Evidome
Copyright (C) 2026 Kenneth L. Jones
ORCID: https://orcid.org/0009-0000-1289-4652

Kenneth L. Jones is the sole author and sole copyright holder of this software.
Copyright is held by him personally and not by Bioinformatic Solutions, LLC.

DUAL LICENSED
=============

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU Affero General Public License, version 3, as published by
the Free Software Foundation. See the LICENSE file for the full text.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

The AGPL permits use, study, modification and redistribution, including for
research. It requires that any modified version which is distributed -- or made
available to others over a network -- be released in full under the same
licence.

Alternatively, a separate commercial licence is available for uses that the
AGPL's conditions do not suit, including incorporating Evidome into a product
or service without releasing the corresponding source. Contact:

    Kenneth L. Jones
    Ken.Jones@bioinformaticsolutions.com

THIRD-PARTY COMPONENTS
======================

Evidome requires two Python packages, which pip installs with it. Neither is
distributed with Evidome.

- matplotlib (https://matplotlib.org), under the Matplotlib License
  (PSF-based, BSD-compatible). It draws the figures.
- scikit-learn (https://scikit-learn.org), under the BSD 3-Clause License.
  It fits the database-value model, and brings NumPy (https://numpy.org) and
  SciPy (https://scipy.org), each under the BSD 3-Clause License.

The evidence browser page (Evidome_Viewer_v<version>.html) loads DuckDB-WASM
(https://github.com/duckdb/duckdb-wasm), under the MIT License, from the
jsDelivr CDN (https://cdn.jsdelivr.net) when it is opened. DuckDB-WASM is not
distributed with Evidome. The page reads the evidence files inside the browser
and sends none of them anywhere.

REFERENCE DATA
==============

Evidome downloads reference data at run time; none of it is distributed with
this software. It comes from:

- Ensembl (https://www.ensembl.org), whose data are available without
  restriction on use; see Ensembl's own terms.
- NCBI Gene (https://www.ncbi.nlm.nih.gov/gene), files gene2ensembl and
  gene_orthologs. NCBI places no restrictions on the use or distribution of
  these data, but notes that submitters of original data may claim rights in
  them; see NCBI's "Website and Data Usage Policies and Disclaimers".
- Gene sets used for enrichment:
  - Reactome (https://reactome.org): data files under CC0 1.0.
  - Gene Ontology (http://geneontology.org), annotations as distributed in
    NCBI Gene's gene2go: CC BY 4.0. Attribution: the Gene Ontology Consortium.
  - WikiPathways (https://www.wikipathways.org): CC0 1.0.
  - MSigDB Hallmark gene sets (https://www.gsea-msigdb.org): CC BY 4.0,
    copyright Broad Institute, Inc., Massachusetts Institute of Technology and
    Regents of the University of California. Attribution: Liberzon A. et al.
    (2015) The Molecular Signatures Database Hallmark Gene Set Collection.
    Cell Systems 1:417-425. Other MSigDB collections (KEGG, BioCarta) carry
    other terms and are not used.
- Upstream-regulator networks: the OmniPath web service (https://omnipathdb.org),
  queried with license=commercial, so that only records supported by
  resources whose licences allow for-profit use are returned (OmniPath's own
  per-resource licence tracking). Datasets: CollecTRI transcription-factor
  regulons (Mueller-Dott S. et al. (2023) Nucleic Acids Research 51:10934) and
  OmniPath's curated signalling network (Tuerei D. et al., OmniPath).

Any further knowledge source added later (pathway, regulator, miRNA, drug
databases) is recorded here with its licence before it is used, because a
licence that is free for academic use is not necessarily free for commercial
use.

Evidome runs Paralome, when installed, as a separate program (to ask where
its shared locations are). Paralome is not distributed with Evidome.
