MIAPA ontology

[Hilmar Lapp]

Hi all,

At the Phylotastic II hackathon [1] that just concluded in Tucson, AZ, a group of people set out to annotating published trees [2], with the goal to allow users to query a tree store for trees that do or do not match certain criteria [3]. Since much of such criteria is, as one might expect, also part of the attributes in the draft MIAPA checklist, we tied these annotations to MIAPA. As a result, we created the first MIAPA ontology as one of the major outcomes of our group.

The ontology is here: https://github.com/miapa/miapa/blob/master/ontology/miapa.owl

I hope to have it soon registered and available through the OBO library URI as well.

The repository also holds annotation files for 10 source trees as proof-of-concepts and examples for applying the ontology. For one of these, the following graphic shows the annotation graph, primarily here the computational provenance (see [4] for the corresponding OWL file):

http://www.evoio.org/wg/evoio/images/7/7a/PetersGraphic.pdf

We will be using the repository's issue tracker for submitting and tracking change requests (in fact, it's already in use, as you can see), so if you find problems please submit them there. The ontology is really in a draft stage - it is very much usable as the annotation files show, but it also hasn't undergone much external vetting yet. I've already started some of this for the provenance part at the IAO list [5], and over the next days I'll be initiating other queries at the SWO and CDAO lists.

-hilmar

[1] http://www.evoio.org/wiki/Phylotastic

[2] http://www.evoio.org/wiki/Tree_Annotation

[3] http://www.evoio.org/wiki/Advancing_MIAPA#Factors_shaping_our_conception_of_source-tree_annotations

[4] OWL file for this is here: https://github.com/miapa/miapa/blob/master/ontology/peters_miapa-annotation.owl

[5] https://groups.google.com/forum/?fromgroups=#!topic/information-ontology/fKU0QE6lAu8

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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :

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[Hilmar Lapp]

There hasn't been yet. I am going to have to keep effort on this on lower heat for a few weeks, and there are a number of issues with the ontology (the MIAPA one I constructed) that need documenting and sorting out.

That said, I'll be attending the I Annotate workshop in SF in April, and intend to be in a position to make major progress on the below and other MIAPA ontology issues/targets (including, actually, mapping to the Open Annotation ontology vocabulary) on the hackday that's part of that event.

(cc'ing the MIAPA list so that group is in the loop)

-hilmar

On Feb 19, 2013, at 4:07 PM, Philippe wrote:

> Hi Hilmar Alan,
>
> Was there a follow-up on this and resolution? If yes can you update us?
>
> Best
>
> Philippe
>
> On 04/02/2013 15:54, Hilmar Lapp wrote:
>>
>> On Feb 4, 2013, at 8:38 AM, Alan Ruttenberg wrote:
>>
>>> The first thing that comes to my attention are the relations, e.g.
>>> wasInfluencedBy, used, is_annotation_of, etc, which could be replaced
>>> by better defined relations used in IAO/OBI.
>>
>> wasInfluencedBy and used are from PROV. is_annotation_of I'll have to
>> check - I wouldn't have expected this to be needed.
>>
>>> There's also some distraction by use of both the PROV ontology and
>>> IAO, where I expect IAO/OBI terms could be used in most cases. I would
>>> recommend first using OBI/IAO and after than is done and clear
>>> consider a mapping to PROV.
>>
>> That sounds fine - I just do think that in the end we do want a mapping
>> to PROV.
>>
>>> For example what is an instance of 'Phylogenetic tree construction
>>> (method centric)'?
>>
>> Good question. I wanted to ask that the SWO folks. Who, incidentally,
>> include IAO terms, such as IAO:software.
>>
>>> I have a pretty packed day today, but if you are interested we could
>>> schedule a call to do a walk through either late in the week or next
>>> week.
>>
>> That sounds great, let's plan for that.
>>
>> -hilmar
>> --

>> ===========================================================
>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org

>> <http://informatics.nescent.org> :
>> ===========================================================
>>
>>
>>
>

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