Brainstorm Finterly, Tina - PathVisio/GPML GitHub Wiki
- Focus on documentation for 2013a
- Tree diagram
- Textual documentation for the elements and attributes
- Discuss changes in the 2013a schema for 2021
- Naming conventions
- Add documentation in Schema
- Clean up
- Look at issues https://github.com/PathVisio/GPML/issues
- Discuss extensions for 2021 schema version (complexes, annotations, multi-species pathways)
- Complexes - e.g. add Xref for Group element
- Multi-species - e.g. add Organism element to data node elements
- Annotation elements for pathway, data node, interaction, group, shape
- Upload GPML2013a-doc.xsd
- Upload GPML2021.xsd (copy of GPML2013a-doc.xsd)
- step-by-step process:
- create issue for the change you make, close issue with commit (fix #123)
- element and property naming convention
- cleaning up literature reference
<Citation idGPML="c00" url="https://pubmed.ncbi.nlm.nih.gov/31226023/">
<Xref identifier="31226023" datasource="PubMed"/>
</Citation>
- adding Annotation element
<Annotation idGPML="abc" name="disease pathway">
<Xref id entifier="PW:0000013" datasource="Pathway Ontology"/>
</Annotation>
- renaming graphId
id
gpmlId
idGPML
gpml_id
- allowed groups to have Xrefs
- add author element for pathways (0...unbound number of authors)
- Went over questions and discussion points for GPML 2021
- Resolved some issues including: property renaming, improving modularity (e.g. adding LineStyleAttributes, separating Point and Anchor from GraphicalLine/Interactions)
- Some issues still to be discussed with group:
- Renaming properties
- Pathway property "version/revision"
- Allowing customized border and label color
- How to visually represent and store lines like elbow
- Supporting custom shapes or background images
- Should Interactions and GraphicalLine have labels?
- To keep fontStrikeThru, InfoBox, Legend?
- How is “type” used for Interaction / GraphicalLine
- Should label element have Xref instead of href?
- Where and how should graphID be added?