Working with annotations

Structured annotations permit the attachment of data and metadata outside the OMERO data model to certain types within the model. The annotations are designed for individualized use by both sites and tools. Annotations can be attached to multiple instances simultaneously to quickly annotated all entities in a view. Each annotation has a “name” which can be interpreted as a “namespace” by tools, which can filter out all unknown namespaces. Further, to prevent users from overwriting or editing important information, annotations are immutable, but editing can be simulated via copy and delete.

Annotated and annotating types

Each type which can be annotated implements ome.model.IAnnotated. Currently, these are:

• Project
• Dataset
• Image
• Pixels
• OriginalFile
• PlaneInfo
• Roi
• Channel
• Annotation and all annotation subtypes in order to form hierarchies
• ScreenPlateWell: Screen, ScreenAcquisition, Plate, Well, Reagent
• Folder

Annotation hierarchy

Though they largely are all String or numeric values, a hierarchy of annotations makes differentiating between just what interpretation should be given to the annotation. This may eventually include validation of the input string and/or file.

Annotation (A*) ....................... A name field and a description
  ListAnnotation ...................... Uses AnnotationAnnotation links to form a list of annotations
  BasicAnnotation (A*) ................ Literal or "primitive" values
    BooleanAnnotation ................. A simple true/false flag
    TimeStampAnnotation ............... A date/time
    TermAnnotation .................... A term used in an ontology
    NumericAnnotation (A*) ............ Floating point and integer values
      DoubleAnnotation
      LongAnnotation
  MapAnnotation ....................... A list of key-value pairs
  TextAnnotation (A*) ................. A single text field
    CommentAnnotation ................. A user comment
    TagAnnotation ..................... Interpreted as a Web 2.0 "tag" on an object, tags on tags form tag bundles
    XmlAnnotation ..................... An xml snippet attached to some object
  TypeAnnotation (A*) ................. Links some entity to another (possibly to be replaced by <any/>)
    FileAnnotation .................... Uses the Format field on OriginalFile to specify type

A* = abstract

See also

Schema documentation for Structured Annotations

Section of the auto-generated schema documentation describing the structured annotations

Names and namespaces

Since arbitrary blobs or clobs can be attached to an entity, it is necessary for clients to have some way to differentiate what it can parse. In many cases, the name might be a simple reminder for a user to find the file s/he has annotated. Applications, however, will most likely want to define a namespace, like http://name-of-application-provider.com/name-of-application/file-type/version. Queries can then be produced which search for the proper namespace or match on a part of the name space:

iQuery.findAllByQuery("select annotation from FileAnnotation where "+
 "name like 'http://name-of-application-provider.com/name-of-application/%'");

Tags will most likely begin without a namespace. As a tag gets escalated to a common vocabulary, it might make sense to add a possibly site-specific namespace with more well-defined semantics.

Descriptions

Unlike the previous, ImageAnnotation and DatasetAnnotation types, the new structured annotations do not have a description field. The single description field was limited for multi-user scenarios, and can be fully replaced by TextAnnotations attached to another annotation.

FileAnnotation fileAnnotation = …;
TextAnnotation description = …;
fileAnnotation.linkAnnotation(description);

Immutability

The actual content value of an annotation – the text, long, double, file value, etc – is immutable. Links to and from the annotation, however, can be modified.

Currently the namespace field of annotations is mutable. See #878 for discussion.

Examples

Basics

import ome.model.IAnnotated;
import ome.model.annotations.FileAnnotation;
import ome.model.annotations.TagAnnotation;
import ome.model.core.OriginalFile;
import ome.model.display.Roi;

List<Annotation> list = iAnnotated.linkedAnnotationList();
// do something with list

Attaching a tag

TagAnnotation tag = new TagAnnotation();
tag.setTextValue("interesting");

Roi roi = …; // Some region of interest
ILink link = roi.linkAnnotation(tag);

iUpdate.saveObject(link);

Attaching a file

// or attach something new
OriginalFile myOriginalFile = new OriginalFile();
myOriginalFile.setName("output.pdf");
// upload PDF

FileAnnotation annotation = new FileAnnotation();
annotation.setName("http://example.com/myClient/analysisOutput");
annotation.setFile(myOriginalFile);

ILink link = iAnnotated.linkAnnotation(annotation)
link = iUpdate.saveAndReturnObject(link);

All write changes are intended to occur through the IUpdate interface, whereas searching should be significantly easier through ome.api.Search than IQuery.

See also

Extending OMERO.server

Map annotations