MS-BioGraphs MSA50 | DIPSA: Data-Intensive Parallel Systems and Algorithms

Name	MS-BioGraphs – MSA50
URL	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA50
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	Yes
Number of Vertices	1,757,323,526
Number of Edges	125,312,536,732
Maximum In-Degree	543,117
Maximum Out-Degree	297,981
Minimum Weight	98
Maximum Weight	634,925
Number of Zero In-Degree Vertices	6,437,984
Number of Zero Out-Degree Vertices	8,542,018
Average In-Degree	71.6
Average Out-Degree	71.7
Size of The Largest Weakly Connected Component	117,980,151,055
Number of Weakly Connected Components	363,090,851
Creation Details	MS-BioGraphs: Sequency Similarity Graph Datasets
Format	WebGraph
License	CC BY-NC-SA
QUB IDF	2223-052
DOI	10.5281/zenodo.7820821
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: MSA50-underlying.graph, Size: 410,094,612,576 Bytes File: MSA50-underlying.offsets, Size: 3,504,554,221 Bytes File: MSA50-underlying.properties, Size: 1,493 Bytes Total Size: 413,599,168,290 Bytes These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels)	The weights of the graph in WebGraph format: File: MSA50-weights.labels, Size: 284,756,409,010 Bytes File: MSA50-weights.labeloffsets, Size: 3,374,946,996 Bytes File: MSA50-weights.properties, Size: 186 Bytes Total Size: 288,131,356,192 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: MSA50_edges_shas.txt Size: 224,400 Bytes SHASUM: 6f56a6710ef6b6e7c01e90907f19c7a0099a272c
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: MSA50_offsets.bin Size: 14,058,588,216 Bytes SHASUM: 3272fb9c681648598f18ab5a10bbafb5bf48dca5
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: MSA50-wcc.bin Size: 7,029,294,104 Bytes SHASUM: 82e3ba326bb56c69edbe7fbb90ce70b731e3a7f2
Transposed’s Offsets (Binary)	The offsets array of the transposed 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. It helps to transpose the graph by performing one pass over edges. Name: MSA50_trans_offsets.bin Size: 14,058,588,216 Bytes SHASUM: 812d75359683dd235a1bd948566b306f43e7088d
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: MSA50.ojson Size: 892 Bytes SHASUM: 5767cdd2e0cddba1ba255afe9accfdbe5d5aabd2

Plots

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

In-Degree Distribution
Out-Degree Distribution
Weight Distribution
Vertex-Relative Weight Distribution
Degree Decomposition
Push and Pull Locality
Cell-Binned Average Weight Degree Distribution
Weakly-Connected Components Size Distribution