MS-BioGraphs MS

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NameMS-BioGraphs – MS
URLhttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS
Download Linkhttps://doi.org/10.21227/gmd9-1534
Script for Downloading All Fileshttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-on-IEEE-DataPort/
Validating and Sample Codehttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-Validation/
Graph ExplanationVertices represent proteins and each edge represents the sequence similarity between its two endpoints
Edge WeightedYes
DirectedNo
Number of Vertices1,757,323,526
Number of Edges2,488,069,027,875
Maximum Degree814,957
Minimum Weight98
Maximum Weight634,925
Number of Zero-Degree Vertices6,437,984
Average Degree1,415.8
Size of The Largest WCC2,486,890,448,664
Number of WCC148,861,367
Creation DetailsMS-BioGraphs: Sequency Similarity Graph Datasets
FormatWebGraph
LicenseCC BY-NC-SA
QUB IDF2223-052
DOI10.5281/zenodo.7820808
Citation
Mohsen Koohi Esfahani, Sebastiano Vigna, 
Paolo Boldi, Hans Vandierendonck, Peter Kilpatrick, March 13, 2024, 
"MS-BioGraphs: Trillion-Scale Sequence Similarity Graph Datasets", 
IEEE Dataport, doi: https://doi.org/10.21227/gmd9-1534.
Bibtex
@data{gmd9-1534-24,
doi = {10.21227/gmd9-1534},
url = {https://doi.org/10.21227/gmd9-1534},
author = {Koohi Esfahani, Mohsen and Vigna, Sebastiano and Boldi, 
Paolo and Vandierendonck, Hans and Kilpatrick, Peter},
publisher = {IEEE Dataport},
title = {MS-BioGraphs: Trillion-Scale Sequence Similarity Graph Datasets},
year = {2024} }


Files

Underlying Graph The underlying graph in WebGraph format:
  • File: MS-underlying.graph, Size: 7,342,853,446,646 Bytes
  • File: MS-underlying.offsets, Size: 5,341,385,503 Bytes
  • File: MS-underlying.properties, Size: 1,560 Bytes
Total Size: 7,348,194,833,709 Bytes
These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels) The weights of the graph in WebGraph format:
  • File: MS-weights.labels, Size: 5,037,171,681,279 Bytes
  • File: MS-weights.labeloffsets, Size: 5,070,752,590 Bytes
  • File: MS-weights.properties, Size: 183 Bytes
Total Size: 5,042,242,434,052 Bytes
These files are validated using ‘Edge Blocks SHAs File’ as follows.
Edge Blocks SHAs File (Text) This file contains the shasums of edge blocks where each block contains 64 Million continuous edges and has one shasum for its 64M endpoints and one for its 64M edge weights.
The file is used to validate the underlying graph and the weights. For further explanation about validation process, please visit the https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-Validation.
  • Name: MS_edges_shas.txt
  • Size: 4,449,360 Bytes
  • SHASUM: 85d5b0896f8fa8a2b490ec6560937c45ced8b0d9
Offsets (Binary) The offsets array of the CSX (Compressed Sparse Rows/Columns) graph in binary format and little endian order. It consists of |V|+1 8-Bytes elements.
The first and last values are 0 and |E|, respectively.
This array helps converting the graph (or parts of it) from WebGraph format to binary format by one pass over (related) edges.
  • Name: MS_offsets.bin
  • Size: 14,058,588,216 Bytes
  • SHASUM: 15c3defdbb92f7b1fe48a3fb20530d99fa30c616
WCC (Binary) The Weakly-Connected Compontent (WCC) array in binary format and little endian order.
This array consists of |V| 4-Bytes elements The vertices in the same component have the same values in the WCC array.
  • Name: MS-wcc.bin
  • Size: 7,029,294,104 Bytes
  • SHASUM: 30f12b738dde8f62aecb94239796b169512e6710
Names (tar.gz) This compressed file contains 120 files in CSV format using ‘;’ as the separator. Each row has two columns: ID of vertex and name of the sequence.
Note: If the graph has a ‘N2O Reordering’ file, the n2o array should be used to convert the vertex ID to old vertex ID which is used for identifying name of the protein in the `names.tar.gz` file.
  • Name: names.tar.gz
  • Size: 27,130,045,933 Bytes
  • SHASUM: ba00b58bbb2795445554058a681b573c751ef315
OJSON The charactersitics of the graph and shasums of the files.
It is in the open json format and needs a closing brace (}) to be appended before being passed to a json parser.
  • Name: MS.ojson
  • Size: 700 Bytes
  • SHASUM: e2eb3fcdd0c22838971ed2edea8e1ed081a77282


Plots

For the explanation about the plots, please refer to the MS-BioGraphs paper.
To have a better resolution, please click on the images.

Degree Distribution
Weight Distribution
Vertex-Relative Weight Distribution
Degree Decomposition
Cell-Binned Average Weight Degree Distribution
Weakly-Connected Components Size Distribution


MS-BioGraphs


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