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OMERO and the Image Data Resource: Supporting open science in Dundee and around the world
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OMERO and the Image Data Resource:
Supporting open science in Dundee and around the world
Simon Li
Open Microscopy Environment
Who thinks it's a good idea?
More than 70% of researchers have tried and failed to reproduce another scientist's experiments, and more than half have failed to reproduce their own experiments.
http://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970
Bioinformatics databases are taken for granted in the life sciences
![ensemble](images/ensembl-homepage.png)
![pdf](images/pdb-homepage.png)
![ncbi](images/ncbi-homepage.png)
Image databases have lagged behind though. There are several application-specific repositories:
![emdb](images/emdb-homepage.png)
![lincs](images/lincs-homepage.png)
![jcbdataviewer](images/jcbdataviewer-homepage.png)
>sp|Q96GD4|AURKB_HUMAN Aurora kinase B OS=Homo sapiens GN=AURKB PE=1 SV=3
MAQKENSYPWPYGRQTAPSGLSTLPQRVLRKEPVTPSALV
LMSRSNVQPTAAPGQKVMENSSGTPDILTRHFTIDDFEIG
RPLGKGKFGNVYLAREKKSHFIVALKVLFKSQIEKEGVEH
QLRREIEIQAHLHHPNILRLYNYFYDRRRIYLILEYAPRG
ELYKELQKSCTFDEQRTATIMEELADALMYCHGKKVIHRD
IKPENLLLGLKGELKIADFGWSVHAPSLRRKTMCGTLDYL
PPEMIEGRMHNEKVDLWCIGVLCYELLVGNPPFESASHNE
TYRRIVKVDLKFPASVPMGAQDLISKLLRHNPSERLPLAQ
VSAHPWVRANSRRVLPPSALQSVA
Image data is extremely difficult to automatically annotate
There are 100s of different file formats
Genomics/proteomics data is often text-based
annotations are mandatory for understanding
What is the Image Data Resource?
A repository for reference datasets and images that
“constitute valuable resources for a broader community of users that will often be accessed as a reference or that will be recomputed to extract additional information and knowledge”
Euro-BioImaging - ELIXIR Image Data Strategy
30 data submissions
1 million experiments
2.7 million images
37 million image planes
43 TB raw data
15 million files
All data is carefully curated
Previously inaccessible datasets
![idr0001-example](images/big_data_harddrives.jpg)]
![idr0015-example](images/idr-datasets/idr-0015-image-1976668.jpg)
![idr0015-example](images/idr-datasets/idr0015-example-external2.png)
![idr0008a-example](images/idr-datasets/idr-0008a-plate-230.png)
Genetic HCS
![idr0015-example](images/idr-datasets/idr-0015-plate-4871.png)
Geographic HCS
![idr0006-example](images/idr-datasets/idr-0006-plate-2243.png)
Gene product targeting HCS
![idr0017-example](images/idr-datasets/idr-0017-plate-4263.png)
Chemical HCS
![idr0018-example](images/idr-datasets/idr-0018-image-1919122.jpg)
Histopathology
![idr0021-example](images/idr-datasets/idr-0021-image-1885136.jpg)
3D‑SIM
![idr0023-example](images/idr-datasets/idr-0023-image-1886132.jpg)
Super-resolution
![idr0027-example](images/idr-datasets/idr-0027-image-2858285.jpg)
Chromatin dynamics
Genes and phenotypes in the IDR
<iframe src="https://idr.openmicroscopy.org/mapr/gene/?experimenter=-1 " class="stretch"></iframe>
![Eleanor Williams](images/team/eleanor_williams.png)
609 MB of spreadsheets
334 MB of text files
![idr0020-study.txt](images/spreadsheets/idr0020-study.png)
![idr0020-screenA-annotation.csv](images/spreadsheets/idr0020-annotation.png)
![idr0020-screenA-library.txt](images/spreadsheets/idr0020-library.png)
What about your datasets?
Hi-res live cell imaging of chromatin dynamics
UOD Life Science's own OMERO server
Open to everyone in SLS (and others on request)
You can choose to publish some of your images (viewable without a login)
<iframe data-src="https://omero.lifesci.dundee.ac.uk/figure/file/364215/ " class="stretch"></iframe>
A public curated reference image repository with internal and external cross-references
An OMERO server for publishing datasets within Dundee
OMERO.figure, a full pipeline for creating publication quality figures
Tools for analysing image data in the IDR and OMERO
Reproducibly
And shareably
But why only in OMERO? And why only images?
An online cloud-based analysis platform for running and sharing analysis scripts
Example: searching the IDR for novel gene interactors
Start with a set of genes we're interested in
Obtain a phenotypic profile characterising this set of genes
Query the IDR for other genes with a similar phenotypic profile
Hypothesis: these genes are potentially associated with the complex
1. Start with a set of genes we're interested in
Arp2/3 protein complex
2. Obtain a phenotypic profile characterising this set of genes
Search all studies in the IDR, obtain all phenotypes associated with these genes
3. Query the IDR for other genes with a similar phenotypic profile
This gives us new targets to investigate
![Jupyter ARP2-3 similar genes](images/jupyter/idr-arp23-similargenes.png)
4. Hypothesis: these genes are potentially associated with the complex
Initial validation with StringDB
Remember: this is very preliminary work!
Anyone can have access to:
![figure](images/summary/nightshade-figure-example.png)
OMERO.figure
![analysis](images/summary/idr-jupyter-example.png)
IDR cloud analysis
Contact us for more details: https://www.openmicroscopy.org/support/
![Jason Swedlow](images/team/jason_swedlow.jpg)
Jason Swedlow
![Josh Moore](images/team/josh_moore.jpg)
Josh Moore
![Simon Li](images/team/simon_li.png)
Simon Li
![Eleanor Williams](images/team/eleanor_williams.png)
Eleanor Williams
![Gabriella Rustici](images/team/gabriella_rustici.png)
Gabriella Rustici
![David Gault](images/team/david_gault.png)
David Gault
![Dominik Lindner](images/team/dominik_lindner.png)
Dominik Lindner
![Harald Waxenegger](images/team/harald_waxenegger.png)
Harald Waxenegger
![Helen Flynn](images/team/helen_flynn.png)
Helen Flynn
![Jean-Marie Burel](images/team/jeanmarie_burel.jpg)
Jean-Marie Burel
![June Matthew](images/team/june_matthew.png)
June Matthew
![Kenny Gillen](images/team/kenny_gillen.jpg)
Kenny Gillen
![Mark Carroll](images/team/mark_carroll.jpg)
Mark Carroll
![Petr Walczysko](images/team/petr_walczysko.png)
Petr Walczysko
![Roger Leigh](images/team/roger_leigh.jpg)
Roger Leigh
![Sebastien Besson](images/team/sebastien_besson.jpg)
Sebastien Besson
![Will Moore](images/team/will_moore.png)
Will Moore
![OME](images/team/logo-ome.svg)
![University of Dundee](images/team/logo-dundee.png)
![Rafael Carazo-salas](images/team/rafael_carazosalas.png)
Rafael Carazo-salas
![University of Bristol](images/team/logo-bristol.png)
![BBSRC](images/logos/bbsrc.png)
![Wellcome Trust](images/logos/wellcome.png)
![Alvis Brazma](images/team/alvis_brazma.png)
Alvis Brazma
![Ugis Sarkans](images/team/ugis_sarkans.png)
Ugis Sarkans
![Simon Jupp](images/team/simon_jupp.png)
Simon Jupp
![Tony Burdett](images/team/tony_burdett.png)
Tony Burdett
![ebi](images/team/logo-ebi.png)
![Aleksandra Tarkowska](images/team/aleksandra_tarkowska.jpg)
Aleksandra Tarkowska
![Richard Ferguson](images/team/richard_ferguson.png)
Richard Ferguson
![Simone Leo](images/team/simone_leo.jpg)
Simone Leo
![Bálint Antal](images/team/balint_antal.png)
Bálint Antal
![Anatole Chessel](images/team/anatole_chessel.jpg)
Anatole Chessel