Comments (3)
It shouldn't be too hard to use the hetio
Python package to read in the JSON-formatted permuted hetnet files and then create a network object from that. I think the MultiGraph
is the best networkx
data structure to store hetnets, but it is far from perfect:
From #8 (comment):
networkx
isn't a good option as it's hetnet support is mediocre --- the MultiGraph supports relationship types but not node types and doesn't really provide first-class type support.
Therefore, I personally have avoided using networkx for hetnets, and instead used Neo4j, hetio, and hetmatpy (when doing matrix operations).
@lingling93 what is your use case for converting the permuted hetnets into networkx? I can help you figure out the proper code to use, but I am wondering if networx is the right solution.
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I want to compare the result of permutation graph with Hetio graph. Now I'm trying to input hetio graph and permutation graphs to node2vec(https://github.com/eliorc/node2vec), this package only accept networkx type graph.
from hetionet.
Interesting, I haven't used node2vec, but my understanding is that it does not understand node or edge types, and thus may be of limited utility for hetnets. An alternative method for which I reviewed the manuscript but have not used, is called edge2vec. Tagging @RoyZhengGao, who's an author on that work.
Would love to see what you uncover about the differences between the permuted and unpermuted Hetionets. Note that we have also created additional permuted derivatives of Hetionet for our recent work. The file hetionet-v1.0-permutations.zip
contains 200 permutations using the HetMat format from our new hetmatpy library. CC @zietzm
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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
- Speeding up data import to Neo4j v5 and CSV format data HOT 2
- Inquiry about metapaths from 2017 Paper "Systematic Integration of Biomedical Knowledge Prioritizes Drugs for Repurposing" HOT 7
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