Finding associated diseases of my collection of diseases extracted from DisGeNET
Entering edit mode
18 months ago

Goal: I have 101 diseases. (extract from DisGeNET) I want to get associated diseases of these 101 diseases. to validated disease graph that I created. Note: Associated could be measured by jaccard similarity, shared genes, shared variants, similar gene pathway, similar metabolic pathway. Note: I come from computer science back ground and this is the first time i am dealing with biology realted dataset. I have no clue how it is structures. eg. Where should be the first place to look when I look at xxx related dataset. If i have question about datasets where should I ask for help. reddit? (if there is something similar to stack overflow where experts are there to answer newbie's question) Where are data collected? Can I convert from one id-code to another? DOID to CUI to OMIM to .... (I am so lost. without validation, I don't know if i am wrong, or there is no infomation to be found in the first place.)

Here what I attempted to do, 1. Search for disease graph.

  1. I cannot find any disease graph other than

    1. disease to disease from SNAP grop which i believe is just disease ontology which I do not want.

    2. Human Disease Network (HDN). I also don't want this because the method it used to construct the graph (edges in the graph are form between diseases iff diseases share at least 1 gene)

    3. Search for disease similarity API (After I failed to find any disease to disease graph dataset)


    1. it claims that it used DisGeNET dataset but not all of diseases in DisGeNET can be found from its web based similarity calculation. ( 54 out of 101 are found). I am not sure If I did something wrong or it just does not exist. I can't find way to validate this doubt. (Validation of these doubts are the main problem with these public API and dataset. Published paper seems to be (to me at least) the only source of truth.)
  3. DDA's API offered by DisGeNET

    1. I describe it below. (2.2)
  4. BioLink

    1. I describe it below (2.3)

From 2.2 DDA's API offered by DisGeNET Here is the url to the API: this is the API I am interested in using /dda/variants/disease/{vocabulary}/{disease} My question is What is the Correct into value for disease id?

eg. for DOID:0050144, I put it as 0050144. (omit DOID:) This gave me 405 error. indicating that it is client side error. So I try the following format DOID0050144, DO0050144, DO:0050144. Unfortunately none of them work.

I tried all of the disease ID availables that it mentioned.

(if you know where to find tutorial or example, please let me know)

From 2.3 BioLInk url to the API i am interested in /sim/search Similar to DisGeNET, I tried all of the combination of disease code. BioLInk does not even tell you, what it accepted. it just say disease id. Period. (if you know where to find tutorial or example, please let me know)

gene disease DisGeNET • 379 views

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