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BrainML Model: "brainmetal"
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This is a tabular description of the entities and fields
making up the "brainmetal"
data model. Regular expression notation is used to indicate
quantities -- i.e., '?' following a term means 0 or 1
occurrence, '*' means 0 or more occurrences, '+' means 1 or
more occurrences, and no following character means exactly 1
occurrence.
Fields with names in (parentheses) are attributes in the XML; all
others are subelements with text content. The term "ANY" under
'Contains:' means an element can contain any other element as
content. This description is
also available in XML format.
| This schema specifies top-level elements that BrainML elements should inherit
from, and utility elements to be used by BrainML schemas and/or instance
documents. Included are:
- the Quintessence elements, abstract top-level data "classes"
- a 'link' element for linking between quintessence elements, both within
and between documents, and for referencing external resources such as
journal article PDFs
- a 'unit' element which supports reference to unit definitions defined
in instance documents conforming to the "units" schema
- a 'vocab' element which supports reference to term declarations in
instance documents conforming to the "vocabulary" schema
- utility complex data type elements
- [temporary] elements defining the structure of a data submission, so that
instance documents can be validated directly against this.. these will be
moved to one or more "brainml" schemas defining document types for exchange | | Depends on models: (none) | | Index of Entities | |
| | (dimensions) | token | Describes the dimensions of the dataset, as a space-separated list
consisting of numbers or "*". Each number indicates the number of
values the dataset contains on a dimension. Thus, a one-dimensional
dataset such as a time series will have just one number -- the length
of the time series. A two-dimensional dataset such as a grid of values
has two numbers -- the sizes of the X and Y axes of the grid.
Alternatively, two numbers may be used to indicate a number of tuples
and the length of each tuple. (Containing element should specify which
usage is valid.) For example, "* 2" indicates a list of ordered pairs.
Non-rectangular or unknown length data is accomodated through use of the
special '*' value.
A list of five time series, each of a different length, would have
dimensions "5 *". Each individual time series entry contained under this
would have its own dimensions entry of a single number giving its length. | | (type) | token | The data type of this data set. Valid values are integer, decimal, and
string. Integer and decimal types can be of arbitrary size and
precision, however BrainML applications MAY process these as 4-byte
signed integers, and 8-byte IEEE doubles respectively. Strings are in
whatever encoding the XML document itself declares. |
|
| | (delimiter)? | short text | Character(s) used to delimit individual data values. | | (group)? | short text | Characters used to delimit dimensional groups in the dataset. The left
and right delimiters should be given, as in "()". Group delimiters are
required to express multi-dimensional nonrectangular datasets. For
example, an integer dataset with dimensions "2 *" might be expressed
as '(23,25,29) (25,26)'. | | (dimensions) | token | Describes the dimensions of the dataset, as a space-separated list
consisting of numbers or "*". Each number indicates the number of
values the dataset contains on a dimension. Thus, a one-dimensional
dataset such as a time series will have just one number -- the length
of the time series. A two-dimensional dataset such as a grid of values
has two numbers -- the sizes of the X and Y axes of the grid.
Alternatively, two numbers may be used to indicate a number of tuples
and the length of each tuple. (Containing element should specify which
usage is valid.) For example, "* 2" indicates a list of ordered pairs.
Non-rectangular or unknown length data is accomodated through use of the
special '*' value.
A list of five time series, each of a different length, would have
dimensions "5 *". Each individual time series entry contained under this
would have its own dimensions entry of a single number giving its length. | | (type) | token | The data type of this data set. Valid values are integer, decimal, and
string. Integer and decimal types can be of arbitrary size and
precision, however BrainML applications MAY process these as 4-byte
signed integers, and 8-byte IEEE doubles respectively. Strings are in
whatever encoding the XML document itself declares. |
|
| | (dimensions) | token | Describes the dimensions of the dataset, as a space-separated list
consisting of numbers or "*". Each number indicates the number of
values the dataset contains on a dimension. Thus, a one-dimensional
dataset such as a time series will have just one number -- the length
of the time series. A two-dimensional dataset such as a grid of values
has two numbers -- the sizes of the X and Y axes of the grid.
Alternatively, two numbers may be used to indicate a number of tuples
and the length of each tuple. (Containing element should specify which
usage is valid.) For example, "* 2" indicates a list of ordered pairs.
Non-rectangular or unknown length data is accomodated through use of the
special '*' value.
A list of five time series, each of a different length, would have
dimensions "5 *". Each individual time series entry contained under this
would have its own dimensions entry of a single number giving its length. | | (type) | token | The data type of this data set. Valid values are integer, decimal, and
string. Integer and decimal types can be of arbitrary size and
precision, however BrainML applications MAY process these as 4-byte
signed integers, and 8-byte IEEE doubles respectively. Strings are in
whatever encoding the XML document itself declares. | | (formatType) | short text | A short string describing the format of the referenced unit. This could
be a MIME string if such exists for this data type. | | (formatRef) | uri | A URL to a specification or description of the format of the referenced
unit. | | (info)? | long text | Any required additional information describing this file or its relation to
others in this dataset may go here. |
|
| | (dimensions) | token | Describes the dimensions of the dataset, as a space-separated list
consisting of numbers or "*". Each number indicates the number of
values the dataset contains on a dimension. Thus, a one-dimensional
dataset such as a time series will have just one number -- the length
of the time series. A two-dimensional dataset such as a grid of values
has two numbers -- the sizes of the X and Y axes of the grid.
Alternatively, two numbers may be used to indicate a number of tuples
and the length of each tuple. (Containing element should specify which
usage is valid.) For example, "* 2" indicates a list of ordered pairs.
Non-rectangular or unknown length data is accomodated through use of the
special '*' value.
A list of five time series, each of a different length, would have
dimensions "5 *". Each individual time series entry contained under this
would have its own dimensions entry of a single number giving its length. | | (type) | token | The data type of this data set. Valid values are integer, decimal, and
string. Integer and decimal types can be of arbitrary size and
precision, however BrainML applications MAY process these as 4-byte
signed integers, and 8-byte IEEE doubles respectively. Strings are in
whatever encoding the XML document itself declares. | | datum* | token | A single data point, possibly multi-dimensional. |
|
| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
|
| | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | (href) | uri | Reference to linked resource; should be a URL or URN. | | (role)? | uri | Should be a URL referring to a relation defined in a file conforming to
"relations.xsd". | | (dest)? | uri | If this is a link to another BrainML element (not an external resource),
the definition of this element is given here, in the form
URI,element, as in "urn:bml/brainml.org:internal/BrainML/1,experiment". |
|
| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
|
| container: (none) | contains: (none) | | inherits: (none) | links: (none) |
| | (name)? | token | (Optional) Name of the unit (excluding hierarchical context). | | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| container: (none) | contains: (none) | | inherits: (none) | links: (none) |
| | (domain)? | token | Domain of applicability for the term (including hierarchical context). | | (term)? | token | Name of the term (including hierarchical context). | | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
|
| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
|
| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
|
| | (id) | token | | | (name)? | token | Optional name for the collection. | | (ordered)? | boolean | Order of contents may be ignored unless present and set to "true". |
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BrainML Model: "units"
|
This is a tabular description of the entities and fields
making up the "units"
data model. Regular expression notation is used to indicate
quantities -- i.e., '?' following a term means 0 or 1
occurrence, '*' means 0 or more occurrences, '+' means 1 or
more occurrences, and no following character means exactly 1
occurrence.
Fields with names in (parentheses) are attributes in the XML; all
others are subelements with text content. The term "ANY" under
'Contains:' means an element can contain any other element as
content. This description is
also available in XML format.
| This schema specifies the format for unit definitions. Definitions occur
in special-purpose documents containing nothing else, that are made
accessible on the internet. BrainML instance documents may refer to these
by use of a 'unit' element that is defined in the main brainml schema.
They may NOT define units themselves. If a unit needs to be added, a schema
authority should submit a unit definitions document to the schema repository. | | Depends on models: (none) | | Index of Entities | |
| | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| | (id) | token | This is the identifier by which the unit will be referenced. Valid
characters in identifiers are ONLY letters, numbers, underscore,
period, and dash, and an identifier cannot start with a number. The
identifier for a domain should be unique within its containing document
among both domains and terms. | | class | token | Quantity measured by unit. E.g., "electric-potential". | | symbol | short text | Symbol used for unit. E.g., "kg". |
|
| | base-name | token | Stem of unit name (e.g., "gram", "meter"). | | prefix? | token | Power-of-ten prefix (e.g., "kilo", "centi"). |
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BrainML Model: "relations"
|
This is a tabular description of the entities and fields
making up the "relations"
data model. Regular expression notation is used to indicate
quantities -- i.e., '?' following a term means 0 or 1
occurrence, '*' means 0 or more occurrences, '+' means 1 or
more occurrences, and no following character means exactly 1
occurrence.
Fields with names in (parentheses) are attributes in the XML; all
others are subelements with text content. The term "ANY" under
'Contains:' means an element can contain any other element as
content. This description is
also available in XML format.
| This schema specifies the format for lists of allowable relations.
Lists occur in special-purpose documents containing nothing else,
that are made accessible on the internet. BrainML links
documents may refer to these by use of an 'xlink:role' attribute that is
defined in the main brainmetal schema. They may NOT define relations
themselves. If terms need to be added, a schema authority should
submit a relation definitions document to the schema repository.
Relation definitions are a bit simpler than term definitions -- there is
no domain, and hierarchy is available but not often used. | | Depends on models: (none) | | Index of Entities | |
| | (id) | token | This is the identifier by which the relation will be referenced. Valid
characters in identifiers are ONLY letters, numbers, underscore,
period, and dash, and an identifier cannot start with a number. The
identifier for a relation should be unique within its containing document. |
|
| container: relation | contains: (none) | | inherits: (none) | links: (none) |
| | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| container: relation | contains: (none) | | inherits: (none) | links: (none) |
| | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| container: (none) | contains: relation+ | | inherits: (none) | links: (none) |
|
BrainML Model: "vocabulary"
|
This is a tabular description of the entities and fields
making up the "vocabulary"
data model. Regular expression notation is used to indicate
quantities -- i.e., '?' following a term means 0 or 1
occurrence, '*' means 0 or more occurrences, '+' means 1 or
more occurrences, and no following character means exactly 1
occurrence.
Fields with names in (parentheses) are attributes in the XML; all
others are subelements with text content. The term "ANY" under
'Contains:' means an element can contain any other element as
content. This description is
also available in XML format.
| This schema specifies the format for vocabulary lists. Lists occur
in special-purpose documents containing nothing else, that are made
accessible on the internet. BrainML instance documents may refer to these
by use of a 'vocab' element that is defined in the main BrainMetaL schema.
They may NOT define vocabulary themselves. If terms need to be added,
a schema authority should submit a vocabulary definitions document to the
schema repository. | | Depends on models: (none) | | Index of Entities | |
| container: domain, term | contains: (none) | | inherits: (none) | links: (none) |
| | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| container: term | contains: (none) | | inherits: (none) | links: (none) |
| | (href) | uri | Reference to linked resource; should be a URL or URN. |
|
| container: (none) | contains: domain+ | | inherits: (none) | links: (none) |
|
| | (id) | token | This is the identifier by which the domain will be referenced. Valid
characters in identifiers are ONLY letters, numbers, underscore,
period, and dash, and an identifier cannot start with a number. The
identifier for a domain should be unique within its containing document
among both domains and terms. By convention, this ID should be an
underscore followed by a number beginning with 1,2,3, or 4. This
should be added automatically by the VocabConverter tool, and if you
are hand-editing a file just put "_". | | (name) | token | This is the simple name of the domain, without any hierarchy or context. | | (description)? | token | Description of the domain's meaning and intended usage. (Optional) |
|
| | (id) | token | This is the identifier by which the term will be referenced. Valid
characters in identifiers are ONLY letters, numbers, underscore,
period, and dash, and an identifier cannot start with a number. The
identifier for a term should be unique within its containing document
among both domains and terms. By convention, this ID should be an
underscore followed by a number beginning with 5,6,7 or 8. This
should be added automatically by the VocabConverter tool, and if you
are hand-editing a file just put "_". | | (name) | token | This is the simple name of the term, without any hierarchy or context. | | (description)? | token | Description of the term's meaning and intended usage. (Optional) |
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BrainML Model: "citation"
|
This is a tabular description of the entities and fields
making up the "citation"
data model. Regular expression notation is used to indicate
quantities -- i.e., '?' following a term means 0 or 1
occurrence, '*' means 0 or more occurrences, '+' means 1 or
more occurrences, and no following character means exactly 1
occurrence.
Fields with names in (parentheses) are attributes in the XML; all
others are subelements with text content. The term "ANY" under
'Contains:' means an element can contain any other element as
content. This description is
also available in XML format.
| This schema specifies the format for citations, which come under the
"reference" quintessence element.
Two top-level citation tags are defined. The first is a BrainML-specific
format, defining tags for journal articles, book chapters, and books.
The second allows the use of external citation schemas such as bibtex-ml.
It acts as a container for tags from these external schemas, but allows
some standard tags from the BrainML format as well. | | Depends on models: (none) | | Index of Entities | |
| | (type) | token | Declares the type of material being cited. Valid values are "article",
"chapter", or "book". | | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
|
| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
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| container: reference_element, method_element, citation_external, author, citation, editor, person_full, model_element, entity_element, data_element, person, collection | contains: (none) | | inherits: (none) | links: (none) |
| | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | (href) | uri | Reference to linked resource; should be a URL or URN. | | (role)? | uri | Should be a URL referring to a relation defined in a file conforming to
"relations.xsd". | | (dest)? | uri | If this is a link to another BrainML element (not an external resource),
the definition of this element is given here, in the form
URI,element, as in "urn:bml/brainml.org:internal/BrainML/1,experiment". |
|
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | initials? | short text | Initials of name (use instead of first/middle). | | first? | short text | First given name. | | middle? | short text | Second and subsequent given names. | | prelast? | short text | Prefix such as "van" or "von der". | | last | short text | Surname. | | lineage? | short text | Suffixes such as "Jr.", "III". | | email? | short text | Email address. | | phone? | short text | Phone number, including international dialing codes. | | institution? | short text | Institution or company where researcher works. | | homepage? | short text | Home page of researcher, lab, or institution. |
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| container: (none) | contains: link* | | inherits: (none) | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. |
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| | (type) | token | Declares the type of material being cited. Valid values are "article",
"chapter", or "book". | | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | title | short text | Title of work being cited (article, chapter, or book). | | year | integer | Year of publication. | | journal? | short text | Journal (abbreviation preferred) an article is published in. | | volume? | short text | Volume of journal an article is published in. | | pubmedID? | integer | PubMed numerical ID (PMID) of an article. | | collection_title? | short text | Title for book or proceedings volume an article is in. | | pages? | short text | Page range of an article or chapter. | | publisher? | short text | Publisher (not required for journals). |
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| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | initials? | short text | Initials of name (use instead of first/middle). | | first? | short text | First given name. | | middle? | short text | Second and subsequent given names. | | prelast? | short text | Prefix such as "van" or "von der". | | last | short text | Surname. | | lineage? | short text | Suffixes such as "Jr.", "III". | | email? | short text | Email address. | | phone? | short text | Phone number, including international dialing codes. | | institution? | short text | Institution or company where researcher works. | | homepage? | short text | Home page of researcher, lab, or institution. |
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| container: (none) | contains: link* | | inherits: person | links: (none) |
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | initials? | short text | Initials of name (use instead of first/middle). | | first? | short text | First given name. | | middle? | short text | Second and subsequent given names. | | prelast? | short text | Prefix such as "van" or "von der". | | last | short text | Surname. | | lineage? | short text | Suffixes such as "Jr.", "III". | | email | short text | Email address. | | phone | short text | Phone number, including international dialing codes. | | institution | short text | Institution or company where researcher works. | | homepage? | short text | Home page of researcher, lab, or institution. |
|
| | (id)? | token | This attribute is needed so that others may link to it. | | (base)? | uri | See http://www.w3.org/TR/xmlbase/ for
information about this attribute. | | initials? | short text | Initials of name (use instead of first/middle). | | first? | short text | First given name. | | middle? | short text | Second and subsequent given names. | | prelast? | short text | Prefix such as "van" or "von der". | | last | short text | Surname. | | lineage? | short text | Suffixes such as "Jr.", "III". | | email? | short text | Email address. | | phone? | short text | Phone number, including international dialing codes. | | institution? | short text | Institution or company where researcher works. | | homepage? | short text | Home page of researcher, lab, or institution. |
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