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==Preface==
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<strong>Note:</strong> This page has moved to: https://github.com/rvosa/bio-nexml/wiki/NeXML-API-for-BioRuby
The following document exhaustively covers the NeXML elements. The coverage is purely technical and I have linked to the appropriate schema definitions from the NeXML site for completeness. A knowledge of the XML Schema Definition( XSD ) is unnecessary to read the document. A discussion on the schema design can be found here: [http://nexml.org/nexml/html/doc/schema-1/#discussion NeXML schema discussion]. Note that this documentation is not final yet.
 
 
 
==Root==
 
The root element of NeXML is called <code>nexml</code>. This element is an instance of the [http://nexml.org/nexml/html/doc/schema-1/nexml/#Nexml Nexml] class.
 
 
 
Attributes:
 
* <code>version</code> - a decimal number indicating the nexml schema version. At present this value is 0.8.
 
* <code>generator</code> - an optional attribute, which is used to identify the program that generated the file. The attribute's value is a free form string.
 
 
 
Namespaces: (Where it says "by convention" in the list below, the convention applies to the three-letter prefixes which are free to
 
vary in most cases, not the namespaces themselves):
 
* the xml namespace prefix that identifies xml schema semantics that might be inlined in the file. By convention this is of the format <code>xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"</code> so that parts of schema language used inside nexml (e.g. where a concrete subclass must be specified) are identified by the <code>xsi</code> prefix.
 
* the nexml namespace prefix, by convention of the format <code>xmlns:nex="http://www.nexml.org/1.0"</code>, so that locations where nexml specific types are referenced (e.g. data type subclasses) these are identified by their <code>nex</code> prefix.
 
* the default namespace, <code>xmlns="http://www.nexml.org/1.0"</code>, which is necessary for namespace aware processors (such as the NeXML-to-CDAO xslt stylesheet produced by an EvoInfo subgroup at the Spring 2009 hackathon).
 
* the xml namespace prefix, required to be of the format <code>xmlns:xml="http://www.w3.org/XML/1998/namespace</code>". This may be used, for example, to specify the base address of the document (using the xml:base attribute).
 
 
 
Lastly, to associate the instance document with the nexml schema, it requires an attribute to specify the nexml schema location, and the namespace it applies to. This is of the format <code>xsi:schemaLocation="http://www.nexml.org/1.0 http://www.nexml.org/1.0/nexml.xsd"</code>. Notice that this attribute is a schema language snippet (identified by the xsi:prefix) that identifies a namespace http://www.nexml.org/1.0) and associates it with a physical schema location (http://www.nexml.org/1.0/nexml.xsd).
 
 
 
The root element can be annotated.
 
 
 
==OTUS==
 
OTUS means Organizational Taxonomic Units. The <code>otus</code> element defines a collection of taxon. An <code>otus</code> is an instance of the [http://nexml.org/nexml/html/doc/schema-1/taxa/taxa/#Taxa Taxa] class.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
* <code>label</code> - a human readable description of the otus.
 
 
 
===OTU===
 
An <code>otu</code> element defines a taxon. An <code>otu</code> is an instance of the [http://nexml.org/nexml/html/doc/schema-1/taxa/taxa/#Taxon Taxon] class.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
* <code>label</code> - a human readable
 
* <code>class</code> - takes the id of a class element. This attribute is optional.
 
 
 
==Class==
 
A set is defined in NeXML with a <code>class</code> element. A <code>class</code> is an instance of the [http://nexml.org/nexml/html/doc/schema-1/abstract/#Class Class] class.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
* <code>label</code> - a human readable description of the class. A label is optional.
 
 
 
==Trees==
 
 
 
Trees in NeXML are described following the GraphML syntax by defining nodes and edges using the <code>node</code> and <code>edge</code> element. Phylogenetic tree or network is defined with the <code>tree</code> and <code>network</code> element respectively. A <code>trees</code> element is a conatainer for both tree and network. In a network the in-degree of nodes is lessened, so that a node can have multiple parents.
 
 
 
Attribute:
 
* <code>id</code> - a file level unique id
 
* <code>otus</code> - takes the id of an otus element defined previously
 
* <code>label</code> - a human readable description of the trees. A label is optional.
 
 
 
===Tree===
 
Phylogenetic trees are defined in NeXML with the <code>tree</code> tag. With NeXML two types of tree can be defined: int and float. While an IntTree can only have integer edge length a FloatTree has an IEEE 754-1985 compliant floating point number for its edge length.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
* <code>xsi:type</code> - can be either <code>IntTree</code> or a <code>FloatTree</code>
 
* <code>label</code> - a human readable description of the tree. A label is optional.
 
 
 
With the [http://nexml.org/nexml/html/doc/schema-1/trees/abstracttrees/#AbstractTree AbstractTree] class at the root of the hierarchy the following sub types are defined.
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/tree/#FloatTree FloatTree]
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/tree/#IntTree IntTree]
 
 
 
===Network===
 
Phylogenetic networks are defined with the <code>network</code> tag.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
* <code>xsi:type</code> - can take any of the two values: IntNetwork, FloatNetwork
 
* <code>label</code> - a human readable description of the tree. A label is optional.
 
 
 
A network is modeled by the [http://nexml.org/nexml/html/doc/schema-1/trees/abstracttrees/#AbstractNetwork AbstractNetwork] class and two concrete implementations exist:
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/network/#FloatNetwork FloatNetwork]
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/network/#IntNetwork IntNetwork]
 
 
 
The difference between a float and int network is same as that between a float and an int tree.
 
 
 
===Nodes===
 
A <code>node</code> tag defines a node of a tree or a network. A tree node is modelled by the [http://nexml.org/nexml/html/doc/schema-1/trees/tree/#TreeNode TreeNode] class and a network node by the [http://nexml.org/nexml/html/doc/schema-1/trees/network/#NetworkNode NetworkNode] class; both of which inherit from the [http://nexml.org/nexml/html/doc/schema-1/trees/abstracttrees/#AbstractNode AbstractNode] class.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id.
 
* <code>otu</code> - id of a previously defined otu element. This is optional.
 
* <code>root</code> - takes <code>true</code> if the node is a root node, <code>false</code> otherwise.
 
 
 
The tree is considered rooted, multiply rooted or unrooted based on how many root nodes does it have.
 
 
 
===Edges===
 
An <code>edge</code> tag defines an edge in a tree or a network.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
* <code>source</code> - id of the node to be served as the source
 
* <code>target</code> - id of the node to server as the target
 
* <code>length</code> - length of the edge
 
 
 
Edges can be of the following type based on whether it is defined for a tree( int or float ) or a network( again, int or float ):
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/network/#NetworkFloatEdge NetworkFloatEdge]
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/network/#NetworkIntEdge NetworkIntEdge]
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/tree/#TreeFloatEdge TreeFloatEdge]
 
* [http://nexml.org/nexml/html/doc/schema-1/trees/tree/#TreeIntEdge TreeIntEdge]
 
 
 
==Characters==
 
The <code>characters</code> element defines comparative data. NeXML dictates that the allowed parameter space for the observations be declared with a <code>format</code> element and the actual observation with the <code>matrix</code> element; both nested within the <code>characters</code> element. Two broad observation categories are allowed: raw character sequences and granular character state observations. Under both these categories NeXML provides means of describing observed DNA, RNA, Protein, Restriction, Standard, and Conitnuous data.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id.
 
* <code>otus</code> - takes the id of an otus element defined previously.
 
* <code>xsi:type</code> - can be one of the following: <code>DnaSeqs</code>, <code>DnaCells</code>, <code>RnaSeqs</code>, <code>RnaCells</code>, <code>RestrictionSeqs</code>, <code>RestrictionCells</code>, <code>StandardSeqs</code>, <code>StandardCells</code>, <code>ContinuousSeqs</code>, <code>ContinuousCells</code>.
 
* <code>label</code> - a human readable description of the character block. A label is optional
 
 
 
The [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractBlock AbstractBlock] class is at the root of the <code>characters</code> hierarchy with the following subtypes:
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractSeqs  AbstractSeqs ] - superclass for character blocks that consist of raw character sequences
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DnaSeqs DnaSeqs]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#ProteinSeqs ProteinSeqs]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RnaSeqs RnaSeqs]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionSeqs RestrictionSeqs]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardSeqs StandardSeqs]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousSeqs ContinuousSeqs]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractCells AbstractCells] - superclass for character blocks that consist of granular character state observations
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DnaCells DnaCells]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#ProteinCells ProteinCells]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RnaCells RnaCells]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionCells  RestrictionCells]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardCells StandardCells]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousCells  ContinuousCells]
 
 
 
===Format===
 
The <code>format</code> element defines the the allowed characters and states in a matrix, and their ambiguity mapping. Within <code>format</code> is enclosed <code>states</code> and <code>char</code> definition.
 
 
 
Attributes: none.
 
 
 
<code>format</code> is modeled by the [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractFormat AbstractFormat] type with the following concrete types:
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAFormat AAFormat]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousFormat ContinuousFormat]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAFormat DNAFormat]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAFormat RNAFormat]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionFormat RestrictionFormat]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardFormat StandardFormat]
 
 
 
Atleast one <code>states</code> element must be defined for any type of <code>format</code> except <code>ContinuousFormat</code>. <code>char</code> must be defined for all type of <code>format</code>.
 
 
 
====states====
 
<code>states</code> is a container for defined states and their mappings. A <code>states</code> can have zero or more <code>state</code>, <code>uncertain_state_set</code>, <code>polymorphic_state_set</code> elements.
 
 
 
Attributes:
 
* <code>id</code> - a file level unique id
 
 
 
With [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractStates AbstractStates] class at the root of the hierarchy <code>states</code> can take up one of the following concrete implementations based on the type of <code>format</code>
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAStates AAStates]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAStates DNAStates]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAStates RNAStates]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionStates RestrictionStates]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardStates StandardStates]
 
 
 
The type of <code>states</code> depends on the type of its parent <code>format</code>. Continuous data is stateless, hence there is no <code>states</code> type corresponding to it. Restriction data implies only two states: presence( 1 ) or absence( 0 ). Naturally, two( and only two ) <code>state</code> are defined for the <code>RestrictionStates</code> type. All other types may have zero or more <code>state</code> defined for them.
 
 
 
=====state=====
 
<code>state</code> defines a possible observation state with its <code>symbol</code> attribute.
 
 
 
Attributes:
 
* id - a file level unique id
 
* symbol - a simple type that restricts from [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractSymbol AbstractSymbol]
 
 
 
<code>state</code> is of the [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractState AbstractState] type. A <code>state</code> can be of the following kind depending on the type of the parent <code>states</code> element:
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAState AAState] - takes a [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAToken AAToken] for <code>symbol</code>
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAState  DNAState] - takes a [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAToken DNAToken] for <code>symbol</code>
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAState  RNAState] - takes a [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAToken RNAToken] for <code>symbol</code>
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionState RestrictionState] - takes a [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionToken RestrictionToken] for <code>symbol</code>
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardState StandardState] - takes a [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardToken StandardToken] for <code>symbol</code>
 
 
 
=====polymorphic_state_set=====
 
[http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractPolymorphicStateSet AbstractPolymorphicStateSet]
 
=====uncertain_state_set=====
 
[http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractUncertainStateSet AbstractUncertainStateSet]
 
 
 
====char====
 
A <code>char</code> specifies which <code>states</code> apply to which matrix columns. A <code>char</code> is of the [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractChar AbstractChar] type.
 
 
 
Depending on the type of the parent <code>format</code> element, a <code>char</code> can be an instance of the following type:
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAChar AAChar]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousChar ContinuousChar]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAChar DNAChar]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAChar RNAChar]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionChar RestrictionChar]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardChar StandardChar]
 
 
 
Attributes:
 
With the type of the char in place, a char can take one or more of the following attributes:
 
* <code>id</code> - a file level unique id is a must for all the char elements
 
* <code>states</code> - the value being the id of a pre defined states element. Except the ContinuousChar type all chars take a states attribute.
 
* <code>codon</code> - specify the codon position. DnaChar and RnaChar optionally take the codon attribute.
 
 
 
===Matrix===
 
A <code>matrix</code> element holds the state observations. One or more <code>row</code> can be defined in a <code>matrix</code>. Depending on the characters type, matrix element can  be of 2 abstract types each with 6 concrete type.
 
 
 
*[http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractSeqMatrix AbstractSeqMatrix] - contains row which hold raw character sequences
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AASeqMatrix AASeqMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousSeqMatrix ContinuousSeqMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNASeqMatrix DNASeqMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNASeqMatrix RNASeqMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionSeqMatrix RestrictionSeqMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardSeqMatrix StandardSeqMatrix]
 
*[http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractObsMatrix AbstractObsMatrix] - contains rows which hold granular state observations
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAObsMatrix AAObsMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousObsMatrix ContinuousObsMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAObsMatrix DNAObsMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAObsMatrix RNAObsMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionObsMatrix RestrictionObsMatrix]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardObsMatrix StandardObsMatrix]
 
 
 
Attributes: none
 
 
 
====Row====
 
The <code>row</code> element defines a single row of a <code>matrix</code>.
 
 
 
Attributes:
 
* id - a file level unique id
 
* label - a human readable description of the row. A label is optional.
 
* otu - takes the id of an otu defined previously
 
 
 
Just like its parent matrix, row can be of two abstract types each with 6 concrete type.
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractSeqRow AbstractSeqRow] - A <code>seq</code> element must be defined for each row with raw character data.
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAMatrixSeqRow AAMatrixSeqRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousMatrixSeqRow ContinuousMatrixSeqRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAMatrixSeqRow DNAMatrixSeqRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAMatrixSeqRow RNAMatrixSeqRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionMatrixSeqRow RestrictionMatrixSeqRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardMatrixSeqRow StandardMatrixSeqRow]
 
* [http://nexml.org/nexml/html/doc/schema-1/characters/abstractcharacters/#AbstractObsRow AbstractObsRow] - One or more <code>cell</code> is defined for each row corresponding to multiple observations.
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/protein/#AAMatrixObsRow AAMatrixObsRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/continuous/#ContinuousMatrixObsRow ContinuousMatrixObsRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/dna/#DNAMatrixObsRow DNAMatrixObsRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/rna/#RNAMatrixObsRow RNAMatrixObsRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/restriction/#RestrictionMatrixObsRow RestrictionMatrixObsRow]
 
** [http://nexml.org/nexml/html/doc/schema-1/characters/standard/#StandardMatrixObsRow StandardMatrixObsRow]
 
 
 
=====seq=====
 
=====cell=====
 
 
 
==Semantic Annotation==
 
Fundamental data objects in NeXML can be annotated using RDFa. This way, the annotationsare directly available to any off-the-shelf RDFa parser but are also simple to integrate into non- RDF-aware processing libraries. The annotations are expressed using recursively nested meta elements, and are essentially triples whose subjects are identified by the about attribute. To specify that a NeXML element such as a tree is the subject, the about attribute and the id attribute of the element must match. This way, core NeXML elements can be converted to RDF (for example by using an XSL stylesheet), RDFa annotations can be extracted from the NeXML (using another stylesheet), and the two resulting graphs can be aligned by the subjects of their respective triples.
 
 
 
* If the triple’s object value is a literal such as a string or a number, the exact data type is specified by the datatype attribute; these types are typically core XML schema types such as xsd:string for atomic types, or rdf:Literal for nested XML element structures that are to be parsed as opaque literals in an RDF graph. The object value is enclosed inside the meta element and the predicate is specified using the property attribute (whose value must be a CURIE). meta elements of this type are of the subclass nex:LiteralMeta.
 
* If the triple’s object value is a remote resource, its location is specified using the href attribute. The predicate for this class of triples is specified as a CURIE using the rel attribute. meta elements of this type are of the subclass nex:ResourceMeta.
 
* If the triple’s object value is a nested annotation, its predicate is specified as a CURIE using the rel attribute. Since this enclosing meta element is to be transformed into an anonymous RDF node, it needs to be identified as the subject of a reification by assigning it an about attribute (as per the RFa rules for identifying triple subjects).
 
  
 
[[Category:NeXML and RDF API for BioRuby]]
 
[[Category:NeXML and RDF API for BioRuby]]

Latest revision as of 19:04, 22 September 2011

Note: This page has moved to: https://github.com/rvosa/bio-nexml/wiki/NeXML-API-for-BioRuby