We're Hiring!

"Attributes" of image data in OMERO

General user discussion about using the OMERO platform to its fullest. Please ask new questions at https://forum.image.sc/tags/omero
Please note:
Historical discussions about OMERO. Please look for and ask new questions at https://forum.image.sc/tags/omero

There are workflow guides for various OMERO functions on our help site - http://help.openmicroscopy.org

You should find answers to any basic questions about using the clients there.

"Attributes" of image data in OMERO

Postby Kouichi_C_Nakamura » Wed Jun 13, 2018 5:01 pm

In this example in IDR,

https://idr.openmicroscopy.org/webclien ... ge-1920105

the image has Attributes that hold information about Gene and Organism etc. I'd like to use this feature myself in our server as well, but could not find information. Is it related to OMERO.mapr?

How can I add Attributes to an image?
Last edited by Kouichi_C_Nakamura on Thu Jun 14, 2018 8:41 am, edited 1 time in total.
Kouichi_C_Nakamura
 
Posts: 165
Joined: Thu Oct 19, 2017 1:35 pm

Re: "Attributes" of image data in OMERO

Postby jmoore » Wed Jun 13, 2018 6:47 pm

Hi Kouichi,

These Attributes are just MapAnnotations. First, we added configuration to change the standard "Key-Value Pairs" section to "Attributes":

Code: Select all
/opt/omero/web/OMERO.web/bin/omero config get | grep Attr
omero.web.ui.metadata_panes=[{"index": 0, "name": "map", "label": "Attributes"}, {"index": 1, "name": "table", "label": "Tables"}, {"index": 2, "name": "file", "label": "Attachments"}, {"index": 3, "name": "comment", "label": "Comments"}, {"index": 4, "name": "tag", "label": "Tags"}, {"index": 5, "name": "rating", "label": "Ratings"}, {"index": 6, "name": "other", "label": "Others"}]


Then, the specific information on Genes & Organisms does indeed come from OMERO.mapr:

Code: Select all
$ /opt/omero/web/OMERO.web/bin/omero config get | grep mapr
omero.web.apps=["django_prometheus", "omero_mapr"]
omero.web.mapr.config=[{"menu": "gene", "config": {"default": ["Gene Symbol"], "case_sensitive": true, "all": ["Gene Symbol", "Gene Identifier"], "ns": ["openmicroscopy.org/mapr/gene"], "label": "Gene"}}, {"menu": "genesupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/gene/supplementary"], "label": "Gene supplementary"}}, {"menu": "sirna", "config": {"default": ["siRNA Identifier"], "all": ["siRNA Identifier", "siRNA Pool Identifier"], "ns": ["openmicroscopy.org/mapr/sirna"], "label": "siRNA"}}, {"menu": "sirnasupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/sirna/supplementary"], "label": "siRNA supplementary"}}, {"menu": "phenotype", "config": {"case_sensitive": true, "all": ["Phenotype", "Phenotype Term Accession"], "default": ["Phenotype"], "label": "Phenotype", "wildcard": {"enabled": true}, "ns": ["openmicroscopy.org/mapr/phenotype"]}}, {"menu": "compound", "config": {"default": ["Compound Name"], "case_sensitive": true, "all": ["Compound Name"], "ns": ["openmicroscopy.org/mapr/compound"], "label": "Compound"}}, {"menu": "compoundsupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/compound/supplementary"], "label": "Compound supplementary"}}, {"menu": "organism", "config": {"default": ["Organism"], "all": ["Organism"], "ns": ["openmicroscopy.org/mapr/organism"], "wildcard": {"enabled": true}, "label": "Organism"}}, {"menu": "antibody", "config": {"default": ["Antibody Identifier"], "case_sensitive": true, "all": ["Antibody Identifier"], "ns": ["openmicroscopy.org/mapr/antibody"], "label": "Antibody"}}, {"menu": "antibodysupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/antibody/supplementary"], "label": "Antibody supplementary"}}, {"menu": "orf", "config": {"default": ["ORF Identifier"], "all": ["ORF Identifier"], "ns": ["openmicroscopy.org/mapr/orf"], "label": "ORF"}}, {"menu": "orfsupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/orf/supplementary"], "label": "ORF supplementary"}}, {"menu": "cellline", "config": {"default": ["Cell Line"], "all": ["Cell Line"], "ns": ["openmicroscopy.org/mapr/cell_line"], "wildcard": {"enabled": true}, "label": "Cell Lines"}}, {"menu": "celllinesupplementary", "config": {"default": [], "all": [], "ns": ["openmicroscopy.org/mapr/cell_line/supplementary"], "label": "Cell Lines supplementary"}}, {"menu": "others", "config": {"default": ["Others"], "all": ["Others"], "ns": ["openmicroscopy.org/omero/bulk_annotations"], "label": "Others"}}]
omero.web.public.url_filter=^/(webadmin/myphoto/|mapr/|webclient/(?!(action|annotate_(file|tags|comment|rating|map)|script_ui|ome_tiff|figure_script))|webgateway/(?!(archived_files|download_as)))
omero.web.ui.top_links=[["Studies", {"query_string": {"experimenter": -1}, "viewname": "webindex"}, {"title": "Image Data Repository"}], ["Genes", {"query_string": {"experimenter": -1}, "viewname": "maprindex_gene"}, {"title": "Genes browser"}], ["Phenotypes", {"query_string": {"experimenter": -1}, "viewname": "maprindex_phenotype"}, {"title": "Phenotypes browser"}], ["Cell Lines", {"query_string": {"experimenter": -1}, "viewname": "maprindex_cellline"}, {"title": "Cell Lines browser"}], ["siRNAs", {"query_string": {"experimenter": -1}, "viewname": "maprindex_sirna"}, {"title": "siRNAs browser"}], ["Antibodies", {"query_string": {"experimenter": -1}, "viewname": "maprindex_antibody"}, {"title": "Antibodies browser"}], ["Compounds", {"query_string": {"experimenter": -1}, "viewname": "maprindex_compound"}, {"title": "Compounds browser"}], ["Organisms", {"query_string": {"experimenter": -1}, "viewname": "maprindex_organism"}, {"title": "Organisms browser"}], ["About", "https://idr.openmicroscopy.org/about/", {"title": "About the Image Data Resource"}]]


You'll likely want to start with a much simpler configuration to test that everything is working. See for example https://github.com/ome/omero-mapr/#config-settings.

Cheers,
~Josh
User avatar
jmoore
Site Admin
 
Posts: 1591
Joined: Fri May 22, 2009 1:29 pm
Location: Germany


Return to User Discussion

Who is online

Users browsing this forum: No registered users and 1 guest