This README file accompanies the dataset representing the multiplex microbiome network. If you use this dataset in your work either for analysis or for visualization, you should acknowledge/cite the following papers:
“Dynamics and associations of microbial community types across the human body”
T. Ding and P. Schloss
Nature 2014 509, 357–360
“Spectral Entropies as Information-Theoretic Tools for Complex Network Comparison”
M. De Domenico and J. Biamonte
Physical Review X 2016 6, 041062
that can be found at the following URLs:
https://www.nature.com/articles/nature13178
https://journals.aps.org/prx/abstract/10.1103/PhysRevX.6.041062
We consider different types of microbial communities across the human body, building an interaction network for each of 18 distinct human body sites. We have elaborated the resulting network from the original work by Ding and Schloss (see above).
The multiplex network used in the paper makes use of the following layers:
- Anterior_nares
- Buccal_mucosa
- Hard_palate
- Keratinized_gingiva
- L_Antecubital_fossa
- L_Retroauricular_crease
- Mid_vagina
- Palatine_Tonsils
- Posterior_fornix
- R_Antecubital_fossa
- R_Retroauricular_crease
- Saliva
- Stool
- Subgingival_plaque
- Supragingival_plaque
- Throat
- Tongue_dorsum
- Vaginal_introitus
There are 305 nodes, labelled with integer ID between 1 and 305, and 4433 connections. The multiplex is undirected and unweighted, stored as edges list in the file
HumanMicrobiome_multiplex.edges
with format
layerID nodeID nodeID weight
(Note: weight is 1 for all edges)
The IDs of all layers are stored in
HumanMicrobiome_layers.txt
The IDs of nodes, together with their name can be found in the file
HumanMicrobiome_nodes.txt
This HUMAN MICROBIOME MULTIPLEX NETWORK DATASET is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0/. Any rights in individual contents of the database are licensed under the Database Contents License: http://opendatacommons.org/licenses/dbcl/1.0/
You should find a copy of the above licenses accompanying this dataset. If it is not the case, please contact us (see below).
A friendly summary of this license can be found here:
http://opendatacommons.org/licenses/odbl/summary/
and is reported in the following.
====================================================== ODC Open Database License (ODbL) Summary
This is a human-readable summary of the ODbL 1.0 license. Please see the disclaimer below.
You are free:
- To Share: To copy, distribute and use the database.
- To Create: To produce works from the database.
- To Adapt: To modify, transform and build upon the database.
As long as you:
-
Attribute: You must attribute any public use of the database, or works produced from the database, in the manner specified in the ODbL. For any use or redistribution of the database, or works produced from it, you must make clear to others the license of the database and keep intact any notices on the original database.
-
Share-Alike: If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL.
-
Keep open: If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures.
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If you find any error in the dataset or you have questions, please contact
Manlio De Domenico
University of Padua
Padua (Italy)
email: manlio.dedomenico@unipd.it