1- A simplified and personalized OMERO data model (ODM)
OMERO is based on complex and rich data model to implement objects and annotations following dedicated workflows. Most of them are captured automatically at the import or analysis workflows. User’s manual annotations are possible at each level to enrich and share the content. A complete data model can be found here.
The diagram below includes most visible and familiar data objects, personalised to emphasis on manual annotations to add in the system. The blue objects are from ODM, and are already implemented. However, light blue objects in dashed boxes are not from the ODM, and are illustrated as logical compounds to show the meta-data missed and not captured from the bioimaging experiences. You will see in the next paragraph how to use Tag and tagset features to annotate data in OMERO.
2- Adding manual annotations
In order to make annotation variables and values used by research team members harmonised and reusable, a minimum essential tagsets dictionary was created. The pair Tagset/tag is used as Key/Value concept, which means that a tagset can have many tags, and tags are in fact, modalities of a tagset!
The screen capture below, illustrate the implementation of the dictionary structure in OMERO. We recommend OMERO users to implement the tags inside the tagsets, following the indications below:
- tagsets must be in english, lower cases, starting with a chronological number in 2 digits. The pattern is: ‘xx–tageset_name‘, where ‘_’ (underscore) is used for composed names to avoid spaces between words.
- tags must be in english, lower cases (except for acronyms) and must include description information (with synonyms if possible).
- some unit-dependant tags like age or temperature, for example, must follow a defined pattern: ‘age+nb+(y/m/d)’ like age3m, age2,5y, age20d or ‘(+/–)+nb+deg’ like ‘+5deg’, for temperature.
- Before any new tagset or tag creation, OMERO user should check their existence in the Tags tree. If any synonym is found, please update the existing tag’s description with the synonym, and avoid any new creation.
3- Tagset/tag dictionnary
This is a main and minimum tagset dictionnary. Please, refer to this table when creating new tags or tagsets.
|
|
Category |
Description |
Modalities example
|
Reference/Ontology |
Experiment description |
experiment_type |
|
histology, protein localization, in situ hybridization (OBI_0001686), gene deletion screen (EFO_0007552), RNAi screen (EFO_0007551), protein screen (EFO_0005398), compound screen (EFO_0007553). |
|
HCS_stage |
An experimental stage describing stages of high content screen analysis. |
primary HCS, secondary HCS, validation HCS |
EFO_0007555 |
|
platform |
The ICM microscopy platform where image was acquired. |
ICM-QUANT, ICM-CELIS, ICM-HITOMICS |
|
|
Sample description |
organism |
A material entity that is an individual living system |
human, mouse, drosophilia, zebrafish, virus, bacteria |
OBI_0100026 |
strain |
A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics |
|
EFO_0005135 |
|
organism_Part |
The part of organism’s anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). |
brain, spin, |
EFO:0000635 |
|
sex |
|
male, female |
PATO_0000047 |
|
age |
A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism |
age3m, age3w, age3y, age3d, embryonic |
EFO_0000246 |
|
biosample_type |
|
whole tissue, cell, commecial cell line, cultured cell |
OBI:0001479 |
|
genetic_background |
a genetic characteristics information which is a part of genotype information that identifies the population of organisms |
mt, wt, ko, CD20-, |
OBI:0001225 |
|
disease |
the sample donor’s disease status or disorder. |
control, normal, |
EFO_0000408 |
|
cell_type |
A cell type is a distinct morphological or functional form of cell. |
glial cell, stem cell |
EFO_0000324 |
|
ENCODE_cell_line |
for commercial only |
hela, mcf7, jurkat, … |
EFO_0002926 |
|
Experiment conditions |
experiment_mode |
|
in-vivo, in-vitro, ex-vivo |
|
biosample_preparation |
|
embedded tissue, fixation method, |
FBbi:00000001 |
|
temperature |
|
4deg, 37deg |
EFO_0000718 |
|
staining_method |
Any of the various methods that use a dye, reagent, or other material for producing coloration in tissues or microorganisms for microscopic examination. |
IHC, ISH, H&E |
NCIT:C23010 |
|
washing |
The process of applying a solvent (e.g. water) or some solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds. |
water, SSC/SDS |
EFO_0000735 |
|
reagent_identifier |
The siRNA, ORF, compound, etc, used to perturb the cells |
s25501, s22776, |
|
|
gene_symbol |
Gene name |
TP53, GFAP, NEUROD1 |
Ensembl gene name http://www.ensembl.org/index.html |
|
treatment_protocol |
A protocol in which the aim is to treat a sample, collection of samples, organism or group of organisms for some experimental analysis of outcome. |
|
EFO_0003969 |