MS-BioGraphs MSA200 | DIPSA: Data-Intensive Parallel Systems and Algorithms

Name	MS-BioGraphs – MSA200
URL	https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA200
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	Yes
Number of Vertices	1,757,323,526
Number of Edges	500,444,322,597
Maximum In-Degree	658,879
Maximum Out-Degree	709,176
Minimum Weight	98
Maximum Weight	634,925
Number of Zero In-Degree Vertices	6,437,984
Number of Zero Out-Degree Vertices	7,471,315
Average In-Degree	285.8
Average Out-Degree	286.0
Size of The Largest Weakly Connected Component	496,880,685,957
Number of Weakly Connected Components	221,467,156
Creation Details	MS-BioGraphs: Sequency Similarity Graph Datasets
Format	WebGraph
License	CC BY-NC-SA
QUB IDF	2223-052
DOI	10.5281/zenodo.7820815
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: MSA200-underlying.graph, Size: 1,558,147,532,780 Bytes File: MSA200-underlying.offsets, Size: 4,319,801,854 Bytes File: MSA200-underlying.properties, Size: 1,517 Bytes Total Size: 1,562,467,336,151 Bytes These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels)	The weights of the graph in WebGraph format: File: MSA200-weights.labels, Size: 1,105,784,580,128 Bytes File: MSA200-weights.labeloffsets, Size: 4,123,546,304 Bytes File: MSA200-weights.properties, Size: 187 Bytes Total Size: 1,109,908,126,619 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: MSA200_edges_shas.txt Size: 895,200 Bytes SHASUM: de1ac0ddce536168881ca2e49e6d5f0cf5b82bb5
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: MSA200_offsets.bin Size: 14,058,588,216 Bytes SHASUM: c241d2dc4bdf46f60c1cd889ac367504d3f58805
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: MSA200-wcc.bin Size: 7,029,294,104 Bytes SHASUM: 2cb256d5e49e5dd0989715cb909fd8f27bfbd04c
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: MSA200_trans_offsets.bin Size: 14,058,588,216 Bytes SHASUM: 47787ac64fb4485da02e3bcdc1696a814adfdb86
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: MSA200.ojson Size: 897 Bytes SHASUM: 18e371cbb4bd9dbe6515e4528956ff32fb2e30c4

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