in pixels
in % relative to the image dimensions
URL to the image itself, not a web page containing the image. This URL will be used to download or embed the image in a website.
URL to the image in original format.
URL to the image thumbnail itself, not a web page containing the image. This URL will be used to download or embed the thumbnail in a website. This should be provided for3D or large 2D images.
URL linking back to the image page on the original website, if they have single image pages.
In pixels.
Machine used to generate the image.
Date when the image was taken. We highly advise to put the date in, as your image will be sorted lower without a date (as if it was an old image).
Lab/center/institute that produced the images.
Lab/center/institute that further procesed the images, for example who generated the 3D rendering from the original images.
Lab/center/institute that produced the sample/organism.
URL to the website where all the images are accessible. This should be a link to a generic page such as a search page or a home page.
The ontology terms accepted are children of "imaging method" in FBBI, see http://www.ebi.ac.uk/ols/ontologies/fbbi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbi_00000222
The ontology terms accepted are children of "sample prearation" in FBBI, see http://www.ebi.ac.uk/ols/ontologies/fbbi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbi_00000001
If any licence restrictions apply to the image, please note the licensing model here. This will be displayed on each page.
One or more publication describing the image production process. Publication which should be cited if the image is used in any other publication.
Age should ideally be presented in days with a further specification, i.e. post conception or post natal
Organism taxon name, ideally the label provided by NCBI. Example: Mus musculus.
Organism taxon id provided by NCBI (if existing). Example NCBITaxon_862507. http://www.ebi.ac.uk/ols/ontologies/ncbitaxon .
Developmental stage. If an ontology term is provided it should come from a public developmental stage ontology i.e. from https://code.google.com/p/developmental-stage-ontologies/ .
Label, as provided in the ontology. This is provided for human readability of the XML. If it doesn't match the most up-to-date label, this will be replaced.
Short form OWL style id, with underscores after namespace not colon. Example MP_0002919
Gene identifier from a public, established resource, representative for the model organism. Examples: MGI, ENSEMBL
Genetic feature (such as allele) identifier from a public, established resource, representative for the model organism. Examples: MGI, ENSEMBL
If an ontology term is provided, see the Sequence ontology ontology. Please contact us if you want to use a different ontology, as this should be possible. See SO ontology: http://www.ebi.ac.uk/ols/ontologies/so/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FSO_0001059
Must be consistent over different data exports or the images will be imported multiple times.
Mutant genetic features. Expressed features should be associated to the channel, not the image itself!
Conditions of the experiment.
Observations relevant to the image and/or experiment that did not fit any of the tags provided. If you think a new XML element should be provided, please contact us.
Id of the region(s) of intereste associated with this image.
Id of the channel(s) associated with the image.
Use most general anatomy term describing the anatomical part depicted in the image. It is not necessarily the anatomical part of interest, but merely what is depicted in the image.
Must be consistent over different data exports.
Information on staining, markers and such. For ontology terms Visualization method children should be provided, from the Fbbi ontology: http://www.ebi.ac.uk/ols/ontologies/fbbi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbi_00000031
Image id with which the Channel is associated.
Regions of interest associated with this channel.
Gene(s)/genetic feature(s) visibly expressed in the image.
Must be consistent over different data exports. Image document must link to this id in associated_roi.
Must always be associated to the right image and back.
Must always be associated to the right channel and back.
Roi coordinates. Current assumption is that Rois are points, rectangles (2 points : upper left corner and lower right corner) and poligons (described by the right sequence of points)
Id of the user who created the annotation.
Group to which the user who created the annotation belongs.
Date when the annotation was created by the owner.
Last edit date.
Anatomy structure depicting gene expression in the current region of interest.
Not all images that depict expression of some gene or transgene in a particular structure depict the expression pattern of that gene or transgene. The depicted expression might be experimentally generated. Or the image may depict some clonal fragment of the expression pattern, with other cells in the image being part of the expression pattern but not showing expression. Because of this, it is not possible to conclude from the fact that some depicted structure expresses X that an image depicts the expression pattern of X.
Anatomical structure presenting some sort of abnormality.
Phenotypes present in the region of interest.
Any notes that don't fit the above annotations.