10. The citation network

Papers cite each other. Within your library, those citations draw a map: the papers everyone builds on, and the groups that read each other.

Fetching the citations

$ mosaic index --enrich-citations
Warning: full_text_index is enabled but pymupdf is not installed.
Run: pipx inject mosaic-search pymupdf
Falling back to metadata-only indexing.
Indexing 107 papers…
Indexed 0 new paper(s). 107 already indexed.
Enriching citation graph for 107 papers…

Citation edges stored for 42 paper(s). 3 skipped (already enriched or no local matches).

--enrich-citations asks OpenAlex, then Crossref, for the reference list of every cached paper, and keeps the references that point to another paper in your cache. A reference to a paper you never searched for is dropped: the map covers your library, not the literature. The citation step needs no embedding model; it runs even when indexing fails.

With rag.citations.enabled = true in the configuration file, mosaic ask also favours papers that are well cited within your library (Citation graph).

The hubs

$ mosaic network --top 5

Citation Network  51 papers · 128 edges

 #      Title                                                    Authors                              Year       Degree
────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 1      Tutorial: Physics and modeling of Hall thrusters         Jean-Pierre Bœuf                     2017           27
 2      Theory for the anomalous electron transport in Hall      Trevor Lafleur et al.                2016           17
        effect thrusters. II. Kinetic model
 3      Latest progress in Hall thrusters plasma modelling       Taccogna, F. & Garrigues, L.         2019           14
 4      E × B electron drift instability in Hall thrusters:      Jean-Pierre Bœuf & Laurent           2018           14
        Particle-in-cell simulations vs.…                        Garrigues
 5      3D particle-in-cell study of the electron drift          W. Villafana et al.                  2023           10
        instability in a Hall Thruster using…
Showing top 5 of 51 papers by degree.

mosaic network lists the papers with the most citation links inside your library, cited or citing. In a library built from searches on one subject, these are the reviews and the founding papers.

Clusters and a graph file

$ mosaic network --query "thruster" --cluster --top 3 --output graph.json
Graph written to: graph.json

Citation Network  49 papers · 127 edges

─────────────────────── Cluster 1 — Tutorial: Physics and modeling of Hall thrusters (12 papers) ───────────────────────
 Hub    Tutorial: Physics and modeling of Hall thrusters                     Jean-Pierre Bœuf     2017        degree=27
        Near-Wall Pathways of Anomalous Electron Transport in Hall           Zhe Liu et al.       2026         degree=7
        Thrusters Revealed by 3D PIC…
        Numerical Study of Electron Cyclotron Drift Instability:             Zahra Asadi et al.   2019         degree=6
        Application to Hall Thruster
  … and 9 more paper(s)

─────────────────────────── Cluster 2 — Concept of the generalized reduced-order… (9 papers) ───────────────────────────
 Hub    Concept of the generalized reduced-order particle-in-cell scheme   M. Reza et al.         2023        degree=10
        and verification in an…
        Enhancing one-dimensional particle-in-cell simulations to          Farbod Faraji et al.   2022         degree=9
        self-consistently resolve…
        Effects of the neutral dynamics model on the particle-in-cell      Farbod Faraji et al.   2023         degree=8
        simulations of a Hall…
  … and 6 more paper(s)

────────────────────── Cluster 3 — Latest progress in Hall thrusters plasma modelling (8 papers) ───────────────────────
 Hub    Latest progress in Hall thrusters plasma modelling         Taccogna, F. & Garrigues, L.   2019        degree=14
        Kinetic effects in a Hall thruster discharge               Igor Kaganovich et al.         2007         degree=5
        Full Particle-In-Cell Simulation Methodology for           James Szabo et al.             2013         degree=4
        Axisymmetric Hall Effect Thrusters
  … and 5 more paper(s)

───────────────────────────── Cluster 4 — Plasma oscillations in Hall thrusters (8 papers) ─────────────────────────────
 Hub    Plasma oscillations in Hall thrusters                               Edgar Choueiri        2001        degree=10
 Hub    3D particle-in-cell study of the electron drift instability in a    W. Villafana et al.   2023        degree=10
        Hall Thruster using…
        Investigation of the Optical Emission of Hall Effect Thrusters      Tarek Ben Slimane     2023         degree=5
        using a Collisional…
  … and 5 more paper(s)

──────────────────────── Cluster 5 — Theory for the anomalous electron transport in… (7 papers) ────────────────────────
 Hub    Theory for the anomalous electron transport in     Trevor Lafleur et al.                  2016        degree=17
        Hall effect thrusters. II. Kinetic model
        E × B electron drift instability in Hall           Jean-Pierre Bœuf & Laurent Garrigues   2018        degree=14
        thrusters: Particle-in-cell simulations vs.…
        Anomalous cross-field transport in a Hall          Brown ZA & Jorns BA.                   2023         degree=5
        thruster inferred from direct measurement of…
  … and 4 more paper(s)

────────────────────────── Cluster 6 — Electron-wall interaction in Hall thrusters (5 papers) ──────────────────────────
 Hub    Electron-wall interaction in Hall thrusters                      Yevgeny Raitses et al.   2005         degree=5
        Anomalous cross field electron transport in a Hall effect        C. Boniface et al.       2006         degree=4
        thruster
        Effect of Anode Dielectric Coating on Hall Thruster Operation    L. Dorf et al.           2003         degree=3
  … and 2 more paper(s)

• --query starts from the cached papers matching the words and follows citations --depth hops out (2 by default).
• --cluster groups papers that cite each other, with Louvain community detection when the analysis extra (networkx) is installed, by connected components otherwise.
• --output writes the graph: .json for D3 or Gephi, .dot for Graphviz, .md for a Mermaid diagram that GitHub, Obsidian and this site render.

What you learned

mosaic index --enrich-citations, mosaic network for hubs, clusters and graph files. Guides: Citation graph, Citation network; reference: network.

The tutorial ends here. The Cookbook has a recipe for each task, and the Reference every option.