Require Simpson index

[Dongze]

Hi,

           I’m a master student in Bioinformatics, and I saw your database, it’s really interesting. now I have a question, you mentioned that you select interections according to their Simpson index, could you please tell me whether I could get the Simpson index value? If I can, how could I get it?

 

Dongze

 

[Dénes Türei]

Hi Dongze,

I used Simpson index to quantify the similarity between resources.
Simpson index is a simple similarity metric used mainly in community ecology.
Staying at the example of comparing networks, it is calculated by
dividing the number of shared edges by the number of edges in the
smaller resource.
E.g. if Signor has 5000 edges and SignaLink has 3000 and 2000 of these
is in agreement, Simpson index is 2000 / 3000 = 0.66
PyPath instances have the method `database_similarity()` which
calculates the Simpson index for edges and nodes for all currently
loaded resources.
I haven't tested it in the past 2 years, if you experiencing any
issues just send a bug report on github.

Best wishes,

Denes

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Denes Turei, Ph.D.

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