CellML Metadata Specification 1.1 Roadmap

CellML Metadata Specification 1.1

Prime directives:

• Convert all as much metadata to Dublin Core compliance as possible.
• Implement modular specification structure
• Achieve final draft of Metadata 1.1 specification by 4th April 2009 for presentation at CellML Workshop 2009
  
• The CellML Metadata 1.1 specification should provide a platform for metadata handling in PMR2.

• proposal to split into an 'umbrella' specification and submodules
  • graphing
  • simulation
  • common annotations
  • biological annotation
• in which case 'core' CellML Metadata specification will primarily just define how modules are organised and how the metadata is serialised in RDF/XML.
• Andre: "Core specification... simply says that any element can have a cmeta:id and that ID can be used to resolve metadata references. And that any element can have rdf:RDF child elements. Then all annotations are defined in separate specifications."
• Need to work out what namespaces will be.
  

• _{See http://www.cellml.org/specifications/metadata/graphs}
  

• _{current graphing metadata spec draft needs to be implemented (in PCEnv or Andre's tools) to be tested before it gets codified in the specification}
• _{things to add:}
  • _{add ability to represent axes (ticks, linear/logarithmic/etc, colour(?))}
  • _gridlines
  • _{line thickness}
  • _{background colour}
  • _{need to rationalise how RDF containers are dealt with in the specification}

_{Timeframe: Unlikely to be completed by the time of the workshop, since testing in PCEnv and other environments is required. Current draft state is reasonable, however.}

_Simulation

• _{See http://www.cellml.org/specifications/metadata/simulations}
  

• _{most components of simulation metadata (as currently used by PCEnv) are non-standard}
• _{should be standardised at some point in the future}

_{Timeframe: The current simulation spec as is (see link above,) could be finalised pending testing within PCEnv, although it would definitely be advantageous to implement it in David (Andre) Nickerson's CellMLSimulator. Andre would like to have CellMLSimulator implement the current simulation spec, but does not forsee having time for this before April 2009.}

Common annotations

Citations:

• See Tracker Item 414
  

• remove BQS, replace with DC citations
•  adding an identifier where one exists as well as the citation would provide for both machine and human readable citations - reccommend this. A URN could also fit in here if required, but CellML Metadata compliant software would not be required to necessarily resolve it.
  • e.g. MIRIAM (LSID?)

• See tracker item 1407
  

• rework keywords in metadata (currently implemented in BQS - use DC citations 'subject')
• serialise keywords, suggest in spec that constrained vocab be used
  • e.g. NCBI's Taxonomy Browser, foundational model of anatomy

• to allow, for example, a modification note that says "changed value of X from 1 to 2, as per [citation]', where in some cases it might also be appropriate to make X a reference to the variable in question (e.g., if we for some reason, wanted very detailed document histories)
  
  

Biological annotation

• See Tracker Item 1408
  
• Clean up this section slightly
• notice of deprecation for cmeta:sex, cmeta:species (?)
  
  • unnecessary to use cmeta for these annotations, should be replaced by an extensible approach - could use DC:keywords, although this is a less granular solution. OWL ontology will cover this.
    

Replace rdf examples with less verbose versions using identifiers, such as GO. Also give example of MIRIAM URN-based annotation. Make note about using structured ontologies within bioentity such as go - see

Timeframe: little to be changed. draft achievable by workshop although controversial.

Defining distribution / usage license of models in metadata

• See Tracker Item 1422
  
• MIRIAM community curation standard requires this
• We currently support dcterms:rights
  
  • Since the draft Metadata 1.0 spec was written, the DC term 'license' (http://purl.org/dc/terms/license) has been added under dcterms:rights, which allows identification of licenses via their URI
  • See http://www.intertwingly.net/wiki/pie/License and http://dublincore.org/usage/decisions/2004/2004-01.Rights-terms.shtml
    
• We should probably provide a small set of licenses to choose from rather than an open ended framework