[ome-users] What did OME ever do for us?

[Graham Klyne]

Ilya,

thanks for your various pointers and comments...


At 10:19 18/07/05 -0400, Ilya Goldberg wrote:
>>So to my specific questions:
>>
>>1. How are custom annotations intended to be used?
>
>There are two types of ad-hoq annotations available in the release.
>One is called simply annotation, which allows you to add a text field (or 
>other type of semantically-typed data) to an image.  The other is 
>classification.  They differ in that a classification allows you to sort 
>an image into one or more groups of mutually exclusive categories.  The 
>weakness here is that the web user-interface is completely general, so its 
>not targeted at what you're trying to do specifically.
>We are currently developing an HTML templates framework which will allow 
>users to use different templates to annotate/search/view their 
>data.  Currently, all of the web-ui display is also done with templates, 
>but they are global and "fixed" (though still easily edited).#

Aha!  (I'm not sure I really want to go here, but can you point me to the 
editable templates?)

I think I'm getting the idea of categories and groups and annotations.  As 
I mentioned in my response to Jason, I see the requirement for categories 
within a group to be mutually exclusive might be onerous.

>We are also involved in an in-situ hybridization project, and are 
>addressing these issues by eating our own dog food (as it were).
>We decided to use the ad-hoq classification mechanism to assign semantic 
>tags to images at the time of acquisition.  The categorization mechanism 
>consists of CategoryGroups and Categories, both of which are global 
>structures.  An image is assigned to one or more categories using a 
>Classification mapping.  In our current ad-hoq annotation efforts, we have 
>CategoryGroups defined as Gene Name, Probe, Probe Type, and Embryo Stage 
>(with the obvious categories defined within them).

Ah, OK.  That sounds not-too-dissimilar to the groups I am contemplating.

>   We are in the process of making these more formal by declaring some of 
> these structures as semantic types.  Also, we are developing the 
> customized aanotation/disaply mechanism using this as one of the 
> use-cases.  The result is a customized template that presents a large 
> thumbnail, and a set of drop-downs and other targeted form controls to 
> let the user quickly annotate a newly acquired image using selected fields.

That sounds very much like what we would like to do.  Are your templates 
available in CVS for experimentation?


>>2. How to create new annotation metadata structures?
>
>Metadata structures are called Semantic Types.  These are basically 
>collections of primitives (text, integer, etc) and references.  The 
>structure itself has a name and so do all of its fields.  These are 
>defined using XML (see examples in src/xml/OME).  The XML files can be 
>imported at run-time using the normal file import mechanism without 
>rebuilding or restarting the database.  The database is extended with new 
>tables/columns to accommodate the new definitions.

That sounds quite easy.  I guess that once a new table/column is added, 
it's there for life?  (Or:  we should figure out what it is we want, test 
it, then rebuild the database from scratch before applying the required 
extensions for real use?)

When you say "normal file import mechanism", is this done using the "ome 
import" command?

[...]

>>2. How to create new annotation metadata structures?  A simpler question 
>>with, I suspect, a more complex answer, but hopefully one that can be 
>>addressed by a pointer to relevant documentation.
>>
>>We aim to capture data in a semi-structured form that can be exported to 
>>a semantic web database for further cross-referencing with other 
>>information sources.  The built-in custom annotations seem to support the 
>>right kind of general structures for this purpose.  Are the form displays 
>>linked directly to the XML metadata schema, or is there an additional 
>>presentation-description component?  How do I go about adding additional 
>>metadata to OME?  Can the metadata format be dynamically updated, or does 
>>this require a re-build of the database?
>
>The web-ui mechanism you're using is completely general, so it works 
>directly off of the Semantic Type definitions in the DB (which were 
>declared originally in XML and imported into OME in the last phase of 
>installation).  A mechanism allowing more targeted 
>definition/search/display of these things is forthcoming.  This will 
>obviously add a separate display component on top of the definition of the 
>data model.  The majority of the custom-display mechanism (HTML templates) 
>is already in the release (/OME/html/Templates), but it can only be 
>customized per-site (i.e. you can change the image display for your entire 
>site, but not for a specific user or group).

I think site-wide customizations would be fine for our current goals.

>The best way to figure out how to add additional metadata to OME is to use 
>the examples of how the core semantic model for OME is declared.
>We don't have a tutorial how to do this (a contributed tutorial would be 
>most welcome!).  You've played with the image 
>experiment/experiment/experimenter STs.  You can find their declarations here:
>Image.ome (contains ImageExperiment among others)
>Experiment.ome
>Experimenter.ome (contains Experimenters and Groups)
>
>The Semantic Type Definition (STD) Schema is documented here:
>http://www.openmicroscopy.org/XMLschemas/STD/latest/STD_xsd/index.html

OK, I'll try and follow one of those examples, and see how it works out.

#g


---
Graham Klyne
Image Bioinformatics Research Group (http://www.bioimage.org/)
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447