Databases¶
In this section, we describe the types of networks (databases) you can select to run diffusion methods over. These include the following and are described in detail in this section *:
Select a network representing an individual biological database
Select multiple databases to generate a harmonized network
Select from one of four predefined collections of biological databases representing a harmonized network
Submit your own network † from one of the accepted formats
- *
Please note that all networks available through DiffuPath have been generated using PyBEL v.0.13.2.
- †
If there are duplicated nodes in your network, please take a look at this Jupyter Notebook to address the issue.
Network Dumps¶
Because of the high computational cost of generating the kernel, we provide links to pre-calculated kernels for a set of networks representing biological databases.
Database |
Description |
Reference |
Download |
---|---|---|---|
DDR |
Disease-disease associations |
||
DrugBank |
Drug and drug target interactions |
||
Gene Ontology |
Hierarchy of tens of thousands of biological processes |
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HSDN |
Associations between diseases and symptoms |
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KEGG |
Multi-omics interactions in biological pathways |
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miRTarBase |
Interactions between miRNA and their targets |
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Reactome |
Multi-omics interactions in biological pathways |
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SIDER |
Associations between drugs and side effects |
||
WikiPathways |
Multi-omics interactions in biological pathways |
If you would like to use one of our predefined collections, you can similarly download pre-calculated kernels for sets of networks representing integrated biological databases.
Collection |
Database |
Description |
Download |
---|---|---|---|
#1 |
KEGG, Reactome and WikiPathways |
-omics and biological processes/pathways |
|
#2 |
KEGG, Reactome, WikiPathways and DrugBank |
-omics and biological processes/pathways with a strong focus on drug/chemical interactions |
|
#3 |
KEGG, Reactome, WikiPathways and MirTarBase |
-omics and biological processes/ pathways enriched with miRNAs |
Custom-network formats¶
You can also submit your own networks in any of the following formats:
Minimally, please ensure each of the following columns are included in the network file you submit:
Source
Target
Optionally, you can choose to add a third column, “Relation” in your network (as in the example below). If the relation between the Source and Target nodes is omitted, and/or if the directionality is ambiguous, either node can be assigned as the Source or Target.
Custom-network example¶
Source |
Target |
Relation |
---|---|---|
A |
B |
Increase |
B |
C |
Association |
A |
D |
Association |
You can also take a look at our sample networks folder for some examples networks.
References¶
- 1
Menche, J., et al. (2015). Disease networks. Uncovering disease-disease relationships through the incomplete interactome. Science, 347(6224), 1257601.
- 2
Wishart, D. S., et al. (2018). DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082.
- 3
Ashburner, M., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25(1), 25–9.
- 4
Zhou, X., Menche, J., Barabási, A. L., & Sharma, A. (2014). Human symptoms–disease network. Nature communications, 5(1), 1-10.
- 5
Kanehisa, et al. (2017). KEGG: new perspectives on genomes, pathways, diseases and drugs.. Nucleic Acids Res. 45,D353-D361.
- 6
Huang, H. Y., et al. (2020). miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database. Nucleic acids research, 48(D1), D148-D154.
- 7
Fabregat, A et al. (2016). The Reactome Pathway Knowledgebase. Nucleic Acids Research 44. Database issue: D481–D487.
- 8
Kuhn, M., et al. (2016). The SIDER database of drugs and side effects. Nucleic Acids Research, 44(D1), D1075–D1079.
- 9
Slenter, D.N., et al. (2017). WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research, 46(D1):D661-D667.