[ome-devel] Fwd: [IDR Project] Zegami / IDR
Simon Li
spli at dundee.ac.uk
Tue Jul 12 10:10:52 BST 2016
Hi Damir
If your OMERO.table is only attached to one object (which it should be in your case) deleting the FileAnnotation will also delete the table, so if you've also deleted the MapAnnotations you should be back to your initial state. One thing to note is that in theory the filename or description of the bulk annotations table could change but the namespace of the annotation should always be a know value, in this case: `openmicroscopy.org/omero/bulk_annotations`<http://openmicroscopy.org/omero/bulk_annotations`>.
We might have other namespaces in future, for instance to distinguish calculated features from bulk-annotations.
A bit of background to the design decision for having Bulk-MapAnnotations: In the mainline OMERO bulk-annotation tables are displayed directly in the UI. For the IDR we wanted to customise the display of this metadata including hiding some values or linking to external resources, but these tables can be very large and are derived from the raw data. The map-annotations effectively gave us a customisable "view" of the data in the table. In the long term it'd be nice if this would all be generated on the fly instead of requiring an explicit create/delete/create cycle everytime you wanted to reconfigure the metadata display, but that's something for the future.
Simon
On 12 July 2016 at 04:27, Damir Sudar <dsudar at lbl.gov<mailto:dsudar at lbl.gov>> wrote:
Thanks Simon,
I'm using the tools in our daily workflow now and will have more feedback. But so far, it's all meeting my needs.
For my need to delete the previous bulkmap annotations I kludged up a a few lines of shell script that work. It's pretty ugly but may indicate what's needed:
# identify Screen ID and delete old bulk_annotation
s_id=$(omero hql --style=plain --all -q --limit=10 "select s from Screen s where s.name<http://s.name> = '$arg' " | cut -f3 -d, )
OA=$(omero hql -q --all --style plain --limit 1 "select '/FileAnnotation:'||f.id<http://f.id> from ScreenAnnotationLink l, FileAnnotation f join l.child where l.child = f and l.parent.id<http://l.parent.id> = '$s_id' and f.description = 'bulk_annotations' " | cut -f2 -d,)
if [ "$OA" == "" ]; then omero delete $OA; fi
Am I correct in assuming that deleting the bulk-annotations FileAnnotation deletes the OMERO.table associated with that Screen and makes everything "virgin" again?
Thanks,
- Damir
On 7/8/2016 12:21 PM, Simon Li wrote:
Hi Damir
Thanks for your feedback! Improving the map annotation processing (which may include removing duplicates, deleting, merging and replacing) is definitely on our todo list, along with tools for viewing them, keep an eye on the mailing lists for updates.
If you've got any other suggestions, big or small, let us know. We want to release the metadata work as a production quality tool, so any external feedback is especially welcome.
Simon
On 8 Jul 2016 19:54, "Damir Sudar" <dsudar at lbl.gov<mailto:dsudar at lbl.gov>> wrote:
Hi Eleanor and team,
I've been having a lot of fun with all the tools you all have developed in the IDR context. Most of them work extremely well as is for my purpose. With the CLI metadata tools my whole workflow is quite smooth. I look forward to a bit more documentation but with built-in help and sometimes a look at the source, I figured out most of the functionality. Since I'm still in development mode, the "--context deletemap" option is extremely useful. One thing I'm missing is an option such as "--context delete_bulk_annotations" to conveniently get rid of the previous version.
Per my earlier message, I ran into an issue with plates with more than 26 rows but Will Moore's partial patch got me over that issue for the time being.
Thanks,
- Damir
On 6/27/2016 2:03 PM, Eleanor Williams wrote:
Hi Damir
To convert the omero tables to key-value pairs annotations we are again using the CLI metadata populate script along with a yaml-format configuration file to specify which columns we want to take from the omero tables and put into Key-Value Annotations.
This component of the metadata functionality is still in the development stage and so to use it you need to:
1. use the latest version of omero (5.2.4) and
2. then run as
OMERO_DEV_PLUGINS=1 bin/omero metadata populate --context bulkmap --cfg bulkmap-config.yml Screen:n
where n is the screen number in omero.
An example config file for one of our screens is here
<https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml>https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-bulkmap-config.yml
You can see I have just picked out some of the columns from theannotation.csv<https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-annotation.csv> file, in this case ones that I thought IDR users might use as search terms, and I have specified URLs for some. You can also change the 'display name' of the column using the ' clientname' tag and create URLs using the 'clientvalue' tag.
Let us know if you have any problems running this, or suggestions for improvement.
Best regards
Eleanor
On 27/06/2016 03:04, Damir Sudar wrote:
Hi Eleanor and Josh,
I'm learning a lot from your work on putting the IDR together and I'm applying it for our image repository for our LINCS project (http://www.lincsproject.org/centers/data-and-signature-generating-centers/oregon-u/) that hopefully will go live in a few months. We're also looking at Zegami as a possible way to provide visualizations of that data (Great demo, Roger!! and thanks for the code for that).
I've gotten as far as putting my metadata into a a format that can be used to generate the omero tables using the Populate Metadata script. But I couldn't find how you guys then populate the Key-Value Annotations. It appears to be a subset of what's in the Tables. Do you have some magic scripts for that and are those available?
Cheers,
- Damir
On 6/16/2016 2:21 AM, Eleanor Williams wrote:
Hi Steve and Roger
I think idr0002-heriche-condensation would be a good screen to start with. It is relatively small at 12 plates and has good annotation with control, quality control and phenotype values. It can be found here http://idr-demo.openmicroscopy.org/webclient/?show=screen-102.
I am doing a bit of a stock-take of the annotation files I've produced so far and will be changing a few aspects over the next few weeks, mainly to include more of the information that is currently held in the study files. For example I'd like to get more of the sample attributes such as species and cell line into the annotation.csv file, and then into the omero tables and Map Annotations. Sample attributes for screens were originally recorded in the study file because it didn't vary per screen, but now that we are also looking at non-screen data where this might vary it makes sense to always have it visible with the images. Also we haven't got as far as exposing much of the study information in omero yet.
I would really like to work with you to understand how you are going to use the experimental and analytic annotations and how we can help in providing the metadata you need and in the most usable format. For example would it be useful if I indicate what is sample attribute information in the annotation.csv file by using something like a constistent header format e.g. Characterisics [Organism], Characteristics [Cell Line], Characteristics [Organism Part] etc, or is this not really necessary for your purposes and 'Organism', 'Cell Line' column headings would be enough?
Finally, it was Balaji Ramalingam<https://www.openmicroscopy.org/site/about/development-teams/jason/balaji.png/view> that you were talking to about streaming the thumbnails. I'm sure he would be happy to discuss this further with you.
Best regards
Eleanor
On 15/06/2016 20:59, Josh Moore wrote:
Forwarding this to the mailing list so that anyone who had expressed
interested in http://zegami.com/ at this year's users' meeting can
follow along.
Cheers,
~Josh
P.S. If you weren't able to attend #OME2016, a recap is now up on the
blog http://blog.openmicroscopy.org/community/2016/06/15/user-meeting/
---------- Forwarded message ----------
From: Stephen Taylor <stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk>
Date: Tue, Jun 14, 2016 at 8:17 AM
Subject: Re: [IDR Project] Zegami / IDR
Cc: Roger Noble <roger at zegami.com><mailto:roger at zegami.com>
Hi,
I’ve been look at a few examples from the link Josh sent to me and
there are quite a lot! What would be a good data set to get import
into Zegami from IDR? I am thinking a set that has decent metadata
and a study that people are more familiar with that would make an
interesting use case.
Kind regards,
Steve
From: Stephen Taylor
Sent: 10 June 2016 14:25
Cc: Roger Noble <roger at zegami.com><mailto:roger at zegami.com>; 'e.x.williams at dundee.ac.uk<mailto:e.x.williams at dundee.ac.uk>'
<e.x.williams at dundee.ac.uk><mailto:e.x.williams at dundee.ac.uk>
Subject: RE: [IDR Project] Zegami / IDR
Hi all,
I am interested generally in getting data in and out of OMERO from
both internal and external. Over a WAN the images are less of an issue
since they are streamed on demand but large metadata on the other hand
can get out of hand since it all has to be loaded completely into
Zegami’s database.
Currently I do “OMERO project” to “Zegami collection” using a Zegami
export script (modified version of the OMERO batch export script).
This takes a project or selection of images from OMERO and produces
thumbnails and data in tab delimited Zegami format and then I manually
import that into Zegami for processing. The OMERO id is preserved so I
can link to the original image in OMERO using the OMERO web client. I
only export certain metadata currently (filenames and OMERO tags) and
my plan is to make this more comprehensive and allow MapAnnotations
and Tables to be exported using this mechanism as well. I need to find
out more how to query these data types. Since we have internal
projects at Oxford that need this I’d like to finish this and make
that plugin freely available for other OMERO users to publish their
data in Zegami.
Longer term for IDR/Zegami
One of your team (apologies I didn’t get his name but he was doing
OMERO/ImageJ in the Unconference session) suggested we just stream in
the thumbnail and just have 1 level (i.e. no zoom) and when you want
to see the image just open it up in OMERO. This would not be as nice
to use but may be sufficient for HCS and would allow you to use
Zegami’s facet based query engine and would be probably little (no?)
work for you guys. We need to test this to see what it looks like and
it assumes OMERO can supply a unique thumbnail URL for each image and
that the metadata will provide a primary key so that we can get to
this image via a thumbnail id. To get at the metadata Josh and Eleanor
said they were thinking of making the CSV downloadable for a
collection, which could be loaded into Zegami on the fly (we have
instances where we dynamically load metadata via URL already).
However, major caveat is on how well this would perform over a WAN
with a large amount of data.
BTW we have developer docs for Zegami for those interested at:
https://support.zegami.com/hc/en-us/categories/200350657-Developers
and would welcome feedback.
Kind regards and thanks,
Steve
From: Jason Swedlow (Staff) [mailto:j.r.swedlow at dundee.ac.uk]
Sent: 08 June 2016 13:09
Cc: Eleanor Williams (Staff) <e.x.williams at dundee.ac.uk><mailto:e.x.williams at dundee.ac.uk>
Subject: Re: [IDR Project] Zegami / IDR
Hi Josh et al—
My two cents— can we consider this use case from an external users’
perspective, mindful that distribution of such a solution would
definitely cause us to consider how we ship thumbnails, handle
straws, etc.
Cheers,
Jason
On Wed, Jun 8, 2016 at 1:31 PM, Josh Moore <josh at glencoesoftware.com><mailto:josh at glencoesoftware.com> wrote:
Stephen,
On Wed, Jun 8, 2016 at 9:52 AM, Stephen Taylor
<stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk> wrote:
Hi Josh,
Yes! What would be the best way of bulk downloading the thumbnails for a screen or plate
Interesting question. Guess the reverse question is: do you want to do
this as an external user or as if you had access to the OMERO?
( I notice the "Run Script" button isn't active ).
Correct. This server is stripped down in several ways as a public resource.
~J.
Kind regards,
Steve
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: 08 June 2016 08:07
To: Stephen Taylor <stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk>
Cc: Eleanor Williams <exwilliams at dundee.ac.uk><mailto:exwilliams at dundee.ac.uk>;
e.x.williams at dundee.ac.uk<mailto:e.x.williams at dundee.ac.uk>; j.a.moore at dundee.ac.uk<mailto:j.a.moore at dundee.ac.uk>
Subject: Re: Zegami / IDR
Hi Stephen,
On Wed, Jun 8, 2016 at 8:40 AM, Stephen Taylor
<stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk> wrote:
Hi Eleanor,
Thanks very useful. Is the web site publically available?
You mean http://idr-demo.openmicroscopy.org/webclient ?
Cheers,
~Josh
Kind regards and thanks,
Steve
From: Eleanor Williams [mailto:exwilliams at dundee.ac.uk]
Sent: 07 June 2016 11:09
To: Stephen Taylor <stephen.taylor at imm.ox.ac.uk><mailto:stephen.taylor at imm.ox.ac.uk>;
e.x.williams at dundee.ac.uk<mailto:e.x.williams at dundee.ac.uk>; j.a.moore at dundee.ac.uk<mailto:j.a.moore at dundee.ac.uk>
Subject: Re: Zegami / IDR
Hi Stephen
Here is a link to our workshop presentation but it describes how to
get the data into omero rather than out.
http://downloads.openmicroscopy.org/presentations/2016/Users-Meeting/Workshops/Metadata-at-Scale.pdf
We will be adding the annotation.csv files as attachments to each
screen over the next couple of weeks.
Let us know if you have any more questions.
Best regards
Eleanor
On 07/06/2016 10:41, Stephen Taylor wrote:
Hi Eleanor and Josh,
Great to meet you both at the OME meeting last week.
I'd be interested in trying get some data into Zegami from IDR. I
missed your Unmeeting (ironically I was demoing Zegami) where I think
you went into some of the technical details. Can you send me the link
to your presentation please?
Kind regards and thanks,
Steve
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Eleanor Williams PhD
Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK
The University of Dundee is a registered Scottish Charity, No: SC015096
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T: 510/486-5346<tel:510%2F486-5346> - F: 510/486-5586<tel:510%2F486-5586> - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>
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--
Eleanor Williams PhD
Data Annotator/Software Engineer
Centre for Gene Regulation and Expression
University of Dundee, UK
The University of Dundee is a registered Scottish Charity, No: SC015096
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--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346<tel:510%2F486-5346> - F: 510/486-5586<tel:510%2F486-5586> - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>
http://biosciences.lbl.gov/profiles/damir-sudar-2/
Visiting Scientist, Oregon Health & Science University
The University of Dundee is a registered Scottish Charity, No: SC015096
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http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
The University of Dundee is a registered Scottish Charity, No: SC015096
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--
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346<tel:510%2F486-5346> - F: 510/486-5586<tel:510%2F486-5586> - E: DSudar at lbl.gov<mailto:DSudar at lbl.gov>
http://biosciences.lbl.gov/profiles/damir-sudar-2/
Visiting Scientist, Oregon Health & Science University
The University of Dundee is a registered Scottish Charity, No: SC015096
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