MS-BioGraphs MS | DIPSA: Data-Intensive Parallel Systems and Algorithms

Name	MS-BioGraphs – MS
URL	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS
Download Link	https://doi.org/10.21227/gmd9-1534
Script for Downloading All Files	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-on-IEEE-DataPort/
Validating and Sample Code	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-Validation/
Graph Explanation	Vertices represent proteins and each edge represents the sequence similarity between its two endpoints
Edge Weighted	Yes
Directed	No
Number of Vertices	1,757,323,526
Number of Edges	2,488,069,027,875
Maximum Degree	814,957
Minimum Weight	98
Maximum Weight	634,925
Number of Zero-Degree Vertices	6,437,984
Average Degree	1,415.8
Size of The Largest WCC	2,486,890,448,664
Number of WCC	148,861,367
Creation Details	MS-BioGraphs: Sequency Similarity Graph Datasets
Format	WebGraph
License	CC BY-NC-SA
QUB IDF	2223-052
DOI	10.5281/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