Tagging Images

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Tagging Images

Robb, Sofia

Hello All,

 

Just looking for your thoughts on a new project.

 

I am currently tagging images with terms. Primarily they are anatomy terms and experimental conditions. Those I have covered.

 

I would also like to tag the images with their state or status. This is for a browser for searching images for discovery. Some of the images may be presentation/publication quality while the majority of the images are not publication quality but still informative. I would like to have users label them as such. I found the IDQA ontology. This has a class “Data Image Life-Cycle” with two sub classes that seem like they might fit this purpose: Acquisition and Presentation. There are no definitions, but I think these could work. Any thoughts?

 

I would also like to tag some images as Favorite or Featured or something of the like so that those can appear first, or only those can be selected to be viewed. I cannot find any terms like these. This is something I could just design in house to use. Is anyone using terms like this?

 

Thanks,

Sofia

 

 

 

 

— 

Sofia M.C. Robb, Ph.D

Genomic Scientist

Stowers Institute for Medical Research

 


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Re: Tagging Images

Chris Mungall


On 26 Apr 2017, at 9:45, Robb, Sofia wrote:

> Hello All,
>
> Just looking for your thoughts on a new project.
>
> I am currently tagging images with terms. Primarily they are anatomy
> terms and experimental conditions. Those I have covered.
>
> I would also like to tag the images with their state or status. This
> is for a browser for searching images for discovery. Some of the
> images may be presentation/publication quality while the majority of
> the images are not publication quality but still informative. I would
> like to have users label them as such. I found the
> IDQA<https://bioportal.bioontology.org/ontologies/IDQA> ontology. This
> has a class “Data Image Life-Cycle” with two sub classes that seem
> like they might fit this purpose: Acquisition and Presentation. There
> are no definitions, but I think these could work. Any thoughts?

Unfortunately it looks like this ontology was made with an unconfigured
oboedit (all IDs are of the form ID:nnnnn). Lack of defs also a problem.

Maybe check out:

http://obofoundry.org/ontology/iao.html

http://obofoundry.org/ontology/fbbi.html

http://schema.org/ImageObject

> I would also like to tag some images as Favorite or Featured or
> something of the like so that those can appear first, or only those
> can be selected to be viewed. I cannot find any terms like these. This
> is something I could just design in house to use. Is anyone using
> terms like this?

I think for these kinds of social things, where the social aspect is not
really the subject of study, it's fine just to use some random semweb
vocabulary. Opinions may vary here, but I'd just go with something like:

http://lov.okfn.org/dataset/lov/terms?q=favourite
http://schema.org/LikeAction

There can be subtle issues with bringing RDF ontology properties into an
OWL ontology (they are uncommitted w.r.t. whether they are Object, Data
or Annotation properties). It seems there should be a standard approach
here but I'm not aware of one, maybe this is something we in OBO can
take on.

Now if your interested in doing an analysis of how users interact with
and like images or you want to do reasoning over these properties there
is a good argument for putting into a robust OWL ontology such as one of
the OBO Library ones.

> Thanks,
> Sofia
>
>
>
>
> —
> Sofia M.C. Robb, Ph.D
> Genomic Scientist
> Stowers Institute for Medical Research
> [hidden email]


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> engaging tech sites, Slashdot.org!
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Re: Tagging Images

Marijane White
Re: the issues using an RDF vocabulary with OWL ontologies, I just want to note that TopBraid hosts an OWL implementation of schema.org that uses object and datatype properties.
http://topbraid.org/schema/


-marijane


On 2017/04/26, 12:12 PM, "Chris Mungall" <[hidden email]> wrote:

   
   
    On 26 Apr 2017, at 9:45, Robb, Sofia wrote:
   
    > I would also like to tag some images as Favorite or Featured or
    > something of the like so that those can appear first, or only those
    > can be selected to be viewed. I cannot find any terms like these. This
    > is something I could just design in house to use. Is anyone using
    > terms like this?
   
    I think for these kinds of social things, where the social aspect is not
    really the subject of study, it's fine just to use some random semweb
    vocabulary. Opinions may vary here, but I'd just go with something like:
   
    http://lov.okfn.org/dataset/lov/terms?q=favourite
    http://schema.org/LikeAction
   
    There can be subtle issues with bringing RDF ontology properties into an
    OWL ontology (they are uncommitted w.r.t. whether they are Object, Data
    or Annotation properties). It seems there should be a standard approach
    here but I'm not aware of one, maybe this is something we in OBO can
    take on.
   
    Now if your interested in doing an analysis of how users interact with
    and like images or you want to do reasoning over these properties there
    is a good argument for putting into a robust OWL ontology such as one of
    the OBO Library ones.
   
    > Thanks,
    > Sofia
    >
    >
    >
    >
    > —
    > Sofia M.C. Robb, Ph.D
    > Genomic Scientist
    > Stowers Institute for Medical Research
    > [hidden email]
   
   
    > ------------------------------------------------------------------------------
    > Check out the vibrant tech community on one of the world's most
    > engaging tech sites, Slashdot.org!
    > http://sdm.link/slashdot_______________________________________________
    > Obo-discuss mailing list
    > [hidden email]
    > https://lists.sourceforge.net/lists/listinfo/obo-discuss
   
    ------------------------------------------------------------------------------
    Check out the vibrant tech community on one of the world's most
    engaging tech sites, Slashdot.org! http://sdm.link/slashdot
    _______________________________________________
    Obo-discuss mailing list
    [hidden email]
    https://lists.sourceforge.net/lists/listinfo/obo-discuss
   

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Re: Tagging Images

Sofia Robb
In reply to this post by Robb, Sofia
Hi,

Thank you for your comments about tagging images. These are helpful. Sorry about not responding sooner. My messages were being bounced. I wondered why the list was so quiet these past few days :)




I am leaning towards having a very small ontology that I use in house only. I am thinking of simplifying my system, the user will upload many images and tag all the images with genes, tissues, phenotypes, etc, and tag one/some images as "representative".  My little ontology has only this one term as of now.

But I will definitely go through all the ontologies that you two sent to see if I can find a better solution. 

The way I am thinking of it, is that typically terms are used to qualify final versions of images. Here we are trying to store not just the best (but they need to be fairly good, just not publication quality) so that the researchers can go over a few images to make sure signal/phenotype is consistent. this could help in defining downstream experiments. This is especially important when a graduate student or a post doc leaves a lab, with their data left behind. Some of this could be very informative for others in the lab if it was appropriately labeled with genes, phenotypes, anatomy of expression, etc and searchable. 


Thanks,
Sofia



Re: the issues using an RDF vocabulary with OWL ontologies, I just want to note that TopBraid hosts an OWL implementation of schema.org that uses object and datatype properties.

http://topbraid.org/schema/



-marijane



On 2017/04/26, 12:12 PM, "Chris Mungall" <cjmungall@...> wrote:


    

    

    On 26 Apr 2017, at 9:45, Robb, Sofia wrote:

    

    > I would also like to tag some images as Favorite or Featured or 

    > something of the like so that those can appear first, or only those 

    > can be selected to be viewed. I cannot find any terms like these. This 

    > is something I could just design in house to use. Is anyone using 

    > terms like this?

    

    I think for these kinds of social things, where the social aspect is not 

    really the subject of study, it's fine just to use some random semweb 

    vocabulary. Opinions may vary here, but I'd just go with something like:

    

    http://lov.okfn.org/dataset/lov/terms?q=favourite

    http://schema.org/LikeAction

    

    There can be subtle issues with bringing RDF ontology properties into an 

    OWL ontology (they are uncommitted w.r.t. whether they are Object, Data 

    or Annotation properties). It seems there should be a standard approach 

    here but I'm not aware of one, maybe this is something we in OBO can 

    take on.

    

    Now if your interested in doing an analysis of how users interact with 

    and like images or you want to do reasoning over these properties there 

    is a good argument for putting into a robust OWL ontology such as one of 

    the OBO Library ones.

    

    > Thanks,

    > Sofia

    >

    >

    >

    >

    > —

    > Sofia M.C. Robb, Ph.D

    > Genomic Scientist

    > Stowers Institute for Medical Research

    > smr@...

    

    

    > ------------------------------------------------------------------------------

    > Check out the vibrant tech community on one of the world's most

    > engaging tech sites, Slashdot.org! 

    > http://sdm.link/slashdot_______________________________________________

    > Obo-discuss mailing list

    > Obo-discuss@...

    > https://lists.sourceforge.net/lists/listinfo/obo-discuss

    

    ------------------------------------------------------------------------------

    Check out the vibrant tech community on one of the world's most

    engaging tech sites, Slashdot.org! http://sdm.link/slashdot

    _______________________________________________

    Obo-discuss mailing list

    Obo-discuss@...

    https://lists.sourceforge.net/lists/listinfo/obo-discuss

    


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