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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

Thank you very much for your the Reactome Knowledgebase and the tools to access it. The DAG is a great way to go. Before using the DAG, I used the content service.

I am finding a minor mismatch in the data (Reactome version 67) between the pathway list from the Content Service and from the DAG:

These two Pathways are seen in the DAG, but not seen in ReactomePathways.txt from the content service. These pathways are in other files from the content service, but not ReactomePathways.txt

MATCH (p:Pathway) WHERE p.stId IN ['R-RNO-215126', 'R-SCE-2564818'] RETURN p.stId as ID, p.displayName AS Name

ID | Name
-- | --
"R-RNO-215126" | "Transport of connexins along the secretory pathway"
"R-SCE-2564818" | "Cytosolic iron-sulfur cluster assembly (yeast)"

Grepping for these two pathways in ReactomePathways.txt come back with no results:

$ grep R-SCE-2564818 ReactomePathways.txt

$ grep R-RNO-215126 ReactomePathways.txt

PS: Is this the correct repo for this issue?

Thank you again for Reactome. We are so fortunate to have such a great resource.

Hello,

Thank you so much for the great open-data pathway collection. It is extremely helpful. I am working to become familiar with the layout of the Reactome database in neo4j.

Why are there are multiple identical copies of CatalystActivity (except for dbId)? For example, this neo4j command, results in the csv table that is attached. The CatalystActivity instances are identical except for the dbId. I do not see a stId. Is the dbId hardcoded into the CatalystActivity object, or does it change from run-to-run or version-to-version of the Reactome graph database loaded into Neo4j.

MATCH (src:CatalystActivity{displayName:"SUMO transferase activity of UBA2:SAE1 [nucleoplasm]"}) RETURN src

Regards,

DV

Here are the results of the MATCH command:

export.csv.txt

Thanks for making the amazing Reactome database available to the research community. Storing the Reactome data in a graph database is an astute move.

Is it correct for both (Pathway)s to have the parameter, isInferred returned as set to false When I do this query?:

MATCH (hi:Pathway{stId:"R-HSA-9613829"})<-[inferredTo]-(lo:Pathway) RETURN hi, lo

I see that both Pathways have the parameter, isInferred set to false. Shouldn't one of them be true?

hi

{
  "schemaClass": "Pathway",
  "isInDisease": false,
  "releaseDate": "2019-06-12",
  "displayName": "Chaperone Mediated Autophagy",
  "stId": "R-HSA-9613829",
  "speciesName": "Homo sapiens",
  "diagramHeight": 1817,
  "stIdVersion": "R-HSA-9613829.3",
  "dbId": 9613829,
  "releaseStatus": "UPDATED",
  "name": [
    "Chaperone Mediated Autophagy"
  ],
  "hasDiagram": true,
  "isInferred": false,
  "doi": "10.3180/R-HSA-9613829.1",
  "diagramWidth": 2185
}

lo

{
  "schemaClass": "TopLevelPathway",
  "isInDisease": false,
  "releaseDate": "2019-06-12",
  "displayName": "Autophagy",
  "stId": "R-HSA-9612973",
  "speciesName": "Homo sapiens",
  "diagramHeight": 338,
  "hasEHLD": true,
  "stIdVersion": "R-HSA-9612973.1",
  "dbId": 9612973,
  "releaseStatus": "UPDATED",
  "name": [
    "Autophagy"
  ],
  "hasDiagram": true,
  "isInferred": false,
  "doi": "10.3180/r-hsa-1632852.1",
  "diagramWidth": 626
}