BioModels.net qualifiers

Table of Contents

• Introduction
• List of qualifiers
• Download the list
• How to use them

The qualification of an annotation is important to grasp the relation between a model component and its annotation. The relationships is rarely one-to-one, and the information content of an annotation is greatly increased if one knows what it represents rather than to know it is "related to".

The qualifier of an annotation should reflect the relationships between the biological objects represented by the model element and the annotation:

For more information about the BioModels.net qualifiers, please refer to http://biomodels.net/qualifiers/.

model-qualifiers

Qualifiers for the modelling object represented by the model component.

If you use these qualifiers in a XML based format, please use the following namespace: http://biomodels.net/model-qualifiers/.

is

The modelling object represented by the model component is the subject of the referenced resource. For instance, this qualifier might be used to link the encoded model to a database of models.

isDerivedFrom

The modelling object represented by the component of the encoded model is derived from the modelling object represented by the referenced resource. For instance, they can be the fruit of a refinement or their adaptation for usage in a different context.

isDescribedBy

The modelling object represented by the component of the encoded model is described by the referenced resource. This relation might be used to link a model or a kinetic law to the literature that describes this model or this kinetic law.

biology-qualifiers

Qualifiers for the biological object represented by the model component.

If you use these qualifiers in a XML based format, please use the following namespace: http://biomodels.net/biology-qualifiers/.

encodes

The biological entity represented by the model component encodes, directly or by transitivity the subject of the referenced resource.

hasPart

The biological entity 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.

hasProperty

The subject of the referenced resource is a property of the biological entity represented by the model component. This relation might be used when a biological entity has a given activity or exerts a specific function.

hasVersion

The subject of the referenced resource is a version or an instance of the biological entity represented by the model component.

is

The biological entity 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

The biological entity 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

The biological entity represented by the model component is encoded, directly, or by transitivity, by the subject of the referenced resource.

isHomologTo

The biological entity represented by the model component is homologous to the subject of the referenced resource, i.e. they share a common ancestor.

isPartOf

The biological entity 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.

isPropertyOf

The biological entity represented by the model component is a property of the referenced resource.

isVersionOf

The biological entity represented by the model component is a version or an instance of the subject of the referenced resource.

occursIn

The biological entity represented by the model component takes place in the subject of the reference resource.

Download the qualifiers

If you need the list of BioModels.net qualifiers in a computer readable format, you can download the whole list in different formats.

• XML (this is generated on demand)
• XML Schema

• RDF Beta

How to use BioModels.net qualifiers

Here is an example of the annotation one could add to a model element representing a complex between two proteins:

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
            xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" 
            xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
  <rdf:Description rdf:about="#MyModelElement">
    <bqbiol:hasPart>
      <rdf:Bag>
        <rdf:li rdf:resource="urn:miriam:uniprot:P04551" />
        <rdf:li rdf:resource="urn:miriam:uniprot:P10815" />
      </rdf:Bag>
    </bqbiol:hasPart>
  </rdf:Description>
</rdf:RDF>