GPML2017

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

---

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 (e.g. type attribute for DataNode)
• 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)
• New default group styles defined (Group, Complex, Pathway, Analog and Paralog)

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
• New graphical element Alias similar to Label with a link to a Group (can replace Group in the pathway diagram)

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

Questions

• order of attributes? can we define those?
• libGPML and GPML repo have different versions of GPML2017.xsd - which one to use?
• zOrder in LineGraphicAttributes and ShapeStyleAttributes
• remove href for Alias
• infobox used!
• add x, y, relX, relY to Anchor
• add default styles for DataNodes and Groups
• remove type in interaction and graphicalLine
• clarify pathway attributes!
• boardwith/height - required - rename to width/height
• change shape attribute in anchor to shapeType - https://github.com/PathVisio/GPML/issues/5 (close issue afterwards)
• ontologyterm not referenced in pathway
• enum for interaction types allowed in PV