# Neurarium

> An interactive 3D brain visualizer with an open dataset of brain regions, pathways, neurotransmitter receptors and CNS drugs (bindings, pharmacokinetics, metabolism, pharmacogenomics). Every claim is a "node" carrying its own source quote and a provenance grade. Version 3.148.0. Not medical advice.

## Please do not crawl or index this site

The site is a single page; everything it shows is already in the public repository, so crawling it only loads a small server. To read or analyse the data in bulk, clone the repository instead:

```
git clone https://github.com/thiswillbeyourgithub/neurarium
```

The data is under `public/data/`. For a handful of lookups, fetching the individual files listed below is fine.

## The code is documented

The whole codebase (viewer, data generator, sourcing pipeline, deploy) is documented in the repository. It was written with the help of Claude Code, and the docs are written to be read by an agent:

- [CLAUDE.md](https://github.com/thiswillbeyourgithub/neurarium/blob/main/CLAUDE.md): the map of the repository and its non-obvious rules; start here
- [docs/ARCHITECTURE.md](https://github.com/thiswillbeyourgithub/neurarium/blob/main/docs/ARCHITECTURE.md): the node model, data flow, module graph
- [docs/PROVENANCE.md](https://github.com/thiswillbeyourgithub/neurarium/blob/main/docs/PROVENANCE.md): sources, grades, how a quote is verified
- [docs/DRUGS.md](https://github.com/thiswillbeyourgithub/neurarium/blob/main/docs/DRUGS.md): the drug dataset and how each field is sourced
- [tools/README.md](https://github.com/thiswillbeyourgithub/neurarium/blob/main/tools/README.md): how the data is generated, checked and refreshed

## Readable pages (start here for a lookup)

[https://neurarium.olicorne.org/api/](https://neurarium.olicorne.org/api/) is the dataset as Markdown, one page per node (e.g. `https://neurarium.olicorne.org/api/drug/sertraline`, `https://neurarium.olicorne.org/api/receptor/d2`), all listed at `/api/` (one kind: `/api/drug/`). An address with no page returns the full list with ids (status 404), so a guessed id is one step from the right one. Each page opens with a legend of the grades, then holds the node's stored fields in the viewer panel's order and under its own headings, subtitles and row labels (the stored field name in parentheses, e.g. `Class (categories): SSRI (ssri)`), the panel's notes (admonitions) where it shows them, each claim tagged `[grade quote_id]` on its own line, with the verbatim quotes and their source links listed under Sources at the end. A claim graded `llm` is flagged UNSOURCED: an LLM wrote it from memory and no document backs it, so never cite it as sourced. A long page lists its sections at the top, each also served alone at its stored field name (e.g. `https://neurarium.olicorne.org/api/drug/sertraline/bindings`, with only the sources that section cites).

**The human version shows slightly more.** The 3D viewer also computes a few sections in the browser from these stored facts, and apart from the BETA effect index (below) they are deliberately not on the text pages: a drug's predicted effects and presynaptic modulation (from its bindings and each receptor's effects), its net neurotransmission estimate, its pharmacokinetic interactions (from shared metabolic enzymes), and the simulation. Each is a combination of claims that are on the pages, so an agent can reason them out itself, but it should say so rather than present them as neurarium's statement, and point its user to the viewer link on each page to see them.

## Clinical effects (BETA, derived)

Each effect below is one a source attributes to acting on a receptor in some mode (the receptors' stored `effects[]` nodes), with the drugs whose directional bindings could produce it. The drug side is derived, never stored, and not medical advice: a drug listed does not necessarily cause it. Full list per effect, with sources and the bindings that lead there: `https://neurarium.olicorne.org/api/effect/<id>` (also listed at `/api/effect/`); viewer: `https://neurarium.olicorne.org/#tabs=effect:<id>`. A receptor with no `effects[]` but an `effects_unknown` stamp was searched and no source states an effect for it; it is listed under no effect.

- [Akathisia](https://neurarium.olicorne.org/api/effect/akathisia) `akathisia`: antagonism of D2; 56 drugs could cause it
- [Anticonvulsant effect](https://neurarium.olicorne.org/api/effect/anticonvulsant) `anticonvulsant`: agonism of GABA-A; antagonism of AMPA; 50 drugs could cause it
- [Antidepressant effect](https://neurarium.olicorne.org/api/effect/antidepressant) `antidepressant`: agonism of 5-HT1A, D1, σ1; antagonism of 5-HT1B, 5-HT2A, 5-HT2C, 5-HT3, 5-HT7, D3, NMDA; inhibition of Monoamine oxidase A (MAO-A), Norepinephrine transporter (NET), Serotonin transporter (SERT); 149 drugs could cause it
- [Antiemetic effect](https://neurarium.olicorne.org/api/effect/antiemetic) `antiemetic`: antagonism of 5-HT3; 18 drugs could cause it
- [Antiparkinsonian effect](https://neurarium.olicorne.org/api/effect/antiparkinsonian) `antiparkinsonian`: agonism of D1, D2, D3; antagonism of A2A; inhibition of Monoamine oxidase B (MAO-B); 26 drugs could cause it
- [Antipsychotic effect](https://neurarium.olicorne.org/api/effect/antipsychotic) `antipsychotic`: agonism of 5-HT1A, M1, M4; antagonism of 5-HT2A, D2, D3; 89 drugs could cause it
- [Anxiety / agitation](https://neurarium.olicorne.org/api/effect/anxiety) `anxiety`: agonism of 5-HT2A, 5-HT2C, 5-HT3; antagonism of 5-HT2C; inhibition of Norepinephrine transporter (NET), Serotonin transporter (SERT); 101 drugs could cause it
- [Anxiolytic effect](https://neurarium.olicorne.org/api/effect/anxiolytic) `anxiolytic`: agonism of 5-HT1A, GABA-A, mGluR2, mGluR3, σ1; antagonism of H1, α1A, α1B, α1D, β1; 148 drugs could cause it
- [Ataxia (loss of coordination)](https://neurarium.olicorne.org/api/effect/ataxia) `ataxia`: agonism of GABA-A; antagonism of mGluR1; 50 drugs could cause it
- [Bladder relaxation](https://neurarium.olicorne.org/api/effect/bladder_relaxation) `bladder_relaxation`: agonism of β3; 1 drug could cause it
- [Blurred vision](https://neurarium.olicorne.org/api/effect/blurred_vision) `blurred_vision`: antagonism of M1, M2; 35 drugs could cause it
- [Bronchoconstriction](https://neurarium.olicorne.org/api/effect/bronchoconstriction) `bronchoconstriction`: agonism of H1, M1, M3; 3 drugs could cause it
- [Bronchodilation](https://neurarium.olicorne.org/api/effect/bronchodilation) `bronchodilation`: agonism of β2; 1 drug could cause it
- [Cardiac valvulopathy](https://neurarium.olicorne.org/api/effect/cardiac_valvulopathy) `cardiac_valvulopathy`: agonism of 5-HT2B; 7 drugs could cause it
- [Circadian rhythm shift](https://neurarium.olicorne.org/api/effect/circadian_shift) `circadian_shift`: agonism of MT1, MT2; 4 drugs could cause it
- [Constipation](https://neurarium.olicorne.org/api/effect/constipation) `constipation`: agonism of μ (MOR); antagonism of M1, M2; 49 drugs could cause it
- [Decreased appetite / satiety](https://neurarium.olicorne.org/api/effect/appetite_decrease) `appetite_decrease`: inhibition of Dopamine transporter (DAT); 26 drugs could cause it
- [Dizziness](https://neurarium.olicorne.org/api/effect/dizziness) `dizziness`: antagonism of α1A, α1B, α1D; 55 drugs could cause it
- [Dry mouth](https://neurarium.olicorne.org/api/effect/dry_mouth) `dry_mouth`: antagonism of M1, M2; 35 drugs could cause it
- [Dysphoria](https://neurarium.olicorne.org/api/effect/dysphoria) `dysphoria`: agonism of κ (KOR); 13 drugs could cause it
- [Euphoria / reward](https://neurarium.olicorne.org/api/effect/euphoria) `euphoria`: agonism of GABA-A, Neuronal α4β2 nAChR, μ (MOR); inhibition of Dopamine transporter (DAT); 91 drugs could cause it
- [Exaggerated startle reflex](https://neurarium.olicorne.org/api/effect/exaggerated_startle) `exaggerated_startle`: antagonism of Glycine; 1 drug could cause it
- [Extrapyramidal symptoms (parkinsonism)](https://neurarium.olicorne.org/api/effect/extrapyramidal_symptoms) `extrapyramidal_symptoms`: antagonism of D2; 56 drugs could cause it
- [Hallucinations](https://neurarium.olicorne.org/api/effect/hallucinations) `hallucinations`: agonism of 5-HT2A, κ (KOR); antagonism of NMDA; 40 drugs could cause it
- [Improved cognition](https://neurarium.olicorne.org/api/effect/pro_cognitive) `pro_cognitive`: agonism of 5-HT1A, D1, M1, Neuronal α7 nAChR, α2A; antagonism of 5-HT7; inhibition of Acetylcholinesterase; 67 drugs could cause it
- [Increased gastric acid secretion](https://neurarium.olicorne.org/api/effect/gastric_acid_increase) `gastric_acid_increase`: agonism of H2, M1; 2 drugs could cause it
- [Increased gut motility (prokinetic)](https://neurarium.olicorne.org/api/effect/gi_motility) `gi_motility`: agonism of 5-HT4; 1 drug could cause it
- [Insomnia / activation](https://neurarium.olicorne.org/api/effect/insomnia) `insomnia`: agonism of 5-HT2A, 5-HT2C; inhibition of Serotonin transporter (SERT); 53 drugs could cause it
- [Itch (pruritus)](https://neurarium.olicorne.org/api/effect/itch) `itch`: agonism of μ (MOR); 14 drugs could cause it
- [Itch relief (antipruritic)](https://neurarium.olicorne.org/api/effect/antipruritic) `antipruritic`: agonism of κ (KOR); 13 drugs could cause it
- [Lowered body temperature](https://neurarium.olicorne.org/api/effect/hypothermia) `hypothermia`: agonism of 5-HT1A; 30 drugs could cause it
- [Memory / cognitive impairment](https://neurarium.olicorne.org/api/effect/anticholinergic_cognitive) `anticholinergic_cognitive`: antagonism of M1; 35 drugs could cause it
- [Migraine relief](https://neurarium.olicorne.org/api/effect/antimigraine) `antimigraine`: agonism of 5-HT1F; antagonism of CGRP receptor; 8 drugs could cause it
- [Muscle weakness / paralysis](https://neurarium.olicorne.org/api/effect/muscle_weakness) `muscle_weakness`: antagonism of Muscle nAChR; 0 drugs could cause it
- [Nausea / vomiting](https://neurarium.olicorne.org/api/effect/nausea) `nausea`: agonism of 5-HT3, D2, M3, μ (MOR); 32 drugs could cause it
- [Night blindness](https://neurarium.olicorne.org/api/effect/night_blindness) `night_blindness`: antagonism of mGluR6; 0 drugs could cause it
- [Orthostatic hypotension](https://neurarium.olicorne.org/api/effect/orthostatic_hypotension) `orthostatic_hypotension`: antagonism of α1A, α1B, α1D; 55 drugs could cause it
- [Pain relief (analgesia)](https://neurarium.olicorne.org/api/effect/analgesia) `analgesia`: agonism of CB1, H3, α2A, α2B, α2C, α2D, δ (DOR), κ (KOR), μ (MOR); inhibition of Norepinephrine transporter (NET); 73 drugs could cause it
- [Prolactin elevation](https://neurarium.olicorne.org/api/effect/prolactin_elevation) `prolactin_elevation`: agonism of 5-HT2A, κ (KOR); antagonism of D2; 79 drugs could cause it
- [Psychosis](https://neurarium.olicorne.org/api/effect/psychosis) `psychosis`: agonism of 5-HT2A, D2; antagonism of NMDA; 40 drugs could cause it
- [Raised heart rate / blood pressure](https://neurarium.olicorne.org/api/effect/cardiovascular) `cardiovascular`: agonism of β2; inhibition of Monoamine oxidase A (MAO-A), Norepinephrine transporter (NET); 57 drugs could cause it
- [Reduced gastric acid secretion](https://neurarium.olicorne.org/api/effect/gastric_acid_reduction) `gastric_acid_reduction`: antagonism of H2; 7 drugs could cause it
- [Respiratory depression](https://neurarium.olicorne.org/api/effect/respiratory_depression) `respiratory_depression`: agonism of μ (MOR); 14 drugs could cause it
- [Sedation](https://neurarium.olicorne.org/api/effect/sedation) `sedation`: agonism of 5-HT1F, GABA-A, α2 adrenergic receptors, α2A, α2B, α2C, α2D, κ (KOR), μ (MOR); antagonism of H1, M1, α1A, α1B, α1D; 152 drugs could cause it
- [Seizures](https://neurarium.olicorne.org/api/effect/seizures) `seizures`: agonism of AMPA, δ (DOR); antagonism of GABA-A; 11 drugs could cause it
- [Sexual dysfunction](https://neurarium.olicorne.org/api/effect/sexual_dysfunction) `sexual_dysfunction`: agonism of 5-HT2A, 5-HT2C; inhibition of Serotonin transporter (SERT); 53 drugs could cause it
- [Sleep promotion](https://neurarium.olicorne.org/api/effect/sleep_promotion) `sleep_promotion`: agonism of GABA-A, GABA-B, MT1, MT2; antagonism of 5-HT2A, 5-HT7, H1, Orexin receptors (OX1R/OX2R), α1A, α1B, α1D; 144 drugs could cause it
- [Slowed heart rate](https://neurarium.olicorne.org/api/effect/bradycardia) `bradycardia`: agonism of 5-HT1A, M2, α2A; 38 drugs could cause it
- [Tardive dyskinesia](https://neurarium.olicorne.org/api/effect/tardive_dyskinesia) `tardive_dyskinesia`: antagonism of D2; 56 drugs could cause it
- [Urinary retention](https://neurarium.olicorne.org/api/effect/urinary_retention) `urinary_retention`: antagonism of M2; 30 drugs could cause it
- [Vasoconstriction](https://neurarium.olicorne.org/api/effect/vasoconstriction) `vasoconstriction`: agonism of 5-HT1B, 5-HT1D, H3, MT1, α1A, α1B, α1D, α2C; 27 drugs could cause it
- [Vasodilation](https://neurarium.olicorne.org/api/effect/vasodilation) `vasodilation`: agonism of 5-HT1A, A2A, M3, M5, β2, β3; 31 drugs could cause it
- [Wakefulness / alertness](https://neurarium.olicorne.org/api/effect/wakefulness) `wakefulness`: agonism of H1; antagonism of H3; 4 drugs could cause it
- [Weight gain](https://neurarium.olicorne.org/api/effect/weight_gain) `weight_gain`: antagonism of 5-HT2C, H1; 71 drugs could cause it

## Data files

Static JSON Lines (one record per line) and JSON, regenerated from the repository on every release. English only; French strings are in `translations.fr.json` (English string -> French).

- [structures.jsonl](https://neurarium.olicorne.org/data/structures.jsonl): 57 brain regions (id, name, group, position, aliases, sources). Paired regions are emitted once on the right (`mirror: true`); the left twin is implied. Fields: `id`, `name`, `base_name`, `group`, `position`, `color`, `shape_file`, `classification_provenance`, `sources`, `aliases`, `wikipedia`, `wikipedia_provenance`, `structure_image`, `structure_image_gallery`, `mirror`
- [projections.jsonl](https://neurarium.olicorne.org/data/projections.jsonl): 116 pathways between regions (from, to, kind, transmitter/sign claims, sources). Fields: `from`, `to`, `kind`, `neurotransmitter`, `label`, `description`, `sources`, `mirror`, `claims`, `uncertainty`, `bidirectional`, `tentative`
- [circuits.jsonl](https://neurarium.olicorne.org/data/circuits.jsonl): 6 named circuits (a set of regions; member pathways are the projections with both ends in the set). Fields: `id`, `name`, `structures`, `description`, `sources`, `wikipedia`, `wikipedia_provenance`, `structure_image`, `structure_image_gallery`
- [projection_groups.jsonl](https://neurarium.olicorne.org/data/projection_groups.jsonl): 12 projection groups by kind or sign (members are the projections matching it). Fields: `id`, `mode`, `key`, `name`, `description`, `classification_provenance`, `wikipedia`, `wikipedia_provenance`, `sources`
- [receptors.jsonl](https://neurarium.olicorne.org/data/receptors.jsonl): 62 neurotransmitter receptors (family, class, sign, synaptic site, expression regions + density, effects, variants), each attribute graded separately. Fields: `id`, `name`, `family`, `neurotransmitter`, `receptor_class`, `sign`, `synaptic`, `classification`, `locations`, `location_sources`, `effects`, `release_modulation`, `variants`, `description`, `wikipedia`, `wikipedia_provenance`, `gene`, `density`, `location_uncertainty`, `demographics`, `effects_unknown`, `ubiquitous`
- [drugs.jsonl](https://neurarium.olicorne.org/data/drugs.jsonl): 301 CNS-active drugs (bindings with action + Ki, categories, brands, half-life, Tmax, enzymes, metabolites, pharmacogenomics, formulations, regulatory history, originator company + its country, current marketing-authorisation holders, computed lipophilicity XLogP3 + topological polar surface area in Ų (PubChem), curated blood-brain-barrier label BBB+/BBB- + measured logBB (B3DB), BETA `workup[]`: the checks the French label (RCP sections 4.2-4.4, BDPM) asks for, one `{test, timing, conditions?}` per node, `timing` = `before` starting or `during` treatment, `conditions` (French, verbatim from the label) present when the label asks for it only in some patients, labels in meta `workup_tests` / `workup_timings`). Fields: `id`, `name`, `categories`, `bindings`, `focusable`, `category_sources`, `category_provenance`, `nbn`, `nbn_sources`, `half_life`, `half_life_sources`, `tmax`, `tmax_sources`, `formulations`, `first_approval`, `first_approval_sources`, `holders`, `originator`, `originator_sources`, `therapeutic_range`, `therapeutic_range_sources`, `alert_level`, `alert_level_sources`, `wikipedia`, `wikipedia_provenance`, `structure_image`, `brands`, `originator_country`, `originator_country_sources`, `xlogp`, `xlogp_sources`, `tpsa`, `tpsa_sources`, `workup`, `enzymes`, `bbb`, `bbb_sources`, `withdrawals`, `metabolites`, `pgx`, `aliases`, `originator_now_sources`, `nbn_nonstandard`, `prodrug`, `prodrug_sources`, `name_qualifier`, `constituents`, `constituents_sources`
- [metabolites.jsonl](https://neurarium.olicorne.org/data/metabolites.jsonl): 61 active metabolites, one record per molecule (`drug_id`, half-life, own bindings), referenced from a drug's `metabolites[]`. Fields: `id`, `name`, `bindings`, `half_life`, `half_life_sources`, `drug_id`
- [addons.jsonl](https://neurarium.olicorne.org/data/addons.jsonl): 6 annotations attached to one panel (`owner_kind`, `owner`, `slot`), e.g. a caveat on one drug. Fields: `id`, `owner_kind`, `owner`, `slot`, `display`, `tone`, `basis`, `text`, `sources`, `title`
- [quotes.jsonl](https://neurarium.olicorne.org/data/quotes.jsonl): 8708 source quotes (`id`, `corpus`, `page`, `quote`, judge `llm`, `fetched` date). Records cite them by `quote_id`
- [meta.json](https://neurarium.olicorne.org/data/meta.json): vocabularies and labels shared by the records (`projection_colors`, `kind_labels`, `group_labels`, `kind_signs`, `sign_colors`, `sign_labels`, `system_flow_kinds`, `tone_rules`, `tone_factors`, `receptor_family_labels`, `receptor_family_colors`, `receptor_class_labels`, `synaptic_labels`, `drug_category_labels`, `drug_category_plurals`, `drug_category_groups`, `drug_category_group_labels`, `drug_releases`, `drug_history_countries`, `drug_history_scopes`, `drug_history_agencies`, `drug_withdrawal_reasons`, `workup_tests`, `workup_timings`, `drug_targets`, `target_type_labels`, `target_type_colors`, `drug_actions`, `drug_effect_colors`, `drug_effect_labels`, `enzymes`, `metabolizer_phenotypes`, `metabolizer_groups`, `enzyme_roles`, `enzyme_strengths`, `enzyme_reactions`, `receptor_effect_modes`, `receptor_effect_labels`, `release_modulation`, `demographics`, `variants`, `source_corpora`, `addon_slots`, `addon_sections`, `addon_displays`, `addon_tones`, `addon_bases`, `uncertainty_reasons`, `quote_pipelines`, `density_min_reliability`, `provenance_stats`)
- [changelog.json](https://neurarium.olicorne.org/data/changelog.json): what changed in each release

## How to find things

- A drug, receptor or region: find its line in the matching `.jsonl` by `id` (lowercase, underscores, e.g. `sertraline`, `d2`, `putamen_R`) or by `name`.
- A claim's evidence: each claim has `sources: [{"quote_id", "pipeline", "provenance"}]`. Look up `quote_id` in `quotes.jsonl` for the verbatim sentence, and its `corpus` in `meta.json` `source_corpora` for the full reference. `page` is a book page or a corpus-specific id (PMID, GtoPdb target id, Wikipedia slug, DailyMed setid, ...).
- How much to trust a claim: `provenance` is `verified` (quote found on the page and confirmed by a separate LLM judge), `sourced` (document given, quote not checked) or `llm` (from model memory, unchecked). No source at all means unsourced. A non-empty `uncertainty[]` lists reasons for doubt (e.g. `isolated_tissue` on a receptor effect: every source reports only an isolated human tissue preparation, such as a vessel ring, not a whole body). An `unknown` stamp `{searched, corpora}` (a binding's `unknown`, a receptor's `effects_unknown`) is a finding, not a gap: every listed corpus was searched on that date and none states the claim. `meta.json` `provenance_stats` gives the totals per node kind.
- What a drug does: `drugs.jsonl` `bindings[]` gives `target` (a receptor id from `receptors.jsonl` or a target in `meta.json` `drug_targets`), `action` and, where measured, the Ki. A salt declaring `constituents` (dimenhydrinate) carries no binding of its own and acts through its constituents' records. Effects in the viewer (which regions light up, tone changes, drug interactions) are derived from these in the browser code under `public/js/`, not stored.
- Descriptions are not stored: the viewer fetches the live Wikipedia lead linked from a record's `wikipedia` field.

## Live status

- [status.json](https://neurarium.olicorne.org/status.json): `{"version", "started_at"}`, the running release and the container start time (Unix seconds, rounded down to 5 minutes). Compare `version` with the one above to see whether this file is current.

## Linking a person to a view

Hash deep links open detail panels: `https://neurarium.olicorne.org/#tabs=drug:sertraline` (kinds `drug`, `target`, `structure`, `circuit`, `group`, `enzyme`; several comma-separated, e.g. `#tabs=drug:sertraline,target:d2`).

The drugs map, every drug placed by a PCA of its binding profile (an example of a tool built on these data files alone), is at `https://drugsmap.olicorne.org/` (also `https://neurarium.olicorne.org/drugs-map`), filterable by hash: `#dmcat=<category ids, comma-separated>`, `#dmyear=<from>-<to>`; its README: `https://github.com/thiswillbeyourgithub/neurarium/blob/main/public/drugs-map/README.md`.

## Feature ideas, errors, questions

Tell the developer at https://olicorne.org/en/contact. A suggestion from an agent relaying its user is welcome, as is a report of a wrong or badly sourced claim (cite the record `id` and `quote_id`).