diff --git a/errata.md b/content/errata.md similarity index 100% rename from errata.md rename to content/errata.md diff --git a/content/index.md b/content/index.md index 9ceb8bc..5b2e5c0 100644 --- a/content/index.md +++ b/content/index.md @@ -13,7 +13,7 @@ featured_image: 'background.png' ## Why this book? This book focuses on the _practical side_ of network science — **working with -network data** — to provide a more practical guide for data scientists to use network science. +network data** — to offer a useful guide for data scientists to use network science. We hope that this book can help researchers in day-to-day tasks, starting from the very act of conceptualizing networks through to sophisticated network @@ -70,11 +70,13 @@ the fundamentals of network data. {{< /details >}} -## Datasets and code +## Resources -### Focal networks +### Datasets: Focal networks +- [Readme](wwnd-readme.md) - [wwnd-focal-networks.zip](wwnd-focal-networks.zip) +### Errata - +- [Errata](errata.md) diff --git a/content/wwnd-readme.md b/content/wwnd-readme.md new file mode 100644 index 0000000..183d867 --- /dev/null +++ b/content/wwnd-readme.md @@ -0,0 +1,148 @@ +FOCAL POINTS - Working with network data +======================================== + +Working with network data +James Bagrow and Yong-Yeol Ahn +2024 + +https://cambridge.org/network-data + +Our book uses six *focal points*, real-world networks, as examples to +illustrate common issues and practices. Here we provide these networks for you +to download and use. Some networks come in multiple forms, such as both static +and dynamic representations and many have attributes associated with the nodes +or edges. Each network provided in GraphML and GML files; most libraries +such as NetworkX and igraph support these formats. + +Below we discuss some specifics for each network. Please see our book for more +information. + + + +Zachary Karate Club +------------------- + +The famous Zachary Karate Club. This network represent members of a university +martial arts club who interacted heavily outside the club, according to surveys +gathered by Wayne Zachary during the early 1970s. This club had a disagreement +and split into two groups, one following the club president and the other the +club's karate instructor. This group information is available in the `group` +node attribute. + +Original data `karate.mtx` (retrieved 22 August 2022) available at: +https://www.cise.ufl.edu/research/sparse/matrices/Newman/karate + +Reference: +W. W. Zachary, An information flow model for conflict and fission in small +groups, Journal of Anthropological Research 33, 452-473 (1977). +https://doi.org/10.1086/jar.33.4.3629752 + + + +Plant-pollinator network +------------------------ + +A network where nodes are either plant or pollinator species and links exist +only from plant to pollinator when field observations were made of that +pollinator acting to pollinate that plant. Nodes are identified by species +names. This network was collected from field observations conducted in Spain. + +Original data (network ID `M_PL_058`) (retrieved 22 August 2022) available at: +https://www.web-of-life.es/ + +Reference: +Bartomeus, I., Vilà, M. & Santamaría, L. Contrasting effects of invasive plants +in plant–pollinator networks. Oecologia 155, 761–770 (2008). +https://doi.org/10.1007/s00442-007-0946-1 + + + +Developer collaboration network +------------------------------- + +A network representing software developers contributing to open source projects +hosted by IBM on the GitHub online development platform. Nodes represent +developers (identified by their GitHub usernames) and links connect developers +who have edited one or more source code files in common, a simple measure of +collaboration. We treat the network as weighted by associating with each link a +weight counting the number of files commonly edited by the two developers. + +The `dynamic` directory contains yearly snapshots of the network from 2013--2017. + + +Original data (deposited 26 March 2019) available at: +https://doi.org/10.6084/m9.figshare.7893002.v1 + +Reference: +Bagrow, J., Bollt, E. An information-theoretic, all-scales approach to +comparing networks. Appl Netw Sci 4, 45 (2019). +https://doi.org/10.1007/s41109-019-0156-x + + + +Flavor network +-------------- + +A network representing recipe ingredients and the flavor molecules they +contain, extracted from food science reference texts. Nodes are identified with +integers prepended with "i" if the node is an ingredient or "c" if it is a +flavor chemical. Associated with each ingredient is its name and category. +Associated with each chemical is its name and CAS number. + +The `backbone` directory contains the multiscale backbone (Ch. 10) visualized +in the original reference and in Ch. 1. + +_Note_: +It was discovered by Augustine Koh (ak.augustine.koh@gmail.com) and Lav +Varshney (varshney@illinois.edu) that "Farnesol", a flavor compound, is present +both as an ingredient (ID i339) and compound (ID c951). Thus, you may want to +remove farnesol from the ingredient list and from the ingredient-compound +network. + +Original data `ingr_comp.zip` and `flavor_network_backbone.zip` (retrieved 20 +October 2022) available at: +https://yongyeol.com/2011/12/15/paper-flavor-network.html + +Reference: +Ahn, YY., Ahnert, S., Bagrow, J. et al. Flavor network and the principles of +food pairing. Sci Rep 1, 196 (2011). +https://doi.org/10.1038/srep00196 + + + +Human Reference Interactome +--------------------------- + +A protein-protein interaction network derived from high-throughput assays. +Nodes are represented by standardized IDs that can be connected to GENCODE gene +annotation metadata. + +Original data `HuRI.tsv` (retrieved 22 August 2022) available at: +http://www.interactome-atlas.org/download + +Reference: +Luck, K., Kim, DK., Lambourne, L. et al. A reference map of the human binary +protein interactome. Nature 580, 402–408 (2020). +https://doi.org/10.1038/s41586-020-2188-x + + + +Malawi Sociometer Network +------------------------- + +A face-to-face contact network between 86 individuals living in a rural village +in Malawi. Edge weights denote the number of contacts between individuals +during the study. + +The `dynamic` directory contains the dynamic network stored as a multigraph. +Note that the contact day has been renumbered compared to the original release +to match the contact time. + +Original data `tnet_malawi_pilot.csv` (retrieved 22 August 2022) available at: +http://www.sociopatterns.org/datasets/contact-patterns-in-a-village-in-rural-malawi/ + +Reference: +Ozella, L. et al., Using wearable proximity sensors to characterize social +contact patterns in a village of rural Malawi, EPJ Data Science 10, 46 (2021). +https://doi.org/10.1140/epjds/s13688-021-00302-w + diff --git a/hugo.toml b/hugo.toml index 60adcf1..8d28e1c 100644 --- a/hugo.toml +++ b/hugo.toml @@ -55,4 +55,4 @@ url = "/#why-this-book" name = "Resources" identifier = "resources" weight = 400 -url = "/#datasets-and-code" +url = "/#resources"