MS-BioGraphs MS200 | DIPSA: Data-Intensive Parallel Systems and Algorithms

Name	MS-BioGraphs – MS200
URL	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS200
Download Link	https://dx.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	1,414,493,449
Number of Edges	502,930,788,612
Maximum Degree	745,735
Minimum Weight	460
Maximum Weight	634,925
Number of Zero-Degree Vertices	0
Average Degree	355.6
Size of The Largest WCC	485,867,547,569
Number of WCC	338,348,495
Creation Details	MS-BioGraphs: Sequency Similarity Graph Datasets
Format	WebGraph
License	CC BY-NC-SA
QUB IDF	2223-052
DOI	10.5281/zenodo.7820812
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://dx.doi.org/10.21227/gmd9-1534.
Bibtex	@data{gmd9-1534-24, doi = {10.21227/gmd9-1534}, url = {https://dx.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: MS200-underlying.graph, Size: 1,459,981,767,426 Bytes File: MS200-underlying.offsets, Size: 3,174,012,489 Bytes File: MS200-underlying.properties, Size: 1,515 Bytes Total Size: 1,463,155,781,430 Bytes These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels)	The weights of the graph in WebGraph format: File: MS200-weights.labels, Size: 1,199,053,831,206 Bytes File: MS200-weights.labeloffsets, Size: 3,090,041,102 Bytes File: MS200-weights.properties, Size: 186 Bytes Total Size: 1,202,143,872,494 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: MS200_edges_shas.txt Size: 899,640 Bytes SHASUM: 5bb635fc94aea3ee7b2b6a4aecbbb1fc6f77e1b5
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: MS200_offsets.bin Size: 11,315,947,600 Bytes SHASUM: 9192158aab65e1ca536a46183411d87452cd9ee3
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: MS200-wcc.bin Size: 5,657,973,796 Bytes SHASUM: 027e1b826659b5ec0f62921a4eb3ecd6c83fa76a
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
N2O Reordering (Binary)	The New to Old (N2O) reordering array of the graph in binary format and little endian order. It consists of \|V\| 4-Bytes elements and identifies the old ID of each vertex which is used in searching the name of vertex (protein) in the names.tar.gz file . Name: MS200-n2o.bin Size: 5,657,973,796 Bytes SHASUM: de833f1c36011af07c165f53760b82a49715537d
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: MS200.ojson Size: 757 Bytes SHASUM: 540c0bded9ab8d334574ed7dd7909435b617ecf3

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