MS-BioGraphs MSA50

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NameMS-BioGraphs – MSA50
URLhttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA50
Download Linkhttps://doi.org/10.21227/gmd9-1534
Script for Downloading All Fileshttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-on-IEEE-DataPort/
Validating and Sample Codehttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-Validation/
Graph ExplanationVertices represent proteins and each edge represents the sequence similarity between its two endpoints
Edge WeightedYes
DirectedYes
Number of Vertices1,757,323,526
Number of Edges125,312,536,732
Maximum In-Degree543,117
Maximum Out-Degree297,981
Minimum Weight98
Maximum Weight634,925
Number of Zero In-Degree Vertices6,437,984
Number of Zero Out-Degree Vertices8,542,018
Average In-Degree71.6
Average Out-Degree71.7
Size of The Largest Weakly Connected Component117,980,151,055
Number of Weakly Connected Components363,090,851
Creation DetailsMS-BioGraphs: Sequency Similarity Graph Datasets
FormatWebGraph
LicenseCC BY-NC-SA
QUB IDF2223-052
DOI10.5281/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://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: 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


MS-BioGraphs


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