Qualifiers

The qualification of an annotation is important to grasp the relation between a model component and the resource used to annotate it. The relationship 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".

There are two kinds of qualifiers used for different purposes:

refinement of the relationship between an annotation resource and the modelling concept represented by a model element
refinement of the relationship between an annotation resource and the biological object represented by a model element

One can view the annotation of a model component as a statement with the form of a triple. The resource used in the annotation is the 'object', while the qualifier is the 'predicate'. In the cases of the model qualifiers, the 'subject' of the relation is the modelling concept represented by the model component referenced by the annotation. Such as modelling concept can be the model itself, a mathematical construct, an hypothesis made, that may change the way we understand the model etc. In the cases of the biology qualifiers, the 'subject' of the relation is the biological or biochemical object represented by the enclosing model element.

In the following, the qualifiers of the first type are called model qualifiers. The associated namespace that should be used is http://biomodels.net/model-qualifiers/. The qualifiers of the second type are called biology qualifiers. The associated namespace that should be used is http://biomodels.net/biology-qualifiers/.

If you wish to download these qualifiers in a computer readable format, please refer to MIRIAM Registry website.

Model qualifiers

These kind of qualifiers define the relationship between a modelling object and its annotation:

The following is the list of the current qualifiers in the http://biomodels.net/model-qualifiers/ namespace. This list may grow but no element will be removed. Two forms are provided, a predicate and a noun ones.

is, identity

The modelling object represented by the model element is identical with the subject of the referenced resource (modelling object B). For instance, this qualifier might be used to link an encoded model to a database of models.

isDerivedFrom, origin

The modelling object represented by the model element is derived from the modelling object represented by the referenced resource (modelling object B). This relation may be used, for instance, to express a refinement or adaptation in usage for a previously described modelling component.

isDescribedBy, description

The modelling object represented by the model element is described by the subject of the referenced resource (modelling object B). This relation might be used to link a model or a kinetic law to the literature that describes it.

Biology qualifiers

These kind of qualifiers define the relationship between a biological object represented by a model element and its annotation:

The following is the list of the current qualifiers in the http://biomodels.net/biology-qualifiers/ namespace. This list may grow but no element will be removed.

encodes, encodement

The biological entity represented by the model element encodes, directly or transitively, the subject of the referenced resource (biological entity B). This relation may be used to express, for example, that a specific DNA sequence encodes a particular protein.

hasPart, part

The biological entity represented by the model element includes the subject of the referenced resource (biological entity B), either physically or logically. This relation might be used to link a complex to the description of its components.

hasProperty, property[new]

The subject of the referenced resource (biological entity B) is a property of the biological entity represented by the model element. This relation might be used when a biological entity exhibits a certain enzymatic activity or exerts a specific function.

hasVersion, version

The subject of the referenced resource (biological entity B) is a version or an instance of the biological entity represented by the model element. This relation may be used to represent an isoform or modified form of a biological entity.

is, identity

The biological entity represented by the model element has identity with the subject of the referenced resource (biological entity B). This relation might be used to link a reaction to its exact counterpart in a database, for instance.

isDescribedBy, description

The biological entity represented by the model element is described by the subject of the referenced resource (biological entity B). This relation should be used, for instance, to link a species or a parameter to the literature that describes the concentration of that species or the value of that parameter.

isEncodedBy, encoder

The biological entity represented by the model element is encoded, directly or transitively, by the subject of the referenced resource (biological entity B). This relation may be used to express, for example, that a protein is encoded by a specific DNA sequence.

isHomologTo, homolog

The biological entity represented by the model element is homologous to the subject of the referenced resource (biological entity B). This relation can be used to represent biological entities that share a common ancestor.

isPartOf, parthood

The biological entity represented by the model element is a physical or logical part of the subject of the referenced resource (biological entity B). This relation may be used to link a model component to a description of the complex in which it is a part.

isPropertyOf, propertyBearer

The biological entity represented by the model element is a property of the referenced resource (biological entity B).

isVersionOf, hypernym

The biological entity represented by the model element is a version or an instance of the subject of the referenced resource (biological entity B). This relation may be used to represent, for example, the 'superclass' or 'parent' form of a particular biological entity.

occursIn, container

The biological entity represented by the model element is physically limited to a location, which is the subject of the referenced resource (biological entity B). This relation may be used to ascribe a compartmental location, within which a reaction takes place.

hasTaxon, taxon[new]

The biological entity represented by the model element is taxonomically restricted, where the restriction is the subject of the referenced resource (biological entity B). This relation may be used to ascribe a species restriction to a biochemical reaction.

How to use the BioModels.net qualifiers

Here is an example of the kind of annotation (using RDF) 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/">
        <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>

Here is an example of the kind of annotation (using RDF) one could add to a model in order to describe its BioModels Database prennial identifier and its reference publication:

      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
                   xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
        <rdf:Description rdf:about="#_000001">
          <bqmodel:is>
            <rdf:Bag>
              <rdf:li rdf:resource="urn:miriam:biomodels.db:BIOMD0000000004" />
            </rdf:Bag>
          </bqmodel:is>
          <bqmodel:isDescribedBy>
            <rdf:Bag>
              <rdf:li rdf:resource="urn:miriam:pubmed:1833774" />
            </rdf:Bag>
          </bqmodel:isDescribedBy>
        </rdf:Description>
      </rdf:RDF>