R-HSA-109704: Pathway hasDiagram=True, but no figure relationship

[dvklopfenstein]

Hello,

Thank you very much for Reactome in the graph database format.

I see that the schemaClass, Pathway for stId:"R-HSA-109704" shows hasDiargam:true, but I do not see a figure relationship to a Figure object.

This is the Neo4j query that I am using:

MATCH (p:Pathway{stId:"R-HSA-109704"})-[r]->(dst) RETURN p, r, dst

Regards,

DV

[dvklopfenstein]

FYI: 789 human pathways have hasDiagram==true, but do not appear to have a png or jpg file associated with it (i.e., no 'figure' relationship to a 'Figure' entity which contains the name of the image file)

[fabregat]

Hi DV,

We do not store the images in the graph database, but you can access them via our ContentService. Please check https://reactome.org/ContentService/#/exporter/toRasterUsingGET

Thank you very much for your interest in using Reactome data and software.

I hope it helps!

Best regards,

[dvklopfenstein]

FYI: I know there are no diagrams in the Reactome database for neo4j.

I intended to say "image filenames", not "images" (e.g., the actual image file).

Many pathways that have diagrams have no associated image filenames in neo4j.

Here is what I see:

2,222 Pathways Total for human
  892 Pathways hasDiagram=true
  103 Pathways hasDiagram=true and a have an associated figure filename
  789 Pathways hasDiagram=true have no "figure" relationship or image filename

I am using Reactome version 65

[fabregat]

Hi DV,

Figures and diagrams are two different things:

• Figures are illustrations provided by our designers (working together with curators)
• Diagrams are the SBGN-like description of the pathway.

To download the diagrams from the Content Service please use the StableIdentifier in the link.

Does this answer your question?

[dvklopfenstein]

Yes. That definitely answers my confusion. Thank you for your time and attention. Using the Neo4j tools to query the Reactome data is working really well.

[fabregat]

We're glad you find the tools useful 👍