OMERO and other data repositories

Kia ora, from New Zealand,
My institute is planning a general implementation of new research data management tools that cover data spanning a wide spectrum (various omics, remote instrument data, GIS and microscopy). OMERO is the tool that we (the light and electron microscopy people) want because it is, frankly, the best tool for the job and awesome.

It is likely that, if implemented here, OMERO would have to be part of a ecosystem of other repositories. I’m hoping that some of you may be able to share some thoughts and experiences working between OMERO and other repositories. Currently it looks like CKAN or Figshare may be contenders for a general repository.

The committee working on this asked me the following questions.

  1. Can the image files accessed using OMERO’s tools be stored in a different repository (e.g., CKAN, Figshare or myTardis)?

  2. Is it possible to keep the dataset level metadata (i.e. description of project and data, who owns the data and contact person etc.) with the organisational catalogue/repository and keep this linked to the image level metadata with OMERO (e.g. sample ID, how samples were treated/prepared, instrument parameters etc.)?

  3. Secondly, we will use repository (FigShare or CKAN) to share and publish data. What role could OMERO have in the sharing/publishing of data, mainly to external users?

I know that OMERO can be used in an externally facing repository role. I’m interested in how people make multi-repository environments work. If you have got this far. Thanks for persevering through my long post :smile_cat:.

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@Duane-Agresearch

Hello Duane

Thank you for your post and your kind words about OMERO.
Please see below the answers to your 3 questions.

  1. Principally yes. Nevertheless, OMERO requires the storage of images on a file system. This file system can be on a server which is mounted as a volume on a machine where the OMERO.server is installed (if the data are imported in “in-place” manner) or on the OMERO.server machine itself. OMERO also assumes that the filepaths, the files themselves and filenames of those original files will not be edited after the files have been imported to OMERO. Thus, the recommendation is to make such files and the directory structure which contains them “read-only”. If MyTardis, Figshare or CKAN can live with such conditions, then the scenario suggested by the question is possible.
  2. Yes, there are ways to link external metadata to data stored in OMERO, mainly via URLs pointing to the external sites. See examples of such data in IDR (which is based on OMERO). On the screenshot below, the icon next to “Loratadine” is a clickable link (the link is Loratadine | C22H23ClN2O2 - PubChem) .pointing to that compound (Loratadine) listing in PubChem database. It is also possible to link back from PubChem or other repository by simply citing the link Webclient which brings you to the particular image in IDR. You can link to Projects, Datasets, Screens, Plates, Wells and (as already mentioned) Images in OMERO in that way too.

  1. OMERO has its own sharing/publishing workflow. Please see Prepare data for publication using OMERO — OMERO guide 0.2.0 documentation. We did not explore how this could be matched with what Figshare and CKAN are doing, but one possibility is certainly to publicize the URLs to the images in OMERO which are in a public group via Figshare and CKAN, if these tools support such workflow.

Hope this halps.
Happy to discuss further

All the best

Petr

:heart:

I’ll add one thought to Petr’s point: though this is definitely the situation at the moment, we have run into similar issues ourselves (e.g. wanting to have images from S3 in OMERO) and so there is a trajectory towards the type of set up you are discussing. Getting there will be expedited by having more people involved :slightly_smiling_face:

~Josh

Wow. Thank you Petr and Josh for the useful answers and examples though the links. I was hoping the answers would be very similar to what you said. It will also not surprise me that this issue will grow. From what I can gather from the research data management committee, in these early days of interoperability we find it difficult to shake culture of thinking of data repository tools are alternatives.

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Hi Duane,
Happy to hear you liked our answers :). Good luck with moving forward with OMERO at your institute. Please feel free to ask further questions if needed.
Best wishes
Petr

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