[ome-users] [General Contact] Possible to have own schema besides ome one?

Curtis Rueden ctrueden at wisc.edu
Thu Dec 17 18:09:27 GMT 2009 

Hi Steffen,

first, thanks for your fast replies. What do you mean with "I have CCed the
> OME users list"?
>

There is an OME mailing list for asking questions such as yours:
   http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/

Asking on the list is better for two reasons: 1) there are many developers
on the list with various expertise, who can more effectively answer your
questions; and 2) other users with the same question later can locate the
answer in the archives instead of needing to ask again.

Looks like you are using the forums too, which is fine. But it is best to
use either the mailing list, forums or both, rather than emailing developers
directly.

 > Presumably, you do not actually want to mix and match two different OME
> > schema versions (or if so, why?), but rather want to use your own custom
> > schema along with OME.
>
> Yes, of course I dont want to mix two schema versions. It was just an
> example.
>
> Do you have any xml file that is using structered annotations? Just to have
> an example. As I understand it, it is just possible to add the annotations
> at certain places within the document, as described at
> http://trac.openmicroscopy.org.uk/omero/wiki/StructuredAnnotations.


Sorry, the StructuredAnnotations element is still fairly new, so I do not
have any examples handy. Andrew might, but he is away until Monday.

So if we want to have an additional laser type, say DPSS, it is not possible
> to add it with structered annotations. We would have to wait until it is
> implemented in OME. Is that right or is there any possibility?
>

One thing you could do is set the Laser type to "Other," and create
StructuredAnnotations that reference the Laser ID in question and indicate a
string value of your choice. Ideally, though, you would request DPSS to be
added to the schema proper, and it would be included in the next version.

-Curtis

On Wed, Dec 16, 2009 at 1:21 PM, Steffen Illig <Steffen.Illig at gmx.net>wrote:

> Hey Curtis,
>
> first, thanks for your fast replies. What do you mean with "I have CCed the
> OME users list"?
>
> > Presumably, you do not actually want to mix and match two different OME
> > schema versions (or if so, why?), but rather want to use your own custom
> > schema along with OME.
>
> Yes, of course I dont want to mix two schema versions. It was just an
> example.
>
> Do you have any xml file that is using structered annotations? Just to have
> an example. As I understand it, it is just possible to add the annotations
> at certain places within the document, as described at
> http://trac.openmicroscopy.org.uk/omero/wiki/StructuredAnnotations. So if
> we want to have an additional laser type, say DPSS, it is not possible to
> add it with structered annotations. We would have to wait until it is
> implemented in OME. Is that right or is there any possibility?
>
> -Steffen
>
>
> -------- Original-Nachricht --------
> > Datum: Tue, 15 Dec 2009 14:49:47 -0600
> > Von: Curtis Rueden <ctrueden at wisc.edu>
> > An: Steffen Illig <Steffen.Illig at gmx.net>
> > CC: OME-users mailing list <ome-users at lists.openmicroscopy.org.uk>
> > Betreff: Re: [General Contact] Possible to have own schema besides ome
> one?
>
> > Hi Steffen,
> >
> > I have CCed the OME users list, since your question is relevant to
> others.
> >
> > what I described in my post (below) is not working. Let me give you an
> > > example, probably you will find my mistake.
> > >
> > > In the ome schema of 2009 (see
> > > http://www.openmicroscopy.org/Schemas/OME/2009-09) you will find a tag
> > > called "MiddleName" in "Experimenter", which is not there in the schema
> > of
> > > 2008.
> > >
> > > If you say
> > >
> > > <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09"
> > >  xmlns:ome2009="http://www.openmicroscopy.org/Schemas/OME/2009-09"
> ....>
> > > ...
> > > <Experimenter ID="Experimenter:sillig">
> > >    <FirstName>Stefan</FirstName>
> > >    <ome2009:MiddleName>Bernhard</ome2009:MiddleName>
> > >    <LastName>Schnell</LastName>
> > >    <Email>xyz at mpimf.de</Email>
> > >    <Institution>MaxPlanckInstituteMF</Institution>
> > >    <GroupRef ID="Group:Lightmicroscopy1"/>
> > > </Experimenter>
> > > ...
> > > it will not be validated.
> > >
> >
> > In this case, I believe the problem is that the ome2009:MiddleName
> element
> > needs to appear beneath an ome2009:Experimenter element (not an
> > Experimenter
> > from the 2008-09 schema).
> >
> > Presumably, you do not actually want to mix and match two different OME
> > schema versions (or if so, why?), but rather want to use your own custom
> > schema along with OME. Take a look at how we mix and match between
> > ome.xsd,
> > SA.xsd and others—e.g.:
> > http://www.openmicroscopy.org/Schemas/SA/2009-09/SA.xsd
> >
> > Specifically, we import the base ome.xsd schema first:
> > <xsd:import namespace="http://www.openmicroscopy.org/Schemas/OME/2009-09
> "
> > schemaLocation="
> http://www.openmicroscopy.org/Schemas/OME/2009-09/ome.xsd"/>
> >
> > If you use a similar procedure in your custom schema, you can create
> > elements that can legally appear beneath an <OME>, <Image> or other
> > element
> > from the ome.xsd schema.
> >
> > HTH,
> > Curtis
> >
> > On Tue, Dec 15, 2009 at 12:49 PM, Steffen Illig
> > <Steffen.Illig at gmx.net>wrote:
> >
> > > Hi Curtis,
> > >
> > > what I described in my post (below) is not working. Let me give you an
> > > example, probably you will find my mistake.
> > >
> > > In the ome schema of 2009 (see
> > > http://www.openmicroscopy.org/Schemas/OME/2009-09) you will find a tag
> > > called "MiddleName" in "Experimenter", which is not there in the schema
> > of
> > > 2008.
> > >
> > > If you say
> > >
> > > <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09"
> > >  xmlns:ome2009="http://www.openmicroscopy.org/Schemas/OME/2009-09"
> ....>
> > > ...
> > > <Experimenter ID="Experimenter:sillig">
> > >    <FirstName>Stefan</FirstName>
> > >    <ome2009:MiddleName>Bernhard</ome2009:MiddleName>
> > >    <LastName>Schnell</LastName>
> > >    <Email>xyz at mpimf.de</Email>
> > >    <Institution>MaxPlanckInstituteMF</Institution>
> > >    <GroupRef ID="Group:Lightmicroscopy1"/>
> > > </Experimenter>
> > > ...
> > > it will not be validated.
> > >
> > > Regards Steffen
> > >
> > >
> > > -------- Original-Nachricht --------
> > > > Datum: Mon, 14 Dec 2009 01:22:53 -0600
> > > > Von: Curtis Rueden <ctrueden at wisc.edu>
> > > > An: steffen.illig at gmx.net
> > > > CC: Kevin Eliceiri <eliceiri at wisc.edu>, Andrew Patterson <
> > > ajpatterson at lifesci.dundee.ac.uk>
> > > > Betreff: Re: [General Contact] Possible to have own schema besides
> ome
> > > one?
> > >
> > > > Hi Steffan,
> > > >
> > > > just a short question: Is it possible to embed another schema next to
> > the
> > > > > ome.xsd one to refer our needs?
> > > > > e.g: <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09
> "
> > > > > xmlns:OUR_LAB="http://xyz" ...>
> > > > > How do I do this?
> > > > >
> > > >
> > > > Absolutely, you have the right idea. If you have created your own
> > schema,
> > > > and are hosting it on your web server, you can indeed reference it in
> > > that
> > > > fashion. Then you just use the "OUR_LAB" namespace with elements from
> > > your
> > > > schema.
> > > >
> > > > Of course, anything in your XML blocks not from the OME schema will
> > > likely
> > > > be ignored by Bio-Formats and other OME-compatible software.
> > > >
> > > > Let us know on the OME users mailing list (
> > > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/) if
> you
> > > > have
> > > > any problems with it.
> > > >
> > > > -Curtis
> > > >
> > > > On Mon, Dec 07, 2009 at 6:36 PM, <steffen.illig at gmx.net> wrote:
> > > > >
> > > > > Hi,
> > > > > just a short question: Is it possible to embed another schema next
> > to
> > > > the
> > > > > ome.xsd one to refer our needs?
> > > > > e.g: <OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2008-09
> "
> > > > > xmlns:OUR_LAB="http://xyz" ...>
> > > > > How do I do this?
> > > > > Regards, Steffen
> > > > >
> > >
> > > --
> > > GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
> > > Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
> > >
>
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