Re: [Obo-anatomy] FMA3

[mejino@u.washington.edu <mejino@u.washington.edu>]

Hi Chris,

My comments in-line.


On Thu, 18 Jun 2009, Chris Mungall wrote:

> FMA3 is out, but the version of fma_lite is still at v2.
>
> I got the owlfull from the FMA site. However, we need both the full and a 
> seperate dl file to do the complete conversion. I believe it was Natasha that 
> made this available previously?

Todd Detwiler used Natasha's code to create the FMA 3.0 owlfull release version. Todd, correct me if I got this wrong.

>
> Also I notice that the term 'Motor neuron' is missing from fma3.0.owlfull. You 
> can still find it in the FMA explorer, although it's not linked to anything. It 
> appears this was obsoleted. Any reason?

One of the authors previously re-assigned 'Motor neuron' under 'General anatomical term' where ambiguous and homonymous terms are assigned. However it has been reinstated and is now a subtype of 'Neuron' in the taxonomy in the current copy. However this is not reflected in the release 3.0 version.

  It means that terms such as 'Axon of 
> motor neuron' are now missing parthood information. I haven't checked how much 
> that is present in FMA2 is missing in FMA3. To adhere to obo principles we need 
> to retain a record of the ID plus some metadata that says "this ID has been 
> obsoleted" (preferably with additional metadata stating explanation etc)

This is now being implemented as per OBO guidelines.


With regards to URI's we prefer and encourage using the FMA namespace. Jim and Todd my have other or additional comments on this.

Onard


>