Experimental research software · Synthetic data · Not for clinical use · Not scientifically validated
This is the complete set of papers, theses, specifications, and model records cited or used as evidence in the project documents (commit e3d560e). Bibliographic details are reproduced as written in those documents, and every DOI, PMID, PMCID, and URL was mechanically checked against the repository source. Fields absent from the documents are left blank. “Access scope” records what the project actually read (for example, full text, author manuscript, or abstract only); works read only as abstracts were not used to support relation direction or mapping. Copyright remains with each author or publisher; this site includes bibliographic information and brief citations only.
Claude Sonnet 5.5 extracted this list from repository documents. Codex gpt-6.1-terra then checked 73 identifiers against the repository, finding one omission and one overstatement. The integrator rechecked both against the source text before incorporating them.
[Boppana2023] Boppana et al.. (2023) Sci Data 10:452
Access scope: full text (open access, CC BY 4.0 per S23 table) · Use: Cited as the basis for the current practice of using the UBERON ID first for vascular identifiers and the FMA ID when there is none, which set the anatomy node identifier rule.
Cited in: docs/evidence_review/evidence_cards.md
[BurkhoffTyberg1993] Burkhoff and Tyberg. (1993)
Access scope: abstract only (quotation in c_sources.json is the PubMed abstract) · Use: Cited as a theoretical study in setting the limit that an experiment lowering only left-ventricular contractility must not promise pulmonary edema or a clinical heart-failure phenotype.
[Colunga2020] Colunga et al.. (2020) J Physiol 598:3203
Access scope: quotations only (Wiley Scholar Gateway connector passages) · Use: Cited as an independent restatement showing what reduced derivative models of the Smith model omit and the mmHg-based unit convention.
[S2_Cook2013] Cook, Neal, Bookstein, Gennari. (2013) Ontology of physics for biology: representing physical dependencies as a basis for biological processes. J Biomed Semantics 4:41
Access scope: full text (PubMed/PMC and Europe PMC XML retained in docs/evidence) · Use: Supported, on the basis of the dependency classes of the OPB (Ontology of Physics for Biology), the decision to separate variable-equivalence notation and equation dependencies into different layers.
[deBono2022] de Bono et al.. (2022) Front Physiol 13:795303
Access scope: full text (open access, CC BY per S23 table) · Use: Supported the design of placing valves as compartment-boundary nodes, on the point that route nodes represent compartment boundaries at valves.
Cited in: docs/evidence_review/evidence_cards.md
[Groene2024] Gröne et al.. (2024) J Integr Bioinform 21(3)
Access scope: full text (open access, CC BY 4.0 per S23 table) · Use: Cited as counter-evidence that the ApiNATOMY platform uses FMA, recording a limitation of the identifier rule.
Cited in: docs/evidence_review/evidence_cards.md
[Erdemir2020] Erdemir. (2020)
Access scope: text read (PubMed) · Use: Used for the literature judgement that validation procedures are prescribed but there is no universal numerical acceptance criterion, on which the Smith 2004 RK4 value comparison was set as report-only, with no pass/fail line.
[S1_Gennari2011] Gennari, Neal, Galdzicki, Cook. (2011) Multiple ontologies in action: composite annotations for biosimulation models. J Biomed Inform 2011;44(1):146-154
Access scope: full text (PubMed/PMC author manuscript); quotations only, not redistributed · Use: Used as the basis for designing the variable-semantics distinction rules and the SHACL shape rules, from the grammar of composite annotations (one OPB property and a physical-entity reference) and the limits of exact-match comparison.
[Herr2023] Herr et al.. (2023) Sci Data 10:171
Access scope: full text (open access, CC BY 4.0 per S23 table) · Use: Cited, as current practice in which HRA anatomical structures are linked to Uberon and FMA is used when needed, in support of the identifier rule.
Cited in: docs/evidence_review/evidence_cards.md
[Hicks2015] Hicks. (2015)
Access scope: abstract only · Use: Read as part of the simulation verification and credibility literature review, and included in the list of bases for deciding how to report the RK4 value comparison.
[Imam2025] Imam et al.. (2025) Front Neuroinform 19:1541184
Access scope: full text (open access, CC BY 4.0 per S23 table) · Use: Cited as the basis of the identifier rule, on the point that SCKAN uses UBERON as the backbone of anatomical terms and FMA as a supplement.
Cited in: docs/evidence_review/evidence_cards.md
[Jones2021] Jones et al.. (2021) J Physiol 599:4991
Access scope: quotations only (Wiley Scholar Gateway connector passages) · Use: Cited as an independent restatement for checking parameter units (mmHg, etc.) and identifiability limits in studies derived from the Smith model.
[Lloyd2008_PMR] Lloyd CM, Lawson JL, Hunter PJ, Nielsen PF. (2008) Bioinformatics 2008;24(18):2122-2123
Access scope: not read (citation required by the PMR licence/citation page) · Use: Recorded as the Physiome Model Repository citation required when redistributing the Smith 2004 CellML encoding.
[Meng2026] Meng et al.. (2026) MedComm
Access scope: open access quotation checked against downloaded text (CC BY) · Use: A sentence stating that “Generally” a patent foramen ovale does not cause a hemodynamically clinically significant shunt; used as the basis for keeping small heart valves and the foramen ovale only as catalogue nodes.
Cited in: docs/evidence_review/evidence_cards.md
[Mulugeta2018] Mulugeta. (2018)
Access scope: text read (PubMed) · Use: Used for the literature judgement that validation procedures are prescribed but there is no universal numerical acceptance criterion, on which the Smith 2004 RK4 value comparison was set as report-only.
[Mueller2023] Müller et al.. (2023)
Access scope: open access quotation checked against downloaded text (CC BY 4.0) · Use: Cited as a result of the survey of current closed-loop models, that the ADAVN model uses valve inertia and Bernoulli terms for all four valves.
Cited in: docs/evidence_review/evidence_cards.md
[Munarko2022] Munarko et al.. (2022) Front Physiol 13:820683
Access scope: full text (open access, CC BY per S23 table) · Use: Cited as counter-evidence that the most common ontologies in the Physiome repository are GO, OPB, FMA, and ChEBI, recording a limitation of the identifier rule.
Cited in: docs/evidence_review/evidence_cards.md
[Nawrot2025] Nawrot et al.. (2025) Cardiol J
Access scope: open access quotation checked against downloaded text (CC BY-NC-ND) · Use: A statement that the Eustachian valve has no significance in the adult circulation; used as the basis for keeping small valves only as catalogue nodes.
Cited in: docs/evidence_review/evidence_cards.md
[S13_Neal2014] Neal, Cooling, Smith, Thompson, Sauro, Carlson, Cook, Gennari. (2014) A reappraisal of how to build modular, reusable models of biological systems. PLoS Comput Biol 2014;10(10):e1003849
Access scope: full text (CC BY; Europe PMC XML retained) · Use: Used the distinction that semantic equivalence is a fact detected in annotations whereas the input/output decision changes the equations at composition time, and the non-semantic error types of validity-range violations and identifier drift.
[S14_Neal2015] Neal, Carlson, Thompson, James, Kim, Tran, Crampin, Cook, Gennari. (2015) Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PLoS One 2015;10(12):e0145621
Access scope: full text (CC BY 4.0; Europe PMC XML retained; earlier HTML capture in c_sources.json) · Use: Used the measured result that automatic duplicate detection missed about half of the duplicates found by experts, and the need for numerical verification after merging.
[S3_Neal2019_Harmonizing] Neal, König, Nickerson, Mısırlı, Kalbasi, Dräger, Atalag, Chelliah, Cooling, Cook, Crook, de Alba, Friedman, Garny, Gennari, Gleeson, Golebiewski, Hucka, Juty, Myers, Olivier, Sauro, Scharm, Snoep, Touré, Wipat, Wolkenhauer, Waltemath. (2019) Harmonizing semantic annotations for computational models in biology. Brief Bioinform 2019;20(2):540-550
Access scope: full text (PubMed/PMC; Europe PMC XML retained) · Use: Used to separate semantic errors from numerical and provenance errors, on the basis of distinguishing semantic annotation (what a variable means) from provenance/curation metadata, and of the point that an identifier match is only a sufficient condition for equivalence.
[S5_Neal2019_SemGen] Neal, Thompson, Kim, James, Cook, Carlson, Gennari. (2019) SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics 2019;35(9):1600-1602
Access scope: PMC page read via two WebFetch passes; supplement not retrieved; quotations only · Use: Used as the basis for the connection allow/deny design (Q3) and for unit handling, on the point that the tool proposes duplicates and humans decide, and that unit conflicts are handled with explicit conversion factors.
[S17_Paeme2011] Paeme, Moorhead, Chase, Lambermont, Kolh, D'Orio, Pierard, Moonen, Lancellotti, Dauby, Desaive. (2011) Mathematical multi-scale model of the cardiovascular system including mitral valve dynamics. Biomed Eng Online 2011;10:86
Access scope: full text (CC BY 2.0; Europe PMC XML retained) · Use: Used as an independent restatement in which the E_es, P_0, lambda, R, L values of the Smith CellML are given in mmHg and mL units, to confirm the kPa label problem and the meaning of the variable dictionary.
[Pathmanathan2013] Pathmanathan and Gray. (2013)
Access scope: text read (PubMed) · Use: Used for the literature judgement that validation procedures are prescribed but there is no universal numerical acceptance criterion, on which the Smith 2004 RK4 value comparison was set as report-only.
[Pathmanathan2014] Pathmanathan and Gray. (2014)
Access scope: abstract plus Wiley passages · Use: Used for the literature judgement that validation procedures are prescribed but there is no universal numerical acceptance criterion, on which the Smith 2004 RK4 value comparison was set as report-only.
[S19_Pironet2013] Pironet, Desaive, Kosta, Lucas, Paeme, Collet, Pretty, Kolh, Dauby. (2013) A multi-scale cardiovascular system model can account for the load-dependence of the end-systolic pressure-volume relationship. Biomed Eng Online 2013;12:8
Access scope: full text (CC BY 2.0; Europe PMC XML retained) · Use: Used to confirm the meanings of the symbols, as the third independent restatement of the mmHg-based units, and to confirm that it names the Smith doctoral thesis as the source of a total blood volume of 1500 mL.
[Regazzoni2022] Regazzoni et al.. (2022)
Access scope: open access quotation checked against downloaded text (CC BY 4.0) · Use: A sentence stating that the four chambers (atria and ventricles) are represented as time-varying elastance elements and the four valves as non-ideal diodes; it showed the standard structure of current closed-loop models.
Cited in: docs/evidence_review/evidence_cards.md
[S18_Revie2013] Revie, Stevenson, Chase, Pretty, Lambermont, Ghuysen, Kolh, Shaw, Desaive. (2013) Evaluation of a Model-Based Hemodynamic Monitoring Method in a Porcine Study of Septic Shock. Comput Math Methods Med 2013:505417
Access scope: full text (CC BY; Europe PMC XML retained; also returned by Wiley connector) · Use: Confirmed in Appendix A the meanings of V_spt, P_peri, P_pcd, V_d and the ventricular, septal, and pericardial equations, and found the structural inconsistency in which P_th enters P_vc.
[S4_RosseMejino2003] Rosse, Mejino. (2003) A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003;36(6):478-500
Access scope: abstract only (PubMed); not used for any relation direction or mapping · Use: Referenced for the distinction of anatomical entities separating blood, ventricular cavity, and wall, on the basis of an abstract sentence that FMA distinguishes structures (material entity versus space).
[Santiago2022] Santiago. (2022)
Access scope: text read (PubMed) · Use: Used for the literature judgement that validation procedures are prescribed but there is no universal numerical acceptance criterion, on which the Smith 2004 RK4 value comparison was set as report-only.
[Shanthini2023] Shanthini & Suma. (2023) Cureus
Access scope: open access quotation checked against downloaded text (CC BY 3.0) · Use: A statement that the Thebesian valve "is embryologically the caudal remnant of the right sinoatrial valve"; used as the basis for keeping small valves only as catalogue nodes.
Cited in: docs/evidence_review/evidence_cards.md
[Shi2011] Shi et al.. (2011)
Access scope: PMC page passages quoted in c_sources.json; extent of reading not stated · Use: Cited as the basis for the hydraulic-electrical analogy, compartment ordinary differential equations, choosing the dimensionality to fit the research purpose, and the point that parameter identification becomes harder as the model grows more complex.
[S6_Smith2004] Smith, Chase, Nokes, Shaw, Wake. (2004) Minimal haemodynamic system model including ventricular interaction and valve dynamics. Med Eng Phys 2004;26(2):131-139
Access scope: published article: abstract only (PubMed), paywalled; a 36-page pre-acceptance author manuscript (card S6P) supplied by the user was read in full and is not retained; quotations only · Use: Confirmed the equations, signs, units and state-switching approach as the reference model and compared them with the CellML encoding; it is stated explicitly that the project model is not a reproduction of it.
[S20_SmithThesis2004] Smith BW. (2004) Minimal haemodynamic modelling of the heart & circulation for clinical application. PhD thesis, University of Canterbury
Access scope: not read (located 2026-11-01, but every request returned a Cloudflare bot-check page; not retrieved) · Use: Identified as a candidate primary source of the equations, parameters and units of the model summarized by the 2004 paper; actual verification was deferred until the user downloads it.
[SurlesZeigler2022] Surles-Zeigler et al.. (2022) Front Neuroinform 16:819198
Access scope: full text (open access, CC BY 4.0 per S23 table) · Use: Cited as the basis of the SPARC vocabulary practice of placing valves as nodes with two identifiers (UBERON, FMA) and using UBERON first for terms.
Cited in: docs/evidence_review/evidence_cards.md
[Tonini2024] Tonini. (2024)
Access scope: surveyed by a research subagent (paraphrase); not individually verified in the cards · Use: A survey result that a patent foramen ovale is added only as a branch between the atria; used as the basis for keeping small valves and the foramen ovale as catalogue nodes.
Cited in: docs/evidence_review/evidence_cards.md
[vanOsta2025] van Osta et al.. (2025)
Access scope: open access quotation checked against downloaded text (CC BY 4.0) · Use: Cited as a result of the survey of current models, that CircAdapt uses 6 valve elements including venous–atrial connections and mimics the pericardium with a pouch module.
Cited in: docs/evidence_review/evidence_cards.md
[vanWilligen2024] van Willigen. (2024)
Access scope: surveyed by a research subagent (paraphrase); not individually verified in the cards · Use: A survey result that the foramen ovale appears only in fetal and neonatal models; used as the basis for keeping small valves and the foramen ovale as catalogue nodes.
Cited in: docs/evidence_review/evidence_cards.md
[CB01_HeartValve] (2007) Heart valve macro- and microstructure.
Access scope: full text, relevant sections read; metadata and original paraphrase only saved · Use: Used as the basis of the valve-boundary knowledge template of the LA–mitral–LV auxiliary file, on the points that the attachment structures of the four valves differ from one another and that the atrioventricular boundary is dynamic and non-planar.
[CB02_AVJunctions] (2000) Anatomy of the human atrioventricular junctions revisited.
Access scope: full text, relevant sections read; metadata and paraphrase only saved · Use: Used as the basis of the auxiliary file's boundary knowledge template, on the points that the atrioventricular junction surrounds the connection of the valve orifice and leaflets and that the fibrous tissue is non-uniform.
Cited in: src/physiosim/ontology/applied_la_mitral_lv_source_v1.json
[CS_LV_Anatomy] Anatomy and myoarchitecture of the left ventricular wall in normal and in disease.
Access scope: full text read (HTML via official PDF redirect) · Use: Used in the knowledge template of the LA–mitral–LV auxiliary file as the basis for defining the composition of the ventricular wall, septum and free wall, and the papillary muscles and chordae tendineae.
Cited in: src/physiosim/ontology/applied_la_mitral_lv_source_v1.json
[CS_Atria] Anatomy of the atria: A road map to the left atrial appendage. pp 347-351
Access scope: official full-text PDF read (CC BY 4.0) · Use: Used as the basis of the auxiliary file's atrial knowledge template for the appendages, walls and endocardial surfaces of both atria and the distinction of the true septum.
Cited in: src/physiosim/ontology/applied_la_mitral_lv_source_v1.json
[CS_HiPCT] Multidimensional Analysis of the Adult Human Heart in Health and Disease Using Hierarchical Phase-Contrast Tomography.
Access scope: official full-text PDF read (CC BY 4.0) · Use: A specimen-based source in which atrial wall layers and ventricular and conduction structures were imaged in 2 adult donor hearts; used only to confirm the existence of structures.
Cited in: src/physiosim/ontology/applied_la_mitral_lv_source_v1.json
[ROOT_MMWHS] Evaluation of algorithms for Multi-Modality Whole Heart Segmentation: An open-access grand challenge.
Access scope: full text (CC BY 4.0) · Use: Used as the basis of the auxiliary file's boundary definition, on the point that the four atrial and ventricular cavities have blood-pool annotations but the cutting location is a choice of the dataset protocol.
Cited in: src/physiosim/ontology/applied_la_mitral_lv_source_v1.json
[S21_SemGenAnnotationProtocol] SemGen annotation protocol, step 5 — properties of physical energy differentials. SemGen wiki (SemBioProcess/SemGen)
Access scope: text read (captured 2026-10-30); described in the card as an informal community document, not a specification · Use: A convention that chamber pressure specifies no sink and assumes a common ground, while transmural pressure takes the external fluid as the sink; used for the pressure reference notation.
Repository documents differ in their bibliographic details or stated access scope. Both versions are shown without correction.