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

[Nicolas Le n. <le...@eb...>]

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.

-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/