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MIRIAM compliant Annotation in COPASI

This page describes the support of MIRIAM compliant annotation in COPASI. COPASI stores the information in a Resource Description Framework (RDF) graph which is saved in RDF/XML Syntax in the COPASI file. MIRIAM annotation is currently provided for the model, the species, the compartments, the global quantities, the reactions, and the kinetic functions.

Graph

COPASI displays the graph below in the user interface and supports full editing functionality (adding, changing, and deleting).

Supported Graph


User Interface


Supported Predicates

COPASI supports the following predicates (name of edges in the RDF graph).

Terms defined by COPASI

The terms interpreted by COPASI are derived from the MIRIAM Qualifiers found in Biomodels.net. We do not use the qualifiers from Biomodels.net directly since we feel the distinction between model-qualifiers and biology-qualifiers is cumbersome to the user and does not provide any additional information.

The name space for the terms is:
     http://www.copasi.org/RDF/MiriamTerms#

Predicate URI User Interface Definition
 encodes encodes The subject represented by the model component encodes, directly or by transitivity the subject of the referenced resource.
 hasPart has part The subject represented by the model component includes the subject of the referenced resource, either physically or logically. This relation might be used to link a complex to the description of its components.
 hasVersion has version The subject of the referenced resource is a version or an instance of the subject represented by the model component.
 is is The subject represented by the model component is the subject of the referenced resource. This relation might be used to link a reaction to its exact counterpart in KEGG or Reactome for instance.
 isDescribedBy reference The subject represented by the model component is described by the referenced resource. This relation should be used for instance to link a species or a parameter to the literature that describes the concentration of the species or the value of the parameter.
 isEncodedBy is encoded by The subject represented by the model component is encoded, directly, or by transitivity, by the subject of the referenced resource.
 isHomologTo is homolog to The subject represented by the model component is homolog, to the subject of the referenced resource, i.e. they share a common ancestor.
 isPartOf is part of The subject represented by the model component is a physical or logical part of the subject of the referenced resource. This relation might be used to link a component to the description of the complex is belongs to.
 isVersionOf is version of The subject represented by the model component is a version or an instance of the subject of the referenced resource.
 occursIn occurs in The subject represented by the model component takes place in the subject of the reference resource.

The above terms may only refer to resources defined as MIRIAM Resources in Biomodels.net.

Terms defined by VCard

The name space for the terms is:
     http://www.w3.org/2001/vcard-rdf/3.0#

Predicate URI User Interface Definition
 EMAIL Email
 Family Family Name This must be a child of N.
 Given Given Name This must be a child of N.
 N Full Name
 ORG Organization
 Orgname Organization Name This must be a child of ORG.

Terms defined by Dublin Core

The name space for the terms is:
     http://purl.org/dc/terms/

Predicate URI User Interface Definition
 dcterms:creator creator An entity primarily responsible for making the resource.
 dcterms:W3CDTF encoding for dates (hidden) The set of dates and times constructed according to the W3C Date and Time Formats Specification.
 dcterms:created date created Date of creation of the resource.
 dcterms:modified date modified Date on which the resource was changed.
 dcterms:bibliographicCitation bibliographic citation A bibliographic reference for the resource.
 dcterms:description description Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.

COPASI File Format

The schema for Miriam Annotation Element in the CopasiML is shown below
  <xs:element name="MiriamAnnotation" type="cMIRIAM" minOccurs="0"/>

  <xs:complexType name="cMIRIAM" id="copasi.MIRIAM">
    <xs:sequence>
      <xs:any namespace="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
              processContents="skip"/>
    </xs:sequence>
  </xs:complexType>

The Miriam Annotation element may contain any legal RDF/XML Syntax .

SBML Support

Import & Export
COPASI imports and exports SBML annotations in MIRIAM format.




Created by: system. Last Modification: Tuesday 15 of April, 2014 09:02:40 EDT by mendes.