MS-BioGraphs on IEEE DataPort

MS-BioGraph sequence similarity graph datasets are now publicly available on IEEE DataPort: https://dx.doi.org/10.21227/gmd9-1534.

To access the files, you need to register/login to IEEE DataPort and then please visit the datasets’ page. By saving the page as an HTML file such as dp.html, you may download the datasets using the following script:

dsname="MS1"
html_file="dp.html"

urls=`cat $html_file  | sed  -e 's/\&/\&/g'  | grep -Eo "(http|https)://[a-zA-Z0-9./?&=_%:-]*" | grep amazonaws  | sort | uniq | grep -E "$dsname[-_]"`

for u in $urls; do
    wget $u
    if [ $? != 0 ]; then break; fi
done

for f in $(find $1 -type f); do
    if [ $f = ${f%%\?*} ]; then continue; fi
    mv "${f}" "${f%%\?*}"
done

MS-BioGraphs

Related Posts

ParaGrapher Integrated to LaganLighter

Poplar source code has been integrated to LaganLighter and access to different WebGraph formats are available in LaganLighter:

  • PARAGRAPHER_CSX_WG_400_AP
  • PARAGRAPHER_CSX_WG_404_AP
  • PARAGRAPHERCSX_WG_800_AP

For further details, please refer to
– LaganLighter source coder Repository: https://github.com/DIPSA-QUB/LaganLighter, particularly, the graph.c file.
– ParaGrapher source code repository: https://github.com/DIPSA-QUB/ParaGrapher particularly, the src/webgraph.c and src/WG*.java files.

Read more about ParaGrapher and LaganLighter.

Related Posts

ParaGrapher Source Code For WebGraph Types

ParaGrapher source code for accessing WebGraphs have been published. The supported graph types are:

ParaGrapher uses its asynchronous and parallel API to implement these graph types. The user needs to implement a callback function that is called by the API upon completion of reading a block of edges. Poplar uses a shared memory for interaction between its C library and the Java library that deploys the WebGraph framework.

For further details, please refer to Poplar source code repository: https://github.com/DIPSA-QUB/ParaGrapher, particularly, src/webgraph.c and src/WG*.java files.

ParaGrapher

Related Posts

On Overcoming HPC Challenges of Trillion-Scale Real-World Graph Datasets – BigData’23 (Short Paper)

2023 IEEE International Conference on Big Data (BigData’23)
December 15-18, 2023, Sorrento, Italia

DOI: 10.1109/BigData59044.2023.10386309
PDF (Authors Copy)

Progress in High-Performance Computing in general, and High-Performance Graph Processing in particular, is highly dependent on the availability of publicly-accessible, relevant, and realistic data sets.

To ensure continuation of this progress, we (i) investigate and optimize the process of generating large sequence similarity graphs as an HPC challenge and (ii) demonstrate this process in creating MS-BioGraphs, a new family of publicly available real-world edge-weighted graph datasets with up to 2.5 trillion edges, that is, 6.6 times greater than the largest graph published recently. The largest graph is created by matching (i.e., all-to-all similarity aligning) 1.7 billion protein sequences. The MS-BioGraphs family includes also seven subgraphs with different sizes and direction types.

We describe two main challenges we faced in generating large graph datasets and our solutions, that are, (i) optimizing data structures and algorithms for this multi-step process and (ii) WebGraph parallel compression technique.

The datasets are available online on https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs.

BibTex

@INPROCEEDINGS{10.1109/BigData59044.2023.10386309,
   author = {Koohi Esfahani, Mohsen and Boldi, Paolo and Vandierendonck, Hans and Kilpatrick,  Peter and  Vigna, Sebastiano},  
  booktitle={2023 IEEE International Conference on Big Data (BigData'23)},  
  title={On Overcoming {HPC} Challenges of  Trillion-Scale Real-World Graph Datasets}, 
  year={2023},
  volume={},
  number={},
  pages={},
  location={Italy, Sorrento},
  publisher={IEEE Computer Society},
  doi={10.1109/BigData59044.2023.10386309}
}

MS-BioGraphs

Related Posts

Dataset Announcement: MS-BioGraphs, Trillion-Scale Public Real-World Sequence Similarity Graphs – IISWC’23 (Poster)

2023 IEEE International Symposium on Workload Characterization (IISWC’23)
October 1-3, 2023, Ghent, Belgium

DOI: 10.1109/IISWC59245.2023.00029
PDF Version

Progress in High-Performance Computing in general, and High-Performance Graph Processing in particular, is highly dependent on the availability of publicly-accessible, relevant, and realistic data sets.

In this paper, we announce publication of MS-BioGraphs, a new family of publicly-available real-world edge-weighted graph datasets with up to 2.5 trillion edges, that is, 6.6 times greater than the largest graph published recently.

We briefly review the two main challenges we faced in generating large graph datasets and our solutions, that are, (i) optimizing data structures and algorithms for this multi-step process and (ii) WebGraph parallel compression technique. We also study some characteristics of MS-BioGraphs.

The datasets are available on https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs .

Please visit https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-Sequence-Similarity-Graph-Datasets/ for a complete version of this paper.

Bibtex

@INPROCEEDINGS{10.1109/IISWC59245.2023.00029,
   author = {Koohi Esfahani, Mohsen and Boldi, Paolo and Vandierendonck, Hans and Kilpatrick,  Peter and  Vigna, Sebastiano},  
  booktitle={2023 IEEE International Symposium on Workload Characterization (IISWC'23)},  
  title={Dataset Announcement: {MS-BioGraphs}, Trillion-Scale Public Real-World Sequence Similarity Graphs}, 
  year={2023},
  volume={},
  number={},
  pages={},
  location={Belgium, Ghent},
  publisher={IEEE Computer Society},
  doi={10.1109/IISWC59245.2023.00029}
}

MS-BioGraphs

Related Posts

MS-BioGraphs: Sequence Similarity Graph Datasets

DOI: 10.48550/arXiv.2308.16744

PDF Version
arXiv Link

Progress in High-Performance Computing in general, and High-Performance Graph Processing in particular, is highly dependent on the availability of publicly-accessible, relevant, and realistic data sets.

To ensure continuation of this progress, we (i) investigate and optimize the process of generating large sequence similarity graphs as an HPC challenge and (ii) demonstrate this process in creating MS-BioGraphs, a new family of publicly available real-world edge-weighted graph datasets with up to 2.5 trillion edges, that is, 6.6 times greater than the largest graph published recently. The largest graph is created by matching (i.e., all-to-all similarity aligning) 1.7 billion protein sequences. The MS-BioGraphs family includes also seven subgraphs with different sizes and direction types.

We describe two main challenges we faced in generating large graph datasets and our solutions, that are, (i) optimizing data structures and algorithms for this multi-step process and (ii) WebGraph parallel compression technique. We present a comparative study of structural characteristics of MS-BioGraphs.

The datasets are available online on https://blogs.qub.ac.uk/DIPSA/MS-BioGraphs .

BibTex

@article{MS-BioGraphs-arxiv,
    title = {{MS-BioGraphs}: Sequence Similarity Graph Datasets},
    author = {Koohi Esfahani, Mohsen and Boldi, Paolo and Vandierendonck, Hans and Kilpatrick, Peter and Vigna, Sebastiano},
    year = 2023,
    journal = {CoRR},
    volume = {abs/2308.16744},
    doi = {10.48550/arXiv.2308.16744},
    url = {https://doi.org/10.48550/arXiv.2308.16744},
    archiveprefix = {arXiv},
    eprint = {2308.16744}
}

MS-BioGraphs

Related Posts

MS-BioGraphs MS

NameMS-BioGraphs – MS
URLhttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS
Graph ExplanationVertices represent proteins and each edge represents the sequence similarity between its two endpoints
Edge WeightedYes
DirectedNo
Number of Vertices1,757,323,526
Number of Edges2,488,069,027,875
Maximum Degree814,957
Minimum Weight98
Maximum Weight634,925
Number of Zero-Degree Vertices6,437,984
Average Degree1,415.8
Size of The Largest WCC2,486,890,448,664
Number of WCC148,861,367
Creation DetailsMS-BioGraphs: Sequency Similarity Graph Datasets
FormatWebGraph
LicenseCC BY-NC-SA
QUB IDF2223-052
DOI10.5281/zenodo.7820808
Citation
Koohi Esfahani, Mohsen, Boldi, Paolo, 
Vandierendonck, Hans, Kilpatrick, Peter, 
Vigna,Sebastiano. (2023). 
MS-BioGraphs - MS. 
https://doi.org/10.5281/zenodo.7820808. 
http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS.
Bibtex
@misc{MS-BioGraphs-MS,
year = {2023},
author = {Mohsen Koohi Esfahani and Paolo Boldi and 
Hans Vandierendonck and Peter Kilpatrick and 
Sebastiano Vigna},
title = {{MS-BioGraphs - MS}},
doi = {10.5281/zenodo.7820808},
url = {http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS},
howpublished= {\url{http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS}}}


Files and Download Links

Underlying Graph The underlying graph in WebGraph format:
  • File: MS-underlying.graph, Size: 7,342,853,446,646 Bytes, Download Link
  • File: MS-underlying.offsets, Size: 5,341,385,503 Bytes, Download Link
  • File: MS-underlying.properties, Size: 1,560 Bytes, Download Link
Total Size: 7,348,194,833,709 Bytes
These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels) The weights of the graph in WebGraph format:
  • File: MS-weights.labels, Size: 5,037,171,681,279 Bytes, Download Link
  • File: MS-weights.labeloffsets, Size: 5,070,752,590 Bytes, Download Link
  • File: MS-weights.properties, Size: 183 Bytes, Download Link
Total Size: 5,042,242,434,052 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: MS_edges_shas.txt
  • Size: 4,449,360 Bytes
  • SHASUM: 85d5b0896f8fa8a2b490ec6560937c45ced8b0d9
  • 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: MS_offsets.bin
  • Size: 14,058,588,216 Bytes
  • SHASUM: 15c3defdbb92f7b1fe48a3fb20530d99fa30c616
  • 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: MS-wcc.bin
  • Size: 7,029,294,104 Bytes
  • SHASUM: 30f12b738dde8f62aecb94239796b169512e6710
  • 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: MS.ojson
  • Size: 700 Bytes
  • SHASUM: e2eb3fcdd0c22838971ed2edea8e1ed081a77282
  • 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.

Degree Distribution
Weight Distribution
Vertex-Relative Weight Distribution
Degree Decomposition
Cell-Binned Average Weight Degree Distribution
Weekly-Connected Components Size Distribution


MS-BioGraphs


Related Posts

MS-BioGraphs MSA500

NameMS-BioGraphs – MSA500
URLhttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA500
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 Edges1,244,904,754,157
Maximum In-Degree229,442
Maximum Out-Degree814,461
Minimum Weight98
Maximum Weight634,925
Number of Zero In-Degree Vertices6,437,984
Number of Zero Out-Degree Vertices16,843,087
Average In-Degree711.0
Average Out-Degree715.3
Size of The Largest Weakly Connected Component1,244,203,865,823
Number of Weakly Connected Components148,861,367
Creation DetailsMS-BioGraphs: Sequency Similarity Graph Datasets
FormatWebGraph
LicenseCC BY-NC-SA
QUB IDF2223-052
DOI10.5281/zenodo.7820810
Citation
Koohi Esfahani, Mohsen, Boldi, Paolo, 
Vandierendonck, Hans, Kilpatrick, Peter, 
Vigna,Sebastiano. (2023). 
MS-BioGraphs - MSA500. 
https://doi.org/10.5281/zenodo.7820810. 
http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA500.
Bibtex
@misc{MS-BioGraphs-MSA500,
year = {2023},
author = {Mohsen Koohi Esfahani and Paolo Boldi and 
Hans Vandierendonck and Peter Kilpatrick and 
Sebastiano Vigna},
title = {{MS-BioGraphs - MSA500}},
doi = {10.5281/zenodo.7820810},
url = {http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA500},
howpublished= {\url{http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MSA500}}}


Files and Download Links

Underlying Graph The underlying graph in WebGraph format:
  • File: MSA500-underlying.graph, Size: 3,755,604,574,487 Bytes, Download Link
  • File: MSA500-underlying.offsets, Size: 4,811,273,232 Bytes, Download Link
  • File: MSA500-underlying.properties, Size: 1,537 Bytes, Download Link
Total Size: 3,760,415,849,256 Bytes
These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels) The weights of the graph in WebGraph format:
  • File: MSA500-weights.labels, Size: 2,520,671,185,509 Bytes, Download Link
  • File: MSA500-weights.labeloffsets, Size: 4,554,987,345 Bytes, Download Link
  • File: MSA500-weights.properties, Size: 187 Bytes, Download Link
Total Size: 2,525,226,173,041 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: MSA500_edges_shas.txt
  • Size: 2,226,360 Bytes
  • SHASUM: d9f692b6f4770f282ea62936293baf6a649c2b91
  • 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: MSA500_offsets.bin
  • Size: 14,058,588,216 Bytes
  • SHASUM: 3eab31d99426ed9f96af6b258fd1253544ba5461
  • 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: MSA500-wcc.bin
  • Size: 7,029,294,104 Bytes
  • SHASUM: 30f12b738dde8f62aecb94239796b169512e6710
  • 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: MSA500_trans_offsets.bin
  • Size: 14,058,588,216 Bytes
  • SHASUM: 220a2a5c60baaedc8913720862b535ba6cabb5bd
  • 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: MSA500.ojson
  • Size: 902 Bytes
  • SHASUM: 5eaebdff2dc56925a0b4751f579ebeabb6e3bee5
  • 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

MS-BioGraphs MS200

NameMS-BioGraphs – MS200
URLhttps://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS200
Graph ExplanationVertices represent proteins and each edge represents the sequence similarity between its two endpoints
Edge WeightedYes
DirectedNo
Number of Vertices1,414,493,449
Number of Edges502,930,788,612
Maximum Degree745,735
Minimum Weight460
Maximum Weight634,925
Number of Zero-Degree Vertices0
Average Degree355.6
Size of The Largest WCC485,867,547,569
Number of WCC338,348,495
Creation DetailsMS-BioGraphs: Sequency Similarity Graph Datasets
FormatWebGraph
LicenseCC BY-NC-SA
QUB IDF2223-052
DOI10.5281/zenodo.7820812
Citation
Koohi Esfahani, Mohsen, Boldi, Paolo, 
Vandierendonck, Hans, Kilpatrick, Peter, 
Vigna,Sebastiano. (2023). 
MS-BioGraphs - MS200. 
https://doi.org/10.5281/zenodo.7820812. 
http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS200.
Bibtex
@misc{MS-BioGraphs-MS200,
year = {2023},
author = {Mohsen Koohi Esfahani and Paolo Boldi and 
Hans Vandierendonck and Peter Kilpatrick and 
Sebastiano Vigna},
title = {{MS-BioGraphs - MS200}},
doi = {10.5281/zenodo.7820812},
url = {http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS200},
howpublished= {\url{http://blogs.qub.ac.uk/DIPSA/MS-BioGraphs-MS200}}}


Files and Download Links

Underlying Graph The underlying graph in WebGraph format:
  • File: MS200-underlying.graph, Size: 1,459,981,767,426 Bytes, Download Link
  • File: MS200-underlying.offsets, Size: 3,174,012,489 Bytes, Download Link
  • File: MS200-underlying.properties, Size: 1,515 Bytes, Download Link
Total Size: 1,463,155,781,430 Bytes
These files are validated using ‘Edge Blocks SHAs File’ as follows.
Weights (Labels) The weights of the graph in WebGraph format:
  • File: MS200-weights.labels, Size: 1,199,053,831,206 Bytes, Download Link
  • File: MS200-weights.labeloffsets, Size: 3,090,041,102 Bytes, Download Link
  • File: MS200-weights.properties, Size: 186 Bytes, Download Link
Total Size: 1,202,143,872,494 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: MS200_edges_shas.txt
  • Size: 899,640 Bytes
  • SHASUM: 5bb635fc94aea3ee7b2b6a4aecbbb1fc6f77e1b5
  • 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: MS200_offsets.bin
  • Size: 11,315,947,600 Bytes
  • SHASUM: 9192158aab65e1ca536a46183411d87452cd9ee3
  • 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: MS200-wcc.bin
  • Size: 5,657,973,796 Bytes
  • SHASUM: 027e1b826659b5ec0f62921a4eb3ecd6c83fa76a
  • 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
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: MS200-n2o.bin
  • Size: 5,657,973,796 Bytes
  • SHASUM: de833f1c36011af07c165f53760b82a49715537d
  • 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: MS200.ojson
  • Size: 757 Bytes
  • SHASUM: 540c0bded9ab8d334574ed7dd7909435b617ecf3
  • 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.

Degree Distribution
Weight Distribution
Vertex-Relative Weight Distribution
Degree Decomposition
Cell-Binned Average Weight Degree Distribution
Weekly-Connected Components Size Distribution


MS-BioGraphs


Related Posts

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


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