The CellML Metadata 1.0 Specification Working Draft - 16 January 2002

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2  Background

The CellML development team has decided to use existing standards wherever possible to describe metadata. RDF, Dublin Core, vCard, and BQS are existing standards used to specify metadata. This section describes our use of these standards and our own CellML Metadata.

2.1  Resource Description Framework

Information about RDF can be found on the W3C's Resource Description Framework (RDF) Page.

2.1.1  What is RDF?

RDF, which stands for the "Resource Description Framework", is the W3C's recommendation for handling metadata on the web. The Resource Description Framework is just that: it is a framework that allows you to store descriptions (i.e. metadata) about resources. A resource can be literally anything. For the purposes of CellML, resources can be the model document, the model itself, or components in the model.

2.1.2  The advantages of using RDF

RDF by itself does not allow people to store metadata. It merely provides a standard framework onto which various groups can hang their metadata vocabularies. Some benefits of having this standard framework are:

• It provides a common attribute=value data model for the metadata. All metadata expressed in RDF can be presented as a series of attributes (i.e. properties of the resource) and their values. For instance, one attribute=value pair for a CellML model might be species=Mus musculus.
• It provides an extensible method for storing metadata of increasing complexity. Some metadata properties will have simple values, such as the species property shown above. Other metadata properties will have complex values. In the latter case, the value of the metadata property is itself considered a resource, and additional metadata properties are stored about it. This is made more clear by an example. Consider the case of the creator attribute. This could be given a simple value of the creator's name, such as John Doe. However, it is more powerful to consider the value of the creator property to be a new resource (the person identified by the name "John Doe"). This allows the person's name to be stored as metadata about the new resource. This allows additional metadata to be stored about the person, such as the person's mailing address, phone number, etc. Most importantly, we don't have to know ahead of time what sorts of metadata processing software might want to store about the person. If a particular application wants to store the person's favourite colour, it can do so. Other applications might not recognise the meaning of the particular element that stores the favourite colour, but they will be able to understand that it is some sort of property about the resource (i.e. person) that is the creator of the model. This allows the application to handle the unknown metadata gracefully (most likely, many applications would at least be able to present the attribute=value pair to the user).
• It makes it possible for applications that don't know anything about CellML to understand our metadata. Though not a reality yet, it is part of Tim Berners-Lee's vision of a semantic web. Eventually, search engine tools could become RDF capable. In that case, people would be able to perform much more powerful searches for information on the web. If someone wants to find all web resources created by John Doe, he/she could search explicitly for resources where creator=John Doe, instead of just searching for resources that contain the string "John Doe".
• There are tools out there that use RDF. It is true that RDF is still a fledgling technology. However, there are tools out there that parse RDF and tools that actually use RDF to build databases, knowledge stores, and other such things. For instance, the W3C provides SiRPAC, a Simple RDF Parser and Compiler which returns a graphical representation of the RDF code it is fed to aid in visualization of the attribute=value constructs as well as validate RDF segments. See the W3C's RDF project list for a list of tools and projects using RDF.

2.1.3  The Generalized Structure of RDF

The RDF Model and Syntax Specification specifies a generalized structure. RDF's generalized structure allows many possible methods of storing metadata. RDF's flexible data model gives one the ability to add new classes of information without changing a previously specified schema; intead, the new classes build on the base schema. This extensibility makes RDF particularly appealing for use in CellML.

In order to ensure consistency of notation, the CellML development team has chosen one way of expressing metadata in RDF. This is the recommended way of implementing RDF in CellML, but it is not the only way of representing metadata. From here on, the rdf prefix will be used to indicate that elements and attributes are in the RDF namespace.

2.2  The Dublin Core Metadata Initiative

Information about the Dublin Core Metadata Initiative can be found on the Dublin Core's website.

2.2.1  What is the Dublin Core?

The Dublin Core is a group of metadata properties. These properties were identified as "common" across a large range of resources by a group of library science and knowledge management communities. These properties include attributes like creator, publisher, subject, and date. A full list is found in Table 3, and their corresponding definitions can be found in the Dublin Core Metadata Element Set, Version 1.1: Reference Description.

The Dublin Core Metadata Initiative group has also provided a standard set of "qualifier" elements. These elements add information to the basic elements. Qualifier elements either provide type information or scheme information. Type information classifies the basic element. For instance, the date element can have a type of created, modified, valid, available, or issued. Scheme information indicates how the content of the element is encoded. For instance, the date element can have a scheme of W3C-DTF or DCMI Period. A full list of qualifiers and their allowed values can be found in Table 2, and their corresponding definitions can be found in the Dublin Core Qualifiers document.

It is important to note that Dublin Core does not have to be expressed in RDF. The Dublin Core elements are not elements in the XML sense. They are simply standard names and definitions for common types of metadata. However, the Dublin Core Metadata Initiative has released two articles that suggest a method for implementing an RDF representation of Dublin Core elements and qualifiers: Expressing Simple Dublin Core in RDF/XML and Expressing Qualified Dublin Core in RDF/XML, respectively. These suggestions have been adopted for use in CellML.

2.2.2  The advantages of using Dublin Core

The Dublin Core set of elements is widely referenced, and the W3C designed the Resource Description Framework with the Dublin Core in mind. General purpose tools are more likely to understand the Dublin Core metadata vocabulary than any other vocabulary. Also, using the Dublin Core metadata vocabulary makes it obvious that certain CellML Metadata properties (such as model creator) map directly to metadata properties that are found in other fields.

Henceforth, the prefixes dc and dcterms will indicate that elements and attributes are in the Dublin Core and the Dublin Core Qualifiers namespaces, respectively.

2.3  vCard

At the time of writing, the only existing RDF definition of metadata about people is a note submitted to the W3C in February 2001 entitled Representing vCard Objects in RDF/XML. (This note is the work of Renato Iannella working at the Distributed Systems Technology Centre at the University of Queensland and orginally appeared on their RDF project page.) This note's suggestions are widely used for referencing people in RDF.

As the vCard data model includes some elements that are not necessary for CellML Metadata, such as nickname and birthday, we will not require CellML processing software to recognize those elements. However, model authors are free to use them. That is, the use of vCard elements outside of the list defined in the CellML Metadata specification will not invalidate the metadata, but these elements may not necessarily be recognized by all CellML Metadata compliant processing software.

CellML Metadata compliant processing software is expected to recognize the following "vCard in RDF" elements that meet the information needs of CellML:

• <vCard:N> (the name construct), with all of its subelements:
  • <vCard:Family>: the person's family, or last name
  • <vCard:Given>: the person's given, or first name
  • <vCard:Other>: additional names, used for middle names and initials
  • <vCard:Prefix>: honorific prefixes, such as "Dr."
  • <vCard:Suffix>: suffixes such as "III" and "Jr."

• <vCard:ADR> (the mailing address construct), with all of its subelements:
  • <vCard:Pobox>: post office box
  • <vCard:Street>: street address
  • <vCard:Locality>: city, town, rural route, etc.
  • <vCard:Region>: state, etc.
  • <vCard:Country>: country
  • <vCard:Pcode>: postal code (such as the American zip code)
  • <vCard:Extadd>: extended address field. This is used to include the company or institution name.

• <vCard:EMAIL> (the e-mail address construct)
• <vCard:TEL> (the telephone number construct)
• <vCard:ORG> (the organization construct), with all of its subelements:
  • <vCard:Orgname>: the name of the organization (i.e. "The University of Auckland")
  • <vCard:Orgunit>: the division or department (i.e. "The Bioengineering Research Group")

• <vCard:TITLE>: the person's job title
• <vCard:ROLE>: the person's job role

The <rdf:type> element is used to specify "type parameters" on certain vCard elements. For instance, an address may be typed as domestic, international, postal, parcel, home, work, or preferred. Table 1 lists the vCard properties used in CellML that have a type parameter with their possible values. Note that one address may be given more than one type. See Figure 33 for an example of how to use the <rdf:type> element in vCard.

Table 1 The names, URIs and recommended prefixes of the namespaces referenced in this specification.

Examples throughout the rest of this specification demonstrate the use of vCard elements in RDF. These elements are preceded by the vCard prefix to indicate that they are in the vCard namespace.

2.4  Bibliographic Query Service

No bibliographic standards exist within RDF/XML at the time of writing. However, the Object Management Group has published the Bibliographic Query Service Specification. The DsLSRBibObjects Module from this specification presents an excellent general data model for bibliographic references. The CellML development team recommends an RDF serialization of this data model (henceforth referred to as the "BQS data model") described in detail in Section 5 of this document. BQS metadata is designated by the namespace prefix bqs in this specification.

2.5  CellML Metadata

A CellML Metadata namespace has been created to include all metadata that has not been previously defined by the four standards listed above. These include biology-related attributes (such as species and bio-entities) as well as properties we felt were missing from other standards (such as annotations). We recommend CellML Metadata be designated by the namespace prefix cmeta.

2.6  Namespaces in CellML Metadata

Namespace URIs and recommended prefixes are given in Table 2.

Table 2 The names, URIs and recommended prefixes of the namespaces referenced in this specification.