Comments (2)
Awesome work @nickzren. Nice job finding an efficient import method that works with the latest Neo4j stack.
I took a quick look at the changes and I'll need a little more time to think about where the code belongs... since it could possibly live in dhimmel/integrate
or hetio/hetnetpy
rather than in this repo whose focus is more the data and not the code to generate the data.
Taking a step back, there's a couple contributions that will be of major utility (in order of importance/interest):
- a neo4j dump file that is compatible with neo4j 5 (and possibly future neo4j versions)
- code to generate the neo4j database and dump file (i.e. your
csv
branch) - the
csv
files, but I'm a little cautious in that they have some similarities with the TSV files and we'd want to understand and document the differences.
Any thoughts?
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Thanks @dhimmel
I recognize the primary aim of this repo is data-centric rather than code-centric. However, I respectfully suggest that including data-specific scripts, such as Python and Cypher, could add value. No strong opinion here, and I'll defer to your ultimate decision on the matter.
The CSV data is derived from JSON files and serves as a comprehensive dataset, including all properties for both nodes and edges.
CSV files and Cypher scripts are generated simultaneously to ensure data type consistency, making the data import into Neo4j unaffected by version changes.
Having separate CSV files for nodes and edges not only enhances the framework's comprehensibility but also allows users to easily choose or modify or extend the data.
I encountered difficulties with restoring from Neo4j dump files and couldn't resolve the issues, so I began exploring alternative solutions.
I'm still learning about this and graph databases, so any corrections are welcome.
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Related Issues (20)
- Local files HOT 2
- Multiple Match Queries Not Working HOT 2
- Question About Hetionet's Dictionary HOT 3
- How to add new disease and anatomy nodes HOT 2
- Providing a dump version of Hetionet HOT 11
- http://neo4j.het.io/browser/ time out HOT 4
- Neo4J instance down (?) HOT 7
- Updated TSV version HOT 6
- graph.db database offline in neo4j HOT 3
- neo4j website down HOT 6
- Hetionet Browser is down HOT 4
- Mapping to original databases HOT 2
- Cannot map non-existing file HOT 5
- Do any relations imply another relation? HOT 1
- Connectivity Search Automated Query Question HOT 8
- Docker compatibility question HOT 4
- Question on metrics HOT 1
- What does it mean if something up regulates a disease in this context? HOT 3
- Inquiry about metapaths from 2017 Paper "Systematic Integration of Biomedical Knowledge Prioritizes Drugs for Repurposing" HOT 7
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