MS-BioGraphs MSA200

NameMS-BioGraphs – MSA200
URLhttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA200
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 Edges500,444,322,597
Maximum In-Degree658,879
Maximum Out-Degree709,176
Minimum Weight98
Maximum Weight634,925
Number of Zero In-Degree Vertices6,437,984
Number of Zero Out-Degree Vertices7,471,315
Average In-Degree285.8
Average Out-Degree286.0
Size of The Largest Weakly Connected Component496,880,685,957
Number of Weakly Connected Components221,467,156
Creation DetailsMS-BioGraphs: Sequency Similarity Graph Datasets
FormatWebGraph
LicenseCC BY-NC-SA
QUB IDF2223-052
DOI10.5281/zenodo.7820815
Citation
Koohi Esfahani, Mohsen, Boldi, Paolo, 
Vandierendonck, Hans, Kilpatrick, Peter, 
Vigna,Sebastiano. (2023). 
MS-BioGraphs - MSA200. 
https://doi.org/10.5281/zenodo.7820815. 
http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA200.
Bibtex
@misc{MS-BioGraphs-MSA200,
year = {2023},
author = {Mohsen Koohi Esfahani and Paolo Boldi and 
Hans Vandierendonck and Peter Kilpatrick and 
Sebastiano Vigna},
title = {{MS-BioGraphs - MSA200}},
doi = {10.5281/zenodo.7820815},
url = {http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA200},
howpublished= {\url{http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA200}}}


Files and Download Links

Underlying Graph The underlying graph in WebGraph format:
  • File: MSA200-underlying.graph, Size: 1,558,147,532,780 Bytes, Download Link
  • File: MSA200-underlying.offsets, Size: 4,319,801,854 Bytes, Download Link
  • File: MSA200-underlying.properties, Size: 1,517 Bytes, Download Link
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, Download Link
  • File: MSA200-weights.labeloffsets, Size: 4,123,546,304 Bytes, Download Link
  • File: MSA200-weights.properties, Size: 187 Bytes, Download Link
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
  • Download Link
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
  • Download Link
WCC (Binary) The Weekly-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
  • Download Link
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
  • Download Link
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
  • Download Link
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
  • Download Link


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
Weekly-Connected Components Size Distribution


MS-BioGraphs


Related Posts

Leave a Reply

Your email address will not be published. Required fields are marked *