Data/TCMGeneDIT

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Describe the dataset TCMGeneDIT, its possible links to other datasets, user scenarios for exploiting this dataset.

Description about TCMGeneDIT

The original data are published by the TCMGeneDIT team (http://tcm.lifescience.ntu.edu.tw/), available as tab delimiter files. They are distributed under the terms of the Creative Commons Attribution License, given proper citation to the original work published in BMC Complementary and Alternative Medicine [doi:10.1186/1472-6882-8-58].

Possible linkage to TCMGeneDIT to be implemented

  • With Entrez Gene by gene ids (4e Jun):
    • A tcm:Medicine is associated with a tcm:Gene by the property tcm:association. The symbol of a gene is described using rdfs:label.
  • With Diseasesome by disease names (4c Jun)
    • A tcm:Medicine is associated with a tcm:Disease by the property tcm:treatment. The name of the disease is described using rdfs:label.
  • With Diseasesome by gene symbol or id (3a Anja)
  • With DailyMed by ingredient names (3b Jun)
    • A tcm:Medicine is associated with a tcm:Ingredient by the property tcm:ingredient. The name of the ingredient is described using rdfs:label.
  • With DrugBank by gene (3a Anja)
  • With DBPedia by ingredient, disease, effect, gene, and herb names (2a Jun) (5c Anja)
  • With DrugBank, DailyMed and LinkedCT by drug (similarity) (3d Anja)
    • score is needed for this
  • Priority: 1-5 (5 being the highest priority).
  • Difficulty: a-e (e being the most difficult task)

Example starting point to explore TCMGeneDIT

Top 10 Alzheimer's genes as listed at: Alzgene at Alzforum

  • APOE
  • CHRNB2
  • GAB2
  • CH25H
  • SORL1
  • TNF
  • OTC
  • CST3
  • ACE
  • MAPT/STH

A query using both the TCMGeneDIT and the Entrez Gene info from http://hcls.deri.org:8080/sparql has found 3 out of the 10 Alzheimer's genes, namely,

  • APOE
  • TNF
  • MAPT/STH

A query for genes associated with Alzheimer's genes in TCMGeneDIT has returned 14 other genes:

  • IL6
  • MAPK1
  • CREB1
  • ADAMTS2
  • IL1B
  • NFKB1
  • CASP3
  • CCND1
  • ACHE
  • APLP2
  • ERBB2
  • AGPS
  • APP
  • TTR

Possible following exploration could be:

  • Understand the functions of these genes who are associated with the same herbal medicine, by using the GO dataset, (possibly the one from hcls@deri)
  • Use the effect information from TCM dataset, together with the gene information from GOA, to confirm whether the medicine could potentially have an effect on the Alzheimer's Disease
  • Use annotation from aTags, which will provide additional information about the association between a herbal medicine and its effects, to confirm whether the medicine could potentially have a positive or negative effect on the Alzheimer's Disease

Open questions:

  • How can the ingredient information from TCM could be used, together other domain dataset?

Useful Links