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hetio / hetionet

Hetionet: an integrative network of disease
https://neo4j.het.io
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How to add new disease and anatomy nodes #42

Open Vittoria9 opened 3 years ago

Vittoria9 commented 3 years ago

Hi,

I am new to this area and would greatly appreciate any insight on the following:

  1. What is the process of adding new disease and anatomy nodes? Can these be developed in a modular format?
  2. Is there consensus amongst the computational chemists / toxicologists on the gold standard for nomenclature to use in in silico models / knowledge graphs?

Many thanks. Best regards, V

Vittoria9 commented 3 years ago

Hi Daniel,

Is this project still being actively maintained or has it been deprecated?

Thanks. V

dhimmel commented 3 years ago

Hi @Vittoria9. Apologies for the slow response.

Is this project still being actively maintained or has it been deprecated?

Hetionet v1.0 doesn't receive scheduled updates. We still assist with user questions and are developing downstream applications like connectivity search.

What is the process of adding new disease and anatomy nodes? Can these be developed in a modular format?

The discussion at https://github.com/hetio/hetionet/issues/34 might be helpful here. The integrate.ipynb notebook is what combines all the nodes and edges into a single network. You can look through that notebook to find which datasets are consumed for disease and anatomy nodes. You could then go to those upstream repositories, fork them, and then update the nodes as you wish. For diseases, the upstream repo is https://github.com/dhimmel/disease-ontology and for anatomy nodes it is https://github.com/dhimmel/uberon.

Is there consensus amongst the computational chemists / toxicologists on the gold standard for nomenclature to use in in silico models / knowledge graphs?

Not sure. You can read about what we did for this project at https://doi.org/10.15363/thinklab.d40 and in the manuscript.