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Topic: Annotation

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	Annotation - Wikipedia, the free encyclopedia
		Annotation is extra information associated with a particular point in a document or other piece of information.
		Annotations about bibliographical sources, labeled annotated bibliographies, give descriptions about how each source is useful to an author in constructing a paper or argument.
		Further annotations can also be added by a compiler or programmer in the form of metadata, which is then made available in later stages of building or executing a program.
	en.wikipedia.org /wiki/Annotation (293 words)

	Annotation-Based Web Content Transcoding
		When annotation files are stored in a repository, an appropriate annotation file for a Web document needs to be selected dynamically from the repository either implicitly by means of a structural analysis of the subject document or explicitly by means of a reference contained in the subject document or some other association database.
		Annotation descriptions could be too complicated for a simple source tag editor to maintain, because addressing by XPath/XPointer follows a hierarchy of document elements from the root to a focal element, and alternative contents are structured as a hierarchy of conjunctive/disjunctive elements for replacement.
		Annotation source tags are re-created from internal DOMs [7] for XML annotation by referring to annotating portions of a subject HTML document.
	www9.org /w9cdrom/169/169.html (5344 words)

	Linguistic Annotation
		Annotate is a sophisticated tool which supports human-machine collaboration on the construction of syntactic trees.
		The annotations produced by the Treebank project were published by LDC.
		The annotation scheme includes sentential information (such as a well-formedness score) and also word and sub-string annotation which is stored in tabular form (for analytical information including syntactic constituents and error descriptions).
	www.ldc.upenn.edu /annotation (3735 words)

	Converting Annotation from Coverage to Geodatabase Format
		Annotation for a map can be created in several ways: imported from a coverage, generated by converting labels on a map, or created as a new annotation feature class in ArcCatalog.
		A TAT file is useful for relating the same annotation to more than one geographic feature and drawing text from the TAT file or a related table instead of the text string contained in the TXT file.
		Because the spatial features in the coverage associated with the annotation usually will also be converted and will share the same coordinate space and may be coincident, it is advisable to create a feature dataset to keep these feature classes together.
	www.esri.com /news/arcuser/1001/migrating2.html (927 words)

	GO Annotation Guide
		Collaborating databases annotate their gene products (or genes) with GO terms, according to two general principles: first, annotations should be attributed to a source; second, each annotation should indicate the evidence on which it is based.
		For annotations to "unknown" from any of the three ontologies, curators should cite a reference (either one within their database or the generic GO reference noted in the evidence documentation) that explains that they found no relevant biological information in the literature (or any other sources they may have considered).
		Annotating individual gene products according to attributes of a complex is especially useful for molecular function annotations in cases where a complex has an activity, but not all of the individual subunits do.
	www.geneontology.org /GO.annotation.shtml (4897 words)

	Web annotation - Wikipedia, the free encyclopedia
		The annotations can be thought of as being applied on a layer on top of the existing resource.
		Any particular annotation layer is visible to users who share the same annotation system¹ and can remain transparent to all others.
		In Annozilla web annotations are stored as RDF on a server, using XPointer to identify the region of the Web document being annotated.
	en.wikipedia.org /wiki/Web_annotation (323 words)

	Distributed Annotation System
		For example, a "clone end" annotation may be related to the start of a contig, an "mRNA" annotation may be related to the clone end, and an "exon" annotation may be related to the start of the mRNA.
		Each annotation is unambiguously located by providing its position as the start and stop positions relative to a "reference sequence." The reference sequence can be one of the entry points, or any of the subsequences within the entry point.
		Annotations have an ID that is unique to the server and a structured description that describes its nature and attributes.
	stein.cshl.org /das (5561 words)

	Learn to Use the New Annotation Feature of Java 5.0
		This annotation is used to indicate that a method declaration is intended to override a method declaration in a superclass.
		This annotation is useful in avoiding the situation where you think you are overriding a method, but you misspell the method name in the child class.
		This annotation indicates that the named compiler warnings should be suppressed in the annotated element (and in all program elements contained in the annotated element).
	www.devx.com /Java/Article/27235/1954?pf=true (2615 words)

	Annotations
		The facility consists of a syntax for declaring annotation types, a syntax for annotating declarations, APIs for reading annotations, a class file representation for annotations, and an annotation processing tool.
		Annotations do not directly affect program semantics, but they do affect the way programs are treated by tools and libraries, which can in turn affect the semantics of the running program.
		Annotations can be read from source files, class files, or reflectively at run time.
	java.sun.com /j2se/1.5.0/docs/guide/language/annotations.html (919 words)

	Annotations - Software Reality
		Annotations are, however, a different case because they are so open in scope.
		One thing that strikes me about the move from XML to annotations is the shift from having a many-one relationship between code and XML to a one-one relationship between code and annotations, as well as the move from weakly-typed to more strongly-typed enforced configuration.
		Annotations allows you to stay within the programming language of choice and also don't get lost/broken when you have to refactor your code a lot.
	www.softwarereality.com /programming/annotations.jsp (2432 words)

	On Deep Annotation
		The database representation is specified using a dedicated deep annotation ontology, which is instantiated to describe the physical structure of the part of the database which may facilitate the understanding of the query results.
		In a generic annotation, a piece of text that corresponds to a database field and that is annotated is only considered to be a place holder, i.e.
		What makes deep annotation different from all these approaches is that for the initial discovery of overlaps between different ontologies/schemata they all depend on lexical agreement of part of the two ontologies/database schemata.
	www.www2003.org /cdrom/papers/refereed/p273/p273_handschuh.html (4898 words)

	The Java Community Process(SM) Program - JSRs: Java Specification Requests - detail JSR# 269
		These annotations are typically processed either by build-time tools or by run-time libraries to achieve new semantic effects.
		Annotation processors will be able to specify what annotations they process and multiple processors will be able to run cooperatively.
		Additionally, the processors for different annotations should be able to work cooperatively and the set of processors that are run should be able to depend on what annotations are present in the code being processed.
	www.jcp.org /en/jsr/detail?id=269 (1170 words)

	Java(TM) Boutique - Program Annotation Facility
		The facility allows the annotator to reduce the overhead of carrying the compile time annotations with the class file to the JVM by specifying them to be ‘compile time’ annotations.
		Special kinds of annotation types called marker annotation types and single member annotation types can be defined for special types of annotation types.
		A single member annotation type is a special case of the normal annotation type, which has only one member element within it.
	javaboutique.internet.com /tutorials/annotation (990 words)

	Annotation Technology (Site not responding. Last check: 2007-10-09)
		Annotation Technology is a set of specifications for annotation software design.
		The main claim of the technology is that using this set of recommendations, one can design an easy to use and powerful annotation software that can gradually replace the common practice of making annotations on paper documents.
		Annotator is a pilot implementation of Annotation Technology.
	www-hbp.usc.edu /Projects/annotati.htm (244 words)

	Making Annotations to Principia Cybernetica Web
		An annotation is a comment discussing a given topic, which is directly entered via a form by one of our users (see the guidelines for making annotations).
		Annotations are distinguished from standard pages by their light grey background color, and by the word "ANNOTATION", linked to the present page, preceding the title.
		Unlike annotations, individual contributions are added to the table of contents, alphabetical index and title search index.
	pespmc1.vub.ac.be /MAKANNOT.html (509 words)

	Annotation Markup (Site not responding. Last check: 2007-10-09)
		Inline annotations are one possible solution for a set of accessibility issues: providing alternate text for graphical elements and other places where short, basically text-only, “tool tip style” rendering is appropriate.
		One question is whether the functional distinction in annotations should be exposed to the author by using two elements, analogous to
		Currently annotations are placed inside elements that are annotated.
	norman.walsh.name /2004/09/16/annotationMarkup (1333 words)

	Human Genome Advanced Annotation Tutorial
		GenBank entries themselves are annotated very unevenly, depending on the knowledge and interest level of the sequencing lab (and no one is allowed to fix a bad annotation!).
		By looking at at vertical columns of the annotation graphic, we now have a fair idea of where the annotation-worthy features are located, which ones code for known and unknown proteins, and how large and conserved the respective protein families are.
		Annotation of pseudogenes at GenBank is erratic, seldom informative, and generally just a byproduct of the annotation of a nearby functional gene.
	www.mad-cow.org /00/annotation_tutorial.html (7549 words)

	What is annotation? - A Word Definition From the Webopedia Computer Dictionary
		Many computer applications enable you to enter annotations on text documents, spreadsheets, presentations, and other objects.
		These voice annotations are digitized and stored with the document.
		When a reader of the document selects the annotation icon, the spoken message is played back through the computer's speakers.
	www.webopedia.com /TERM/A/annotation.html (150 words)

	Writing Annotation: Programming Annotation Software, PDF Annotation, Image Annotation Tool, C++ Programming SDK (Site not responding. Last check: 2007-10-09)
		The annotation toolbar has been updated to have a Windows XP look and feel.
		When hovering over any of the eight size handles—an appropriate arrow cursor is displayed depending on the handle and the rotation of the annotation object.
		This can be used to draw the annotations with thick lines, and change the line style from solid to dashed or dotted.
	www.leadtools.com /SDK/Document/Document-Annotation-new14.5.htm (764 words)

	Genotator: A Workbench for Sequence Annotation
		Useful annotations include homologies to known genes, possible gene locations, gene signals such as promoters, etc. We are developing a workbench for automatic sequence annotation and annotation viewing and editing.
		Researchers will then be able to examine all of the annotations (for example, the genes predicted by various gene-finding methods) and select the ones that look the best.
		Color-coded sequence annotations for both strands are displayed on a canvas that can be scrolled and zoomed.
	www.fruitfly.org /~nomi/genotator/about.html (807 words)

	VT76: Structure-Based Functional Annotation
		The insertion of the 7th strand (beta-4) relative to the Rossman fold is observed in the enzyme 1-deoxy-D-xylulose-5-phosphate reductoisomerase (1K5H), which contains a 7 stranded NADPH binding Rossman fold domain formed by two segments from the full-length protein, however the predicted NADPH binding residues of 1K5H are not conserved in VT76.
		VT76 is annotated (Pfam, Interpro) as belonging to a family of possible lysine decarboxylases, although there is no experimental evidence supporting this function.
		As the protein is annotated as a 'possible lysine decarboxylase' (although there does not seem to be experimental evidence supporting this annotation), these negatively charged regions may be the site of lysine (or other substrate) binding.
	honiglab.cpmc.columbia.edu /nesg/VT76/vt76_web.html (433 words)

	newsmessage_view — Annotation Portal
		This will include examples and guides for annotation, but also engineering environments for semantic annotation of unstructured content.
		If this is the first time you have to do with annotation and authoring and you want to know what is meant by this term, you should first read the introduction in our help section.
		If you want to add some content to this portal and you are not registered yet, please register as a new user by sending a request to the Portal Manager.
	annotation.semanticweb.org (214 words)

	Annotation definition - Womens Health and Medical Information on MedicineNet.com
		Annotation: In genetics, the process of identifying the locations and coding regions of genes in a genome and determining what those genes do.
		To annotate (irrespective of the context) is to add a note by way of explanation or commentary.
		Once a genome is sequenced, it needs to be annotated to make sense of it.
	www.medterms.com /script/main/art.asp?articlekey=26317 (174 words)

	Annotation Engine - Berkman Center for Internet & Society
		The Annotation Engine is a set of Perl scripts and a database that allows readers anywhere to add comments to web pages anywhere else.
		The comments, URL, and location pointers are stored in the database here, enabling the Annotation Engine to add them to a page before it is displayed.
		The Annotation Engine is a tool in development.
	cyber.law.harvard.edu /projects/annotate.html (201 words)

	Public Annotation in MaizeGDB
		All public annotations are available to all visitors; the record page for a specific piece of data shows all of the public annotations provided for that record.
		Just log in to the annotation system and visit a record you want to annotate; near the top of that record is a link to add your own annotation (it's just below the name of the record).
		You can return and edit your annotations later, as well as delete ones that are out of date, using the preferences link found on any page on the site (this becomes visible when you log in).
	www.maizegdb.org /annotation.php (309 words)

	Annotation Development Toolkit: Programming Annotation Software, PDF Annotation, Image Annotation Tool, C++ Programming ... (Site not responding. Last check: 2007-10-09)
		When combined with annotation security, the redaction objects provide a means of granting user-level access to parts of an image.
		Annotation objects can be stored as a separate object presentation layer, or can be burned or embedded into the actual image.
		Save an object or group in a file, on the Windows clipboard, as a file in memory (this is useful for database support), or in a database using OLEDB or VB data binding.
	www.leadtools.com /SDK/Document/Document-Annotation.htm (631 words)

	Ruby Annotation (Site not responding. Last check: 2007-10-09)
		This document presents an overview of ruby annotation and defines the markup for it.
		However, this document does not specify any mechanisms for presentation or styling of ruby annotation; this is part of the respective style sheet languages.
		Ruby annotations are used frequently in Japan in many kinds of publications, including books and magazines.
	www.w3.org /TR/ruby (5124 words)

	Linguistic Annotation
		ISO TC37 SC4 is concerned directly with development of a standard linguistic annotation framework that can enable easy interchange and reuse of annotated language resources.
		Recently, a workshop composed of experts from North America, Europe, and Asia produced an outline of a general data model for linguistic annotations and a repository of data categories that will be serve as the core of a proposal for an ISO standard linguistic annotation framework.
		This workshop is intended to follow on and validate this work by soliciting papers from the computational linguistics and language engineering communities that situate current annotation practices with respect to the model as it has developed so far, and identify possible modifications and/or extensions that may be needed to make the standard operable.
	www.cs.vassar.edu /~ide/events/ACL2003-LR (530 words)

	The TIGR Arabidopsis thaliana Genome Annotation Database
		Initial annotation for these sequences, where available, is currently being displayed while we are trying to bring the analysis and annotation up to the format and standard as performed for TIGR-generated sequences.
		The Program to Assemble Spliced Alignments (PASA) and associated annotation pipeline was developed and employed towards the improvement of the Arabidopsis genome annotation by incorporating full-length cDNAs and ESTs into gene structures.
		TIGR's Annotation routine A description on the analysis and annotation performed on the Arabidopsis genomic sequence.
	www.tigr.org /tdb/e2k1/ath1/ath1.shtml (489 words)

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