ontology-metadata.owl
Chris Mungall
> * IAO_0000117 definition editor
> Name of editor entering the definition
Why the name of the editor rather than the editor? The convention in
obo format ontologies has always been to provide a unique identifier
(usually initials) for either a curator or a collection of individuals
at a content meeting.
Also, IAO doesn't stick to it's own guidelines. The values of this
field are of the form "Person:Alan Ruttenberg". This is a curious name
for a person. I normally call Alan "Alan", not "Person:Alan".
What are the conventions for when a definition is edited multiple
times? Is this for the text definition or the equivalentclass axiom?
>
> * IAO_0000119 definition source
> formal citation, e.g. identifier in external database to indicate /
> attribute source(s) for the definition. Free text indicate /
> attribute source(s) for the definition. EXAMPLE: Author Name, URI,
> MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Definition provenance is extremely important, I think it is a mistake
to allow this to be free text. In obo format the definition source is
an identifier (which can be annotated with descriptive free text),
which can also be a URI.
You may as well just stash the two properties above into rdfs:comment,
the metadata would be just as computable.
> * IAO_0000111 preferred term
> The concise, meaningful, and human-friendly name for a class or
> property preferred by the ontology developers. (US-English)
What is the relationship to rdfs:label, both axiomatically and in
terms of usage conventions? Looking at IAO itself it seems the
practice is to redundantly state the rdfs:label
What is the cardinality?
> * IAO_0000115 definition
> The official OBI definition, explaining the meaning of a class or
> property. Shall be Aristotelian, formalized and normalized. Can be
> augmented with colloquial definitions.
Presumably the 'OBI' should be removed. Whilst I agree that
definitions should in general be aristotelian, I think it makes sense
to separate the practice from the description. Note that it is the
definition field I am quoting above, and it is not itself aristotelian.
Undocumented properties:
* has obsolescence reason
* in branch
(is this OBI specific?)
Alan Ruttenberg
>
>
>> * IAO_0000117 definition editor
>> Name of editor entering the definition
>
> Why the name of the editor rather than the editor? The convention in
> obo format ontologies has always been to provide a unique identifier
> (usually initials) for either a curator or a collection of individuals
> at a content meeting.
>
> Also, IAO doesn't stick to it's own guidelines. The values of this
> field are of the form "Person:Alan Ruttenberg". This is a curious name
> for a person. I normally call Alan "Alan", not "Person:Alan".
See: https://wiki.cbil.upenn.edu/obiwiki/index.php/Definition_source
The current syntax is so it is easy to enter. The longer term plan is
to script these into URIs.
> What are the conventions for when a definition is edited multiple
> times? Is this for the text definition or the equivalentclass axiom?
We've been adding definition editors as we go on, occasionally
removing old ones if no longer appropriate. We haven't been doing
editorship at the axiom level, but could in the future. Ongoing notes
are in the editor notes field.
>
>>
>> * IAO_0000119 definition source
>> formal citation, e.g. identifier in external database to indicate /
>> attribute source(s) for the definition. Free text indicate /
>> attribute source(s) for the definition. EXAMPLE: Author Name, URI,
>> MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
>
> Definition provenance is extremely important, I think it is a mistake
> to allow this to be free text. In obo format the definition source is
> an identifier (which can be annotated with descriptive free text),
> which can also be a URI.
See the spec I pointed to.
>
> You may as well just stash the two properties above into rdfs:comment,
> the metadata would be just as computable.
>
>> * IAO_0000111 preferred term
>> The concise, meaningful, and human-friendly name for a class or
>> property preferred by the ontology developers. (US-English)
>
> What is the relationship to rdfs:label, both axiomatically and in
> terms of usage conventions? Looking at IAO itself it seems the
> practice is to redundantly state the rdfs:label
yes. We also decided to change the name from preferred term to "editor
preferred term".
> What is the cardinality?
1. I understand that there is a desire to make editor preferred term
globally unique across foundry ontologies. We haven't implemented
that. Feel encouraged to update the documentation.
>
>> * IAO_0000115 definition
>> The official OBI definition, explaining the meaning of a class or
>> property. Shall be Aristotelian, formalized and normalized. Can be
>> augmented with colloquial definitions.
>
> Presumably the 'OBI' should be removed.
Yes.
> Whilst I agree that
> definitions should in general be aristotelian, I think it makes sense
> to separate the practice from the description.
Agreed.
> Note that it is the definition field I am quoting above, and it is not itself aristotelian.
:)
> Undocumented properties:
>
> * has obsolescence reason
This is relatively new, but we want to grow it out and be adopted more
widely. We need to sync with Werner's reasons.
> * in branch
> (is this OBI specific?)
So far. A hook for modularization. It isn't used by script yet. The
plan was to use such annotations so that we could script cleanup
moving terms from one "branch" to another as needed as the editing
tools don't support us well on this.
Thanks for the review. Would much appreciate if you added appropriate
notes and made fixes directly to the files.
-Alan