Filename: omicsbdml.xsd * Description: XML Schema for OmicsBDML version 1.0.
Author(s): Koji Kyoda, Yukako Tohsato, Kenneth H. L. Ho, Shuichi Onami
UnitKind represents unit of numerical value in the data.
It is based on the definition of the SBML schema (Hucka et al., 2003).
tUnitKind represents unit of time.
BasedOn indicates whether data was produced from an in vivo measurement or from a computer simulation.
UUIDType represents a universally unique identifier (http://tools.ietf.org/html/rfc4122).
Info describes the content of the OmicsBDML file.
Each OmicsBDML file has a unique identifier, which is used to identify the file in sharing and exchange.
License information such as the Creative Commons licenses (http://creativecommons.org/licenses/) should be explicitly indicated
so that unnecessary conflict can be avoided.
Affiliation describes the affiliation of a person in the OmicsBDML file.
E-mail address of the person should be listed, and physical address can be listed.
Person describes detailed information of a person of the OmicsBDML file.
First and last name should be listed. ORCID and affiliation can be listed.
A list of contributors should be described.
Summary provides a concise description of the quantitative data in the OmicsBDML file.
A targeted organism should be provided based on the NCBI taxonomy definition (http://www.ncbi.nlm.nih.gov/taxonomy).
A localID can be used to link the omicsbdmlID of the OmicsBDML file to an internal identifier name in each author or laboratory.
Detailed information of original published paper and/or database can be included.
Contact describes the corresponding author(s) of the OmicsBDML file.
Methods describes procedures used for reproducing spatiotemporal numerical data in the OmicsBDML file.
ScaleUnit indicates scale and unit of coordinates and time.
The scale factor of x, y, z dimensions, and time can be separately defined.
If data only have x and y dimensions, the scale factor of z dimension should be set to zero.
The unit of coordinates and time should be selected from the units predefined in tUnitKind.
Object specifies types of object that is detected from microscope images used in
an in vivo measurement or from the result of a computer simulation.
The number of object is unlimited because the dynamics of more than one object can be obtained from
the in vivo measurement or from the simulation.
XYZ represents three-dimensional coordinates.
Point is used when an object is described as a set of points.
The X, Y, and Z position of the cuboid's western, southern, and highest side, respectively
The cuboid's width
The cuboid's depth
The cuboid's height
Measurement represents spatial information of objects.
Each measurement corresponds to coordinates of position for each object.
Component describes a collection of objects and their spatial information at a given point of time.
Each component must be separated by time (e.g. time frame); therefore it must contain the time element.
It also has a unique identifier, componentID.
A prevID can be used optionally to define a reference or connectivity with another component from a previous time.
Each component requires at least one measurement to describe spatial information of objects.
Data contains spatiotemporal numerical data of biological dynamics.
It has four sub-elements ScaleUnit, Object, Feature and Component.
Series is used to separate data into a series of data files
which are obtained from the same experiment or simulation.
Set is used to represent a set of data files which are referenced in the same article.
omicsbdmlDocument consists of 5 top-level elements (Info, Summary, Contact, Methods, and Data).
There is the optional elements Series and Set, which can be used instead of the Data element.