{
  "abstract": "Protein-protein interaction databases record evidence without weighing it. In BioGRID, an interaction asserted once by a single high-throughput screen and one confirmed by twenty laboratories across a dozen assays are the same kind of row in the same file. Tools built on such databases inherit that flattening: they draw every reported interaction as an edge, and the resulting picture states that two proteins interact without stating how much anyone should believe it. We present ProLiVis 2.0, a rewrite of the literature-centric visualization system of arXiv:2111.12794. It contributes three things. First, a citation-trust model that scores each interaction from seven terms, including a term for the number of independent laboratories behind the supporting publications, obtained by clustering those publications over shared institutional affiliations; a plain count of publications cannot distinguish five confirmations from one group publishing five times. Second, a deterministic reformulation of the center layout, closed-form and $O(n \\log n)$, which replaces the force-directed placement of the original and makes published figures regenerable from a session manifest. Third, an implementation that runs entirely in a web browser, with an embedded analytical database, requiring no installation and uploading no data. On BioGRID release 5.0.260 restricted to SARS-CoV-2, 24,344 of 34,540 reported interactions (70%) rest on a single publication, and raising the trust threshold to 0.2 leaves 11,320 of them. That the large majority of a curated interaction network is unreplicated is a fact no existing view of the database makes visible.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2609.15236",
  "author_total": 4,
  "authors": [
    {
      "name": "Melih Sözdinler"
    },
    {
      "name": "Yalçın Doksanbir"
    },
    {
      "name": "Gökhan Akpınar"
    },
    {
      "name": "Ege Aktan"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b9qq33zhhgvtk.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2609.15236",
  "fulltext_url": null,
  "id": "b9qq33zhhgvtk",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2609.15236",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cs.IR"
    ],
    [
      "arxiv",
      "cs.SI"
    ],
    [
      "arxiv",
      "q-bio.MN"
    ],
    [
      "openalex",
      "1312|Bioinformatics and Genomic Networks"
    ]
  ],
  "openalex": "W7213230758",
  "pdf_url": "https://arxiv.org/pdf/2609.15236",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b9qq33zhhgvtk.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:30Z",
      "native_id": "2609.15236",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2609.15236"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.MN",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "ProLiVis 2.0: Literature-Centric Visualization of Protein--Protein Interaction Networks, with a Citation-Trust Model for Interaction Evidence",
  "title_text": "ProLiVis 2.0: Literature-Centric Visualization of Protein--Protein Interaction Networks, with a Citation-Trust Model for Interaction Evidence",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:30Z",
  "url": "https://research.draconitic.com/paper/b9qq33zhhgvtk",
  "venue": "arXiv",
  "versions": []
}