[ome-users] Ontologies and Omero

[Eleanor Williams]

Forwarding a email thread of ideas for the use of ontologies in OMERO,
and what is already being done in the Image Data Resource, to the
mailing list for further discussion.  Anyone else have suggestions of
how they would like ontology integration with OMERO?


-------- Forwarded Message --------

Hi Peter

Thank you very much for your detailed description of how you envisage
ontologies could be used in Omero.

We are starting to use ontologies in the Image Data Resource [1], which
is built using Omero, to normalize the phenotypes observed in different
studies (e.g. [2]) and map sample attributes such as cell lines.  But of
course would like to increase the use of ontologies for image tagging
and searches across data.

For describing imaging experiments there are several ontologies that
touch on aspects of imaging such as the OBI and Fbbi ontologies ([3] and
[4].  I have been using Fbbi for describing imaging methods. It does
include some terms about sample preparation but maybe doesn't cover
everything you might want.

I'll let you know of progress we make on the use of ontologies in Omero
over the next months.

Best regards

Eleanor

[1] http://idr.openmicroscopy.org/about/

[2] http://idr.openmicroscopy.org/mapr/phenotype/?value=CMPO_0000077

[3] http://www.ebi.ac.uk/ols/ontologies/obi

[4] http://www.ebi.ac.uk/ols/ontologies/fbbi


On 02/06/2017 10:40, Peter Zentis wrote:
> Hi Eleanor, hi Steffi,
> to be honest I do not yet have any exact idea about the ontology implementation. I guess, I was hoping you just mention the topic and someone would come up with an existing implementation of something which could also be useful for us:)
> In the first place I would imagine a link between Omero and an ontology or ontology-system, which would offer the Omero-User to tag her images with tags (and or key-value pairs) derived from the components in the ontology. It then either should not be possible to create custom tags in an ontology-linked Omero-project or it should be transparent to the user if a tag comes from the ontology or is a custom internally generated tag. (I could also imagine an ontology editor in Omero, which would users allow to interact with the external ontology to e.g. suggest alternative labels or add new objects, but I suppose normal users would rarely need this). This synchronisation of tags with ontology could immediately increase the consistency of tags and save people who already work with existing ontologies some effort.
> In a second step I hope it is somehow possible to make Omero aware of the ontology itself. If the relations in the ontology would be available in Omero, so that also the tags would be related this would enable smart suggestions during tagging. E.g. someone would like to tag an image with the label glomerulus from his connected nephrology-ontology, related tags like Bowman's capsule, renal corpuscle, nephron and so on would automatically be added or somehow suggested to the user. Or if a more general ontology is connected if someone wants to tag something as a glomerolus the person would first have to decide which glomerulus exactly (Glomerulus (kidney), Glomerulus (olfaction), Glomerulus (cerebellum) as distinguished in the ontology) is meant and after selection would be offered according suggestions for further tags. After annotating naturally one would like to perform semantic searches on the data...
> So one question would be this on how to connect an ontology to Omero. Another question would be if there are ontologies (ontology systems?) suitable for biological microscopy i.e. reflecting the different aspects of the biology of the specimen, the experimental procedures to obtain/prepare, imaging parameters, analysis parameters and results... I think in medicine for radiology or so there exist (commercial?) solutions which contain such general ontologies I hope someone has developed something similar for the biological context?!
> Cheers,
> Peter

--
Eleanor Williams PhD

Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK


The University of Dundee is a registered Scottish Charity, No: SC015096