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DIGITALSOMA v3.0.0 — LICENCE AND NOTICES
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A Dynamic Physiological Digital Twin Engine for Living Animals

Copyright (c) 2024–2026 Dr. ir. Ali Youssef
  ORCID: 0000-0002-9986-5324
  Adjunct Professor, "Computational Bioecosystems"
  Digital Agroecosystems Laboratory, University of Manitoba
  Winnipeg, Manitoba, Canada & Founder, BioTwinRs Ltd., Leuven, Belgium

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PART I — LICENCE
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DigitalSoma is released under the Creative Commons Attribution –
NonCommercial – ShareAlike 4.0 International Licence (CC BY-NC-SA 4.0).

Full legal text:
  https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode

                         PLAIN-LANGUAGE SUMMARY

You are free to:

  Share    Copy, download, and redistribute DigitalSoma and any
           derivative works in any medium or format.

  Adapt    Remix, transform, extend, and build upon DigitalSoma —
           adding new solvers, species templates, integrations, or
           derived frameworks.

Under the following conditions:

  Attribution (BY)
           Every use, distribution, or publication that incorporates
           DigitalSoma or any derivative of it must give clear and
           prominent credit to the original author. The minimum required
           attribution is:

             Youssef, A. (2026). DigitalSoma: A Dynamic Physiological
             Digital Twin Engine for Living Animals (v3.0.0).
             Digital Agroecosystems Laboratory, University of Manitoba
             & BioTwinRs Ltd., Leuven, Belgium.
             https://github.com/Pierianspring/digitalsoma
             ORCID: 0000-0002-9986-5324

           You must also indicate clearly if you have modified the
           original work and may not imply that the original author
           endorses your use, your modifications, or your conclusions.

  NonCommercial (NC)
           You may not use DigitalSoma, in whole or in part, for
           commercial purposes without explicit prior written permission
           from the copyright holder.

           See Part II of this licence for the precise definition of
           commercial use and the process for obtaining a commercial
           licence.

  ShareAlike (SA)
           If you distribute, publish, or release any derivative of
           DigitalSoma — including modified versions of the source code,
           extended frameworks, or new software systems that incorporate
           DigitalSoma components — you must release your derivative work
           under this same licence: CC BY-NC-SA 4.0.

           You may not release derivatives under any more restrictive
           licence, nor under any licence that permits commercial use,
           without explicit written permission from the copyright holder.

                              GENERAL NOTICES

  No warranties are given. DigitalSoma is provided "as is", without
  warranty of any kind, express or implied, including but not limited to
  the warranties of merchantability, fitness for a particular purpose,
  and non-infringement.

  In no event shall the author or copyright holder be liable for any
  claim, damages, or other liability arising from, out of, or in
  connection with the software or the use or other dealings in the
  software — including but not limited to adverse animal welfare outcomes,
  incorrect clinical assessments, or errors in regulatory submissions
  arising from use of DigitalSoma output.

  This licence does not grant any right to use the name "DigitalSoma",
  "BioTwinRs", or the name of the copyright holder in any advertising,
  promotional, or endorsement context without prior written consent.

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PART II — DEFINITION OF COMMERCIAL USE AND COMMERCIAL LICENSING
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                      WHAT COUNTS AS COMMERCIAL USE

The following uses are considered commercial and require explicit prior
written permission from the copyright holder before any use begins:

  (a) PRODUCT SALE
      Selling, licensing, or otherwise commercialising any software
      product, application, platform, or tool that incorporates
      DigitalSoma in whole or in part — whether as source code, compiled
      binary, API, or cloud-hosted service.

  (b) PAID CONSULTING AND PROFESSIONAL SERVICES
      Using DigitalSoma as part of any paid consulting engagement,
      professional service, or fee-for-service analytical work, whether
      the fee is charged to the client directly or recovered indirectly
      through overhead, project billing, or institutional recharge
      mechanisms outside of publicly funded academic grants.

  (c) COMMERCIAL PRODUCTION AND INDUSTRY USE
      Using DigitalSoma in any commercial livestock production operation,
      commercial aquaculture facility, veterinary practice operating for
      profit, animal health company, precision livestock farming
      technology company, or any other for-profit enterprise — regardless
      of whether the use is internal (operational monitoring) or external
      (client-facing service).

  (d) INDUSTRY-FUNDED RESEARCH
      Using DigitalSoma in any research project where the primary funder
      is a commercial entity (company, industry association, or venture-
      backed organisation), or where any commercial partner holds rights
      to exploit the research outputs for profit. This includes industry-
      academic partnership agreements and collaborative research and
      development agreements (CRDAs) where a commercial entity is a
      named participant.

  (e) SPIN-OUT AND COMMERCIALISATION ACTIVITIES
      Using DigitalSoma as part of a technology transfer, spin-out
      company formation, patent application, or any other activity
      intended to generate commercial value from the software or from
      research results produced using it.

                      WHAT IS EXPLICITLY NOT COMMERCIAL USE

The following uses are explicitly permitted without any fee and without
requiring permission, provided the attribution requirements in Part I
are met:

  (i)  Academic and university research — including thesis work,
       postdoctoral research, and faculty research — at any accredited
       academic institution, regardless of whether the research is
       supported by public grant funding (e.g. NSERC, CIHR, EU Horizon,
       BBSRC, NSF, NIH, or equivalent national research councils).

  (ii) Teaching and educational use — including course demonstrations,
       student assignments, laboratory practicals, and workshop training
       at educational institutions.

  (iii) Non-profit research organisations, government research agencies,
        and intergovernmental bodies (e.g. FAO, OIE/WOAH, WHO) using
        DigitalSoma for public-interest research with no commercial
        exploitation of outputs.

  (iv) Publication of research results, datasets, and methods in peer-
       reviewed scientific literature, preprint servers, or conference
       proceedings — provided the attribution requirement is met and the
       published work itself is not a commercial product.

  (v)  Development of new open-source tools, solvers, or extensions
       released under CC BY-NC-SA 4.0 or a compatible non-commercial
       licence.

                      HOW TO OBTAIN A COMMERCIAL LICENCE

Commercial use requires a separate written licence agreement. To request
a commercial licence:

  Contact:  info@biotwinrs.com
  Subject:  "DigitalSoma Commercial Licence Request"
  Include:  (1) Organisation name and type
            (2) Intended use and deployment context
            (3) Estimated scale of use (number of animals, users, sites)
            (4) Whether the use involves regulatory submissions

Commercial licences are negotiated individually. Terms including fees,
scope, duration, sublicensing rights, and support arrangements are agreed
in writing before any commercial use begins. The copyright holder
reserves the right to decline any commercial licence request.

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PART III — SCIENTIFIC DISCLAIMERS
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DigitalSoma is a research and educational software framework. The
following limitations apply to all built-in computational components.

  BUILT-IN SOLVERS
  The six built-in solvers are provided as initialisation scaffolding and
  working starting points based on established biological principles and
  published equations. They have not been validated as clinical decision-
  support tools in any species or production environment. They are
  intended to be supplemented, replaced, or overridden by user-defined,
  validated computational models appropriate to the specific species, age
  class, production system, and research question at hand.

  PHYSIOLOGICAL STRESS INDEX (PSI)
  The Physiological Stress Index is an original composite formulation
  developed by the author specifically for DigitalSoma. It serves two
  purposes only: (1) to trigger the Threshold Event System alarm when
  multi-system stress is simultaneously detected, and (2) to provide a
  proxy input to the VeDDRA Dyspnoea adverse event flag (PT 506).

  THE PSI HAS NOT BEEN VALIDATED against independent welfare assessments,
  clinical outcomes, or gold-standard stress measures in any species. The
  composite formula, the equal weighting of components, and the 0.70
  threshold are not derived from empirical optimisation. The PSI must not
  be used as a standalone welfare indicator, clinical diagnostic
  criterion, or welfare certification instrument without independent
  species-specific validation.

  VeDDRA ADVERSE EVENT FLAGS
  VeDDRA adverse event flags produced by DigitalSoma are generated by
  rule-based threshold comparison against species-relative baselines.
  These flags are indicators for further investigation, not confirmed
  diagnoses. All adverse event reports must be reviewed by a qualified
  veterinarian before submission to any regulatory authority.

  NO CLINICAL USE WITHOUT VALIDATION
  DigitalSoma output must not be used as the sole basis for clinical
  decisions, treatment choices, welfare certification, or regulatory
  reporting without independent validation of the relevant solver models
  for the specific animal population, production system, and context.

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PART IV — THIRD-PARTY VOCABULARY AND STANDARDS NOTICES
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DigitalSoma uses Uniform Resource Identifiers (URIs) from internationally
recognised ontologies and terminology standards as property identifiers,
observation codes, and unit codes. No ontology content, vocabulary
database, or terminology file is bundled with this distribution. URIs are
used exclusively as stable, globally unique identifiers pointing to
externally maintained definitions.

  ── Uberon Multi-Species Anatomy Ontology ──────────────────────────────
  URI base:  http://purl.obolibrary.org/obo/UBERON_
  Licence:   CC BY 3.0
  Citation:  Mungall, C.J., et al. (2012). Genome Biology, 13, R5.
  Source:    https://obofoundry.org/ontology/uberon.html

  ── SNOMED CT — Systematized Nomenclature of Medicine ─────────────────
  URI base:  http://snomed.info/sct/
  Licence:   SNOMED CT Affiliate Licence (open-source projects)
  Source:    https://www.snomed.org/snomed-ct/get-snomed

  ── NCBITaxon — NCBI Taxonomy Ontology ────────────────────────────────
  URI base:  http://purl.obolibrary.org/obo/NCBITaxon_
  Licence:   Public domain (US Government work)
  Source:    https://www.ncbi.nlm.nih.gov/taxonomy

  ── UCUM — Unified Code for Units of Measure ──────────────────────────
  URI base:  http://unitsofmeasure.org/
  Licence:   Open licence for unit code identifiers
  Citation:  Schadow & McDonald (2009). Regenstrief Institute.
  Source:    https://ucum.org

  ── LOINC — Logical Observation Identifiers Names and Codes ───────────
  URI base:  http://loinc.org/
  Licence:   LOINC Licence Agreement (free for use with attribution)
  Citation:  McDonald, C.J., et al. (2003). Clinical Chemistry, 49(4).
  Source:    https://loinc.org/licence/

  ── VeDDRA — Veterinary Dictionary for Drug Regulatory Activities ──────
  Revision:  EMA/CVMP/PhVWP/10418/2009 Rev.16, effective 1 October 2025
  URI base:  https://www.ema.europa.eu/en/veterinary-regulatory/
  Licence:   EMA open-data policy
  Source:    https://www.ema.europa.eu/en/veterinary-regulatory-overview/
             post-authorisation-veterinary-medicines/pharmacovigilance-
             veterinary-medicines/eudravigilance-veterinary

  ── PATO — Phenotype and Trait Ontology ───────────────────────────────
  URI base:  http://purl.obolibrary.org/obo/PATO_
  Licence:   CC BY 3.0
  Source:    https://obofoundry.org/ontology/pato.html

  ── HP — Human Phenotype Ontology ─────────────────────────────────────
  URI base:  http://purl.obolibrary.org/obo/HP_
  Licence:   hpoplus licence
  Source:    https://hpo.jax.org

  ── MP — Mammalian Phenotype Ontology ─────────────────────────────────
  URI base:  http://purl.obolibrary.org/obo/MP_
  Licence:   CC BY 4.0
  Source:    https://www.informatics.jax.org/

  ── HL7 FHIR R4 ───────────────────────────────────────────────────────
  Standard:  HL7 FHIR Release 4 (v4.0.1)
  Licence:   CC0 (specification); implementation carries own licence
  Source:    https://www.hl7.org/fhir/R4/

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PART V — CONTACT
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  Commercial licensing:   info@biotwinrs.com
  Repository:             https://github.com/Pierianspring/digitalsoma
  PyPI:                   https://pypi.org/project/digitalsoma
  Author ORCID:           https://orcid.org/0000-0002-9986-5324

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END OF LICENCE AND NOTICES
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