GPML2017

We are currently working intensively on an updated GPML schema with lots of improvements and new features.

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Linkouts:

• Current GPML2017.xsd
• Please add comments and suggestions

Summary

• XML element names in upper camel case (e.g. DataNode)
• XML attribute names in lower camel case (e.g. fillColor, dataSource)
• Documentation of the schema definitions included in the XSD file using xsd:annotation / xsd:documentation
• Default definitions supported by PathVisio and WikiPathways included in schema definition
  • DataNode type
  • Group groupType (new group styles defined)
  • Point arrowHead
• Graphics attributes (e.g. centerX, centerY, width) are now included in the main XML element
• Major restructuring of citations and ontology tags (removing dependency on BioPAX)

Attribute renaming

• graphId to elementID
• version in Pathway element to revision
• Style attribute for Group renamed to Type (consistent for all other types except for graphical styles)

New attributes/elements

• New backgroundImage attribute for Pathway element - needs implementation in viewer/GUI!
• New graphical element Alias similar to Label with a link to a Group (can replace Group in the pathway diagram) - needs implementation in GUI!

Elements/Attributes deprecated and removed from schema

• FontDecoration - currently not in use
• FontStrikethru - currently not in use
• Email attribute in Pathway element
• Last-Modified attribute in Pathway element
• Maintainer attribute in Pathway element
• groupId removed - elementID of Group used to reference to it

Old PublicationXrefs and openControlledVocabulary (references and ontology tags)

• New element Citation with internal unique citationID for referencing within the pathway
  • Attributes: title, year, URL, source
  • Elements: Xref and Author
  • URL and Xrefs allow usage of other citations including DOI and other weblinks
• New element OntologyTerm
  • Attributes: term, ontology, ontologyTermID
  • ontologyTermID (e.g. PW:000032) should be unique so it can be used for reference within the document as well