encodement
> 
> The discussions
> ===============
> 
> 1) bqmodel:isDerivedFrom
> 
> bqmodel:progenitor, bqmodel:antecedent, bqmodel:ancestor, bqmodel:basis, 
> bqmodel:base, bqmodel:foundation, bqmodel:origin
> 
> Neil favours "antecedent". I favour "origin".
> 
> 2) bqbiol:isPartOf
> bqbiol:encompassment, bqbiol:assembly, bqbiol:partship, bqbiol:parthood, 
> bqbiol:whole, bqbiol:meronym
> 
> Neil favours "parthood". I favour "whole".
> 
> 3) bqbiol:isPropertyOf
> 
> bqbiol:bearer, bqbiol:carrier
> 
> Neil favours "bearer". I concur
> 
> 4) bqbiol:isVersionOf
> 
> bqbiol:consociate, bqbiol:cohort, bqbiol:superclass, bqbiol:hyponym
> 
> Neil favours superclass. I concur
> 
> 5) bqbiol:occursIn
> 
> This is tricky because we want to split it. At the moment it is used to 
> indicate containment, including "this model of human glycolysis is 
> contained in homo sapiens". This is stretching the containment.
> 
> Physical containment:
> bqbiol:encompassment, bqbiol:containment
> 
> Neil favours containment. I am not too happy with that. "container" would 
> be better, no?
> 
> Taxonomic instantiation:
> bqbiol:instantiation
> 
> I think this is not explicit enough. BTW, we do not want to limit the value 
> to a taxonomic unit. It could be a cell line or something similar.
>