Element Accession is used to capture the local part in a sequence identifier (e.g. 'P17304'
in 'UniProtKB:P17304', in which case the 'source' attribute would be 'UniProtKB').
The annotation of a molecular sequence. It is recommended to annotate by using the optional
'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270',
'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'). Optional element 'desc' allows for a free text
description. Optional element 'confidence' is used to state the type and value of support for a annotation.
Similarly, optional attribute 'evidence' is used to describe the evidence for a annotation as free text
(e.g. 'experimental'). Optional element 'property' allows for further, typed and referenced annotations from
external resources.
Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree.
The parent branch length of a clade can be described either with the 'branch_length' element or the
'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the
'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate
the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications
at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including
parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub
clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level).
A general purpose confidence element. For example this can be used to express the bootstrap
support value of a clade (in which case the 'type' attribute is 'bootstrap').
A date associated with a clade/node. Its value can be numerical by using the 'value' element
and/or free text with the 'desc' element' (e.g. 'Silurian'). If a numerical value is used, it is recommended
to employ the 'unit' attribute to indicate the type of the numerical value (e.g. 'mya' for 'million years
ago'). The elements 'minimum' and 'maximum' are used the indicate a range/confidence
interval
The geographic distribution of the items of a clade (species, sequences), intended for
phylogeographic applications. The location can be described either by free text in the 'desc' element and/or
by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by
'Polygons'.
Element 'mol_seq' is used to store molecular sequences. The 'is_aligned' attribute is used
to indicated that this molecular sequence is aligned with all other sequences in the same phylogeny for
which 'is aligned' is true as well (which, in most cases, means that gaps were introduced, and that all
sequences for which 'is aligned' is true must have the same length).
Element Phylogeny is used to represent a phylogeny. The required attribute 'rooted' is used
to indicate whether the phylogeny is rooted or not. The attribute 'rerootable' can be used to indicate that
the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent
data, such as gene duplications). The attribute 'type' can be used to indicate the type of phylogeny (i.e.
'gene tree'). It is recommended to use the attribute 'branch_length_unit' if the phylogeny has branch
lengths. Element clade is used in a recursive manner to describe the topology of a phylogenetic
tree.
'phyloxml' is the name of the root element. Phyloxml contains an arbitrary number of
'phylogeny' elements (each representing one phylogeny) possibly followed by elements from other namespaces.
The coordinates of a point with an optional altitude (used by element 'Distribution').
Required attributes are the 'geodetic_datum' used to indicate the geodetic datum (also called 'map datum',
for example Google's KML uses 'WGS84'). Attribute 'alt_unit' is the unit for the altitude (e.g. 'meter').
Property allows for typed and referenced properties from external resources to be attached
to 'Phylogeny', 'Clade', and 'Annotation'. The value of a property is its mixed (free text) content.
Attribute 'datatype' indicates the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string',
'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:date', 'xsd:anyURI'). Attribute
'applies_to' indicates the item to which a property applies to (e.g. 'node' for the parent node of a clade,
'parent_branch' for the parent branch of a clade). Attribute 'id_ref' allows to attached a property
specifically to one element (on the xml-level). Optional attribute 'unit' is used to indicate the unit of
the property. An example: <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade"
unit="METRIC:m"> 200 </property>
To represent an individual domain in a domain architecture. The name/unique identifier is
described via the 'id' attribute. 'confidence' can be used to store (i.e.) E-values.
Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated
with a node. 'symbol' is a short (maximal ten characters) symbol of the sequence (e.g. 'ACTM') whereas
'name' is used for the full name (e.g. 'muscle Actin'). 'location' is used for the location of a sequence on
a genome/chromosome. The actual sequence can be stored with the 'mol_seq' element. Attribute 'type' is used
to indicate the type of sequence ('dna', 'rna', or 'protein'). One intended use for 'id_ref' is to link a
sequence to a taxonomy (via the taxonomy's 'id_source') in case of multiple sequences and taxonomies per
node.
This is used to express a typed relationship between two sequences. For example it could be
used to describe an orthology (in which case attribute 'type' is 'orthology').
Element Taxonomy is used to describe taxonomic information for a clade. Element 'code' is
intended to store UniProt/Swiss-Prot style organism codes (e.g. 'APLCA' for the California sea hare 'Aplysia
californica') or other styles of mnemonics (e.g. 'Aca'). Element 'authority' is used to keep the authority,
such as 'J. G. Cooper, 1863', associated with the 'scientific_name'. Element 'id' is used for a unique
identifier of a taxon (for example '6500' with 'ncbi_taxonomy' as 'provider' for the California sea hare).
Attribute 'id_source' is used to link other elements to a taxonomy (on the xml-level).
A uniform resource identifier. In general, this is expected to be an URL (for example, to
link to an image on a website, in which case the 'type' attribute might be 'image' and 'desc' might be
'image of a California sea hare').
value comes from list: {'xsd:string'|'xsd:boolean'|'xsd:decimal'|'xsd:float'|'xsd:double'|'xsd:duration'|'xsd:dateTime'|'xsd:time'|'xsd:date'|'xsd:gYearMonth'|'xsd:gYear'|'xsd:gMonthDay'|'xsd:gDay'|'xsd:gMonth'|'xsd:hexBinary'|'xsd:base64Binary'|'xsd:anyURI'|'xsd:normalizedString'|'xsd:token'|'xsd:integer'|'xsd:nonPositiveInteger'|'xsd:negativeInteger'|'xsd:long'|'xsd:int'|'xsd:short'|'xsd:byte'|'xsd:nonNegativeInteger'|'xsd:unsignedLong'|'xsd:unsignedInt'|'xsd:unsignedShort'|'xsd:unsignedByte'|'xsd:positiveInteger'}
value comes from list: {'domain'|'kingdom'|'subkingdom'|'branch'|'infrakingdom'|'superphylum'|'phylum'|'subphylum'|'infraphylum'|'microphylum'|'superdivision'|'division'|'subdivision'|'infradivision'|'superclass'|'class'|'subclass'|'infraclass'|'superlegion'|'legion'|'sublegion'|'infralegion'|'supercohort'|'cohort'|'subcohort'|'infracohort'|'superorder'|'order'|'suborder'|'superfamily'|'family'|'subfamily'|'supertribe'|'tribe'|'subtribe'|'infratribe'|'genus'|'subgenus'|'superspecies'|'species'|'subspecies'|'variety'|'subvariety'|'form'|'subform'|'cultivar'|'unknown'|'other'}
The XML Instance Representation table above shows the schema component's content as an XML instance.
The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].
Model group information are shown in gray, e.g. Start Choice ... End Choice.
For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in bold.
If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".
Otherwise, the type of the element/attribute is displayed.
If the element/attribute's type is in the schema, a link is provided to it.
For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<pattern = [1-9][0-9]{3}>>.
If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.
Abstract(Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.
Collapse Whitespace PolicyReplace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.
Disallowed Substitutions(Applies to element declarations). If substitution is specified, then substitution group members cannot be used in place of the given element declaration to validate element instances. If derivation methods, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an xsi:type attribute.
Nillable(Applies to element declarations). If an element declaration is nillable, instances can use the xsi:nil attribute. The xsi:nil attribute is the boolean attribute, nil, from the http://www.w3.org/2001/XMLSchema-instance namespace. If an element instance has an xsi:nil attribute set to true, it can be left empty, even though its element declaration may have required content.
Prohibited Derivations(Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.
Prohibited Substitutions(Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.
Replace Whitespace PolicyReplace tab, line feed, and carriage return characters with space character (Unicode character 32).
Substitution GroupElements that are members of a substitution group can be used wherever the head element of the substitution group is referenced.
Substitution Group Exclusions(Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.
Target NamespaceThe target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.