SBML.org — the global portal for all things SBML

Annot

Contents

Annotation Package break-out

These are the meeting notes for the Annotation package break out session during the COMBINE 2010 meeting.

Open issues

  • set annot namespace
  • integration of annot package in sbml (decision)
  • solution to attribute annotations (decision)
  • different types of negations (negative qualifiers, absence, list?)
    • complete list of negative biomodels.net qualifiers
  • provide examples for the draft
    • reification example (The annotation with the ID rdf:about="# 000002.size" has been provided by a person called ’John Doe’.)
    • biologically useful example of alt/seq/list containers
    • examples for different negation types

Discussion notes

(to be edited during break out session)

annot package namespace

xmlns:annot="http://www.sbml.org/sbml/package/annot/version1"

UPDATE (Dagmar) : After checking back with Mike, it turns out there is a standard namespace pattern for SBML L3 packages. So, instead of using the namespace shown above, we will use

http://www.sbml.org/sbml/level3/version1/annot/version1

(as described on the package mechanism web page.)

integration of annot package in sbml (decision)

  • sibling solution preferred
  • cleaner approach, cleaner separation between package and core

solution to attribute annotations

  • adding a . is not distinctive enough
  • . notation is "made up" by the package while XPath is a standard notation
  • prefixing the XPath with xpath namespace is necessary
  • XPath use should be recommended to restrict not to use ordering
  • XPath should use abbreviated paths [element metaID /@attribute]
  • XPath is the suggested solution

negation

  • different types of negations (negative qualifiers, absence, list?)
    • complete list of negative biomodels.net qualifiers
  • christian suggested the use of additional statements to negate previous statements, a bit similar to the eRDF approach
  • no solution found -> open for discussion

containers

  • double specification of amounts (bqbiol:is vs bqbiol:hasPart) has to be explained in the proposal
  • todo: make extensive examples for the use of different containers with different qualifiers... afterwards try what happens if we introduced negative qualifiers -> what is then still missing??

next discussion

planned for Mon 18th/Tue 19th

Retrieved from "http://sbml.org/Events/Forums/COMBINE_2010/Breakout_sessions/Annot"

This page was last modified 05:55, 12 October 2010.



Please use our issue tracking system for any questions or suggestions about this website. This page was last modified 05:55, 12 October 2010.