[ome-users] tags from OMERO tracking data

[Jaime Prilusky]

Dear Jason,

Thank you for the useful references an pointers.

Happy Holidays,

Jaim
__
Dr Jaime Prilusky
R&D Bioinformatics and Data Management
Life Sciences Core Facilities
Weizmann Institute of Science
76100 Rehovot - Israel

mail: Jaime.Prilusky at weizmann.ac.il<mailto:Jaime.Prilusky at weizmann.ac.il>
tel:  972-8-934-4959
fax: 972-8-934-6006

On 24 Dec 2016, at 11:09 AM, Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>> wrote:

Hi Jaime-

Not sure if this is helpful, but two examples of OMERO-based resources that are annotating cell images are:

IDR:  http://idr-demo.openmicroscopy.org<http://idr-demo.openmicroscopy.org/>; http://biorxiv.org/content/early/2016/11/24/089359. IDR uses CMPO for cell phenotype annotations: http://www.ebi.ac.uk/cmpo/, but the phenotypes recorded there are more conceptual and might or might not be relevant to what you are looking for.

SSBD: http://ssbd.qbic.riken.jp<http://ssbd.qbic.riken.jp/>; http://bioinformatics.oxfordjournals.org/content/32/22/3471.full; and in particular, https://www.researchgate.net/publication/310753318_Development_of_an_Ontology_for_an_Integrated_Image_Analysis_Platform_to_enable_Global_Sharing_of_Microscopy_Imaging_Data

If you want to be more specific about the terms you are thinking about regarding “tracking data”, maybe that might help shake a few more trees.

Cheers,

Jason



On 19/12/2016 07:44, "ome-users on behalf of Jaime  Prilusky" <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of jaime.prilusky at weizmann.ac.il<mailto:jaime.prilusky at weizmann.ac.il>> wrote:

We are collecting terms for CMEO, the Ontology of CMSO (Cell Migration Standardization Organization , https://cmso.science/), and would appreciate your help by providing the tags collected by your OMERO server for tracking data to be used as example.

We will acknowledge your contribution to the Ontology even when the terms themselves will remain anonymous.

The documentation to extract the list of tags from OMERO is at https://www.openmicroscopy.org/site/support/omero5.2/users/cli/tag.html

Thank you in advance,
Regards,
__
Dr Jaime Prilusky
R&D Bioinformatics and Data Management
Life Sciences Core Facilities
Weizmann Institute of Science
76100 Rehovot - Israel

mail: Jaime.Prilusky at weizmann.ac.il<mailto:Jaime.Prilusky at weizmann.ac.il>
tel:  972-8-934-4959
fax: 972-8-934-6006

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