DisSim

Databases

Database Name [Reference]
URL (Date of Download)
Disease Ontology [1] https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo (Jun. 2016)
CTD [2] http://ctdbase.org/ (Jun. 2016)
GeneRIF [3] http://www.ncbi.nlm.nih.gov/gene/about-generif (Jun. 2016)
GAD [4] https://geneticassociationdb.nih.gov/ (Jun 2016)
OMIM [5] http://www.omim.org/ (Jun. 2016)
GO & GOA [6,7] http://www.geneontology.org/ (Jun 2016)
HumanNet [8] http://www.functionalnet.org/humannet/HumanNet.v1.join.txt (Jun. 2016)



Algorithms

Methods [Reference]
URL
Resnik [9] http://arxiv.org/abs/cmp-lg/9511007
Lin [10] http://www.citeulike.org/group/276/article/1238
Wang [11] http://www.ncbi.nlm.nih.gov/pubmed/20439255
PSB [12] http://www.ncbi.nlm.nih.gov/pubmed/22166490
SemFunSim [13] http://www.ncbi.nlm.nih.gov/pubmed/24932637



Downloads

Description
URL
Diseases of DisSim http://123.59.132.21/download/disease_DisSim.txt



References

1. Schriml, L.M., Arze, C., Nadendla, S., Chang, Y.W., Mazaitis, M., Felix, V., Feng, G. and Kibbe, W.A. (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic acids research, 40, D940-946.

2. Davis, A.P. et al. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res 41, D1104-14 (2013).

3. Mitchell, J.A. et al. Gene indexing: characterization and analysis of NLM's GeneRIFs. AMIA Annu Symp Proc, 460-4 (2003).

4. Becker, K.G., Barnes, K.C., Bright, T.J. & Wang, S.A. The genetic association database. Nat Genet 36, 431-2 (2004).

5. Amberger, J., Bocchini, C. & Hamosh, A. A new face and new challenges for Online Mendelian Inheritance in Man. Human mutation 32, 564-567 (2011).

6. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-9 (2000).

7. Barrell, D. et al. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res 37, D396-403 (2009).

8. Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM (2011) Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res 21: 1109-1121.

9. Resnik P (1995) Using information content to evaluate semantic similarity in a taxonomy. arXiv preprint cmp-lg/9511007.

10. Lin D. An information-theoretic definition of similarity; 1998. Proceedings of the 15th international conference on Machine Learning. San Francisco, CA: Morgan Kaufmann. pp. 296-304.

11. Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF (2007) A new method to measure the semantic similarity of GO terms. Bioinformatics 23: 1274-1281.

12. Mathur S, Dinakarpandian D (2012) Finding disease similarity based on implicit semantic similarity. J Biomed Inform 45: 363-371.

13. Cheng L, Li J, Wang YD (2014) SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association. PLOS ONE 9: e99415.




 
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