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Literature and education
Textual scholarship is a discipline that often uses the technique of annotation to describe or add additional historical context to texts and physical documents.
Students often highlight or underline passages in books in order to refer back to key phrases easily, or add marginalia to aid studying. One educational technique when analyzing prose literature is to have students or teachers circle the names of characters and put rectangular boxes around phrases identifying the setting of a given scene.
Annotated bibliographies add commentary on the relevance or quality of each source, in addition to the usual bibliographic information that merely identifies the source.
Learning and instruction
From a cognitive perspective annotation has an important role in learning and instruction. As part of guided noticing it involves highlighting, naming or labelling and commenting aspects of visual representations to help focus learners' attention on specific visual aspects. In other words, it means the assignment of typological representations (culturally meaningful categories), to topological representations (e.g. images). This is especially important when experts, such as medical doctors, interpret visualizations in detail and explain their interpretations to others, for example by means of digital technology. Here, annotation can be a way to establish Common Ground between interactants with different levels of knowledge.  The value of annotation has been empirically confirmed, for example, in a study which shows that in computer-based teleconsultations the integration of image annotation and speech leads to significantly improved knowledge exchange compared with the use of images and speech without annotation. 
Markup languages like XML and HTML annotate text in a way that is syntactically distinguishable from that text. They can be used to add information about the desired visual presentation, or machine-readable semantic information.
The "annotate" function (also known as "blame" or "praise") used in source control systems such as Git, Team Foundation Server and Subversion determines who committed changes to the source code into the repository. This outputs a copy of the source code where each line is annotated with the name of the last contributor to edit that line (and possibly a revision number). This can help establish blame in the event a change caused a malfunction, or identify the author of brilliant code.
A special case is the Java programming language, where annotations can be used as a special form of syntactic metadata in the source code. Classes, methods, variables, parameters and packages may be annotated. The annotations can be embedded in class files generated by the compiler and may be retained by the Java virtual machine and thus influence the run-time behaviour of an application. It is possible to create meta-annotations out of the existing ones in Java.
Since the 1980s, molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation (irrespective of the context) is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it.
For DNA annotation, a previously unknown sequence representation of genetic material is enriched with information relating genomic position to intron-exon boundaries, regulatory sequences, repeats, gene names and protein products. This annotation is stored in genomic databases as Mouse Genome Informatics, FlyBase, and WormBase. Educational materials on some aspects of biological annotation from the 2006 Gene Ontology annotation camp and similar events are available at the Gene Ontology website.
The National Center for Biomedical Ontology (www.bioontology.org) develops tools for automated annotation of database records based on the textual descriptions of those records.
As a general method, dcGO  has an automated procedure for statistically inferring associations between ontology terms and protein domains or combinations of domains from the existing gene/protein-level annotations.
In the digital imaging community the term annotation is commonly used for visible metadata superimposed on an image without changing the underlying master image, such as sticky notes, virtual laser pointers, circles, arrows, and black-outs (cf. redaction).
In the United States, legal publishers such as Thomson West and Lexis Nexis publish annotated versions of statutes, providing information about court cases that have interpreted the statutes. Both the federal United States Code and state statutes are subject to interpretation by the courts, and the annotated statutes are valuable tools in legal research.
In linguistics, annotations include comments and metadata; these non-transcriptional annotations are also non-linguistic. A collection of texts with linguistic annotations is known as a corpus (plural corpora). The Linguistic Annotation Wiki describes tools and formats for creating and managing linguistic annotations.
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- Abstract (summary)
- Automatic image annotation
- Coding (social sciences)
- Comment (disambiguation)
- Java annotation
- Nota Bene
- PDF annotation
- Text annotation
- Web annotation
- XPS annotation
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