MS-BioGraphs MS1 | DIPSA: Data-Intensive Parallel Systems and Algorithms

Name	MS-BioGraphs – MS1
URL	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS1
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	43,144,218
Number of Edges	2,660,495,200
Maximum Degree	14,212
Minimum Weight	3,680
Maximum Weight	634,925
Number of Zero-Degree Vertices	0
Average Degree	61.7
Size of The Largest WCC	124,003,393
Number of WCC	15,746,208
Creation Details	MS-BioGraphs: Sequency Similarity Graph Datasets
Format	WebGraph
License	CC BY-NC-SA
QUB IDF	2223-052
DOI	10.5281/zenodo.7820827
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: MS1-underlying.graph, Size: 6,300,911,484 Bytes File: MS1-underlying.offsets, Size: 77,574,569 Bytes File: MS1-underlying.properties, Size: 1,288 Bytes Total Size: 6,378,487,341 Bytes These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels)	The weights of the graph in WebGraph format: File: MS1-weights.labels, Size: 8,201,441,365 Bytes File: MS1-weights.labeloffsets, Size: 80,797,007 Bytes File: MS1-weights.properties, Size: 184 Bytes Total Size: 8,282,238,556 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: MS1_edges_shas.txt Size: 5,040 Bytes SHASUM: 27974edb4bf8f3b17b00ff3a72a703da18f3807a
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: MS1_offsets.bin Size: 345,153,752 Bytes SHASUM: 0abedde32e1ac7181897f82d10d40acfe14f2022
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: MS1-wcc.bin Size: 172,576,872 Bytes SHASUM: 4c491dd96e3582b70a203ae4a910001381278d75
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: MS1-n2o.bin Size: 172,576,872 Bytes SHASUM: b163320b6349fed7a00fb17c4a4a22e7d124b716
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: MS1.ojson Size: 736 Bytes SHASUM: c60afa0652955fd46f1bb8056380523504d69fa6

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