v1 Parity Gap Inventory — RC Gate Document

Field	Value
Status	Living document
Last audited	2026-05-21 (loop iter 15 surface refresh — counts via scripts/measure_verb_surface.py)
Previous audit	2026-05-18 (Category 7 LOVD variants addition, task:da412dcd) — 4c6b9274
Audited against	origin/main commit 42ccb94b1 (post-PR #2066)
Owner	Substrate ops + architecture review
Purpose	Formal inventory of remaining v1-vs-v2 parity gaps per SPEC-015. Cutover (SPEC-006 Phase C, nginx flip) is gated on all must-have targets reaching DONE.
Method	Codebase scan: verbs, schemas, migrations, routes, economics, runtimes, Prism reconciliation. No code changes — analysis only.

Note on counts: The category tables below count v1 surface area mapped to v2 implementations (parity targets), not v2’s absolute counts. As v2 grows beyond v1 parity, that growth is captured in SPEC-197, not here.

Summary Counts

Category	Parity DONE	CODE_ONLY	MISSING	DEGRADED	Parity Total	v2 Actual (2026-05-21)
Polymorphic verbs (SPEC-001)	419	0	0	0	419	729 (+74%)
REST routes (v1/*)	191	0	0	0	191	919 openapi paths
MCP tools	419	0	0	0	419	matches verbs (729)
Artifact schemas	104	0	0	0	104	128 (+23%)
DB migrations	221	0	0	0	221	263 (+19%)
Economics modules	15	0	0	0	15	15
Tool runtimes	12	0	0	0	12	12
Forge science tools	159	0	0	0	159	204 forge verbs (+28%)
Auth (JWT + OAuth)	5	0	0	0	5	5
HTML page parity (Tier 1)	18	0	0	0	18	(Prism — out of substrate scope)
HTML page parity (Tier 2)	18	0	0	0	18	(Prism)
HTML page parity (Tier 3)	39	0	0	1	40	(Prism)
Corpus migration (ETL)	6	0	0	0	6	6
Live agent population	59	0	0	0	59	59
Skills bundles	23	0	0	0	23	27 native + 138 K-Dense upstream (per VENDOR_VERSIONS.md)
Mimeo policies	11	0	0	0	11	11
Cross-cutting behaviors	11	0	0	0	11	11
Scheduled workers (SPEC-046)	—	—	—	—	(post-parity)	59
Watchdogs (SPEC-048)	—	—	—	—	(post-parity)	4
Ingest pipelines (SPEC-047)	—	—	—	—	(post-parity)	6
TOTAL parity targets	1618	0	0	1	1619	—

Headline

• 1619 parity targets identified across 17 categories per SPEC-015 (includes 119 M15–M39 forge additions beyond original v1 targets).

• 1618 (99.9%) DONE — code merged to main, tests pass (99.0% pytest pass rate per PR #1351).

• 0 CODE_ONLY — all previously pending verifications resolved.

• 0 MISSING — all previously MISSING Tier 3 pages resolved (implemented or retired; audit task:d0e5c26f).

• 1 (0.1%) DEGRADED — /workspace/library (localStorage fallback pending SPEC-066 P2; Prism-side work out of scope for substrate).

Category 1: Polymorphic Verbs (SPEC-001)

Status: DONE (419/419 parity targets)

The category-count of 419 reflects v1-side verb surface area mapped to v2 implementations. v2’s actual verb registry as of 2026-05-21 is 729 verbs (480 read / 249 write) across 20+ namespaces — substantially exceeding the parity floor (scripts/measure_verb_surface.py). Verbs above the 419 parity baseline are v2-native and tracked in SPEC-197.

All v2 verbs are registered via @verb decorator and exposed three ways:

• HTTP: POST /api/scidex/{verb_name} (auto-generated by attach_verb_routes())

• MCP: tool name scidex.xxx.yyy via stdio JSON-RPC

• In-process: callable from any Python context

MCP contract coverage landed in 9f364c86, verifying the @verb registry is fully exposed via the MCP protocol.

Key verb groups (all DONE):

Group	Verbs	SHA evidence
Core CRUD (get/create/update/list/count/search)	12	01dcfd26
Actor management (30+ actor.* verbs)	38	01dcfd26
Signal/vote/subscription	10	01dcfd26
Comment system	6	01dcfd26
Debate + Pantheon debate	22	01dcfd26
Senate governance	14	01dcfd26
Economics (wallet/budget/dividend/market)	35	01dcfd26
Knowledge graph (causal/evidence/graph)	15	01dcfd26
Curation/dedupe/embed	8	01dcfd26
Notebook	8	01dcfd26
Federation/A2A	14	01dcfd26
Forge science tools	39	01dcfd26 + task:dc890a1a + task:df02e6e8 + task:2da4b7b3 + task:f634eac2 + task:26617431 + task:3463b61d + task:8fccd5eb + task:b7d5aa35 + task:78f3dd39 + task:3887741a + task:2fbb48aa + task:59b8c3a5 + task:7d64606a + task:83e2843c + human_protein_atlas (task:dd03d707) + europepmc (task:b84a0b91) + cosmic_mutations (task:0e176703 e3ed379d #1499) + pubchem_compound (task:a6c38059 01009ec1 #1506) + tcga_genomics (task:53cc7967 898d62e5 #1508) + encode_epigenomics (task:fe1be75d 6f933ef7 #1511) + geo_expression (task:8993311d 9d89182c #1496) + ebi_expression_atlas (task:addb4bdc) + ncbi_gene (task:ad19a31e)
Experiment extraction (SPEC-075)	1	task:b5415bc0
Remaining (tiers/roles/review/etc.)	231+	01dcfd26

Experiment extraction (SPEC-075)

scidex.experiment.extract — DONE (task:b5415bc0, 2026-05-17). On-demand read verb that fetches a paper artifact’s abstract and extracts 0..N structured experiment records with seven canonical SPEC-075 dimensions (hypothesis_tested, method, model_system, perturbation, controls, outcome_measure, result_summary) plus structured statistics. Wraps the SPEC-075 §3.6 backfill pipeline’s LLM extractor. In cassette mode (no ANTHROPIC_API_KEY), returns deterministic fixtures keyed by paper_id substring. 36 unit tests in tests/unit/skill/verbs/test_experiment_extract.py.

Category 2: REST Routes (v1/*)

Status: DONE (191/191)

191 REST-style routes across 56 mounted routers in src/scidex_substrate/api/routes/. Key route groups:

Router	Prefix	Status
auth (dev login, OAuth, session, register)	/auth/*, /v1/auth/*	DONE
search	/v1/search	DONE
wiki	/v1/wiki/pages	DONE
gaps	/v1/gaps	DONE
debates + streaming	/v1/debates	DONE
papers	/v1/paper	DONE
hypotheses	/v1/hypotheses	DONE
analyses	/v1/analyses	DONE
economics	/v1/economics/*	DONE
markets	/v1/markets	DONE
senate	/v1/senate/*	DONE
working groups	/v1/working-groups	DONE
federation	/v1/federation	DONE
agents	/v1/agents/*	DONE
actor profile/social/budget	/v1/agents/*	DONE
identity (DID)	/v1/identity	DONE
admin	/v1/admin	DONE
healthz	/healthz	DONE

Plus 8 direct GET endpoints on app (/health, /health/deep, /readyz, /, /v1/mcp/schema.json, /api/scidex/subscribe, /v1/debates/{id}/stream, /v1/debates/{id}/rounds) and 8 ASGI middlewares (CORS, logging, analytics, metrics, rate-limit, x402, scheduler-secret, public-route, api-key-auth).

Category 2.5: SPEC-039 substrate engagement-parity loops (closed iter 14)

Cross-reference: spec-039-three-module-conventions.md. The 2026-04-30 SPEC-039 §1 audit flagged 25 substrate items as “v1-only” — verification through loop iters 12-14 showed 0 are actually missing. The audit had a methodology blind spot (only inspected scheduled_workers/; missed watchdogs/ SPEC-048 and ingest/ SPEC-047). The two items that were genuinely needed (deadline_tick and senate_gate_evaluator scheduled workers) shipped in iters 6-7.

Category 3: Artifact Schemas

Status: DONE (104/104 parity targets; v2 actual = 128 schemas as of 2026-05-21)

The 104 parity targets correspond to v1’s artifact-type inventory. v2 currently ships 128 schemas in src/scidex_substrate/schema_registry/default_schemas/ — the 24 v2-native schemas above the parity baseline (e.g. mechanism_diagram per SPEC-194 Gap D, protein_design, falsification_attempt) are tracked in SPEC-197.

104 registered artifact type schemas in src/scidex_substrate/schema_registry/default_schemas/. All auto-registered at substrate startup. Key types include: hypothesis, paper, analysis, wiki_page, comment, signal, link, skill, tool, gap, debate_outcome, market, persona, arena, notebook, experiment, dataset, benchmark, clinical_trial, protein_design, working_group, gov_proposal, agent_bundle, parity_target, and ~80 more.

Evidence: directory listing against 01dcfd26.

Category 4: DB Migrations

Status: DONE (221/221 parity targets; v2 actual = 263 migrations as of 2026-05-21)

The 221 parity targets correspond to the v1 → v2 schema-transition migrations needed at cutover. v2’s actual migration count is 263 (src/scidex_substrate/migrations/*.sql); the additional 42 migrations beyond the parity baseline cover v2-native primitives shipped post-baseline.

Covers the complete substrate schema from 0001_initial_schema.sql through 0263_*. Includes:

• Initial schema + core tables

• Skills, tools, actor links, scores, signals

• Subscriptions, benchmarks, senate, squads

• Pantheon, arenas, colliders, challenges

• Auth keys, multisig, wallets, token ledger

• Economics pricing, write metering

• AT Protocol federation prework

• Working groups, LMSR markets, quality warnings

• Agent memory (4-layer), personality, reflection

• x402 invoices, hypothesis arenas, blob storage

Evidence: ls src/scidex_substrate/migrations/*.sql | wc -l = 221 (some migration numbers have multiple files).

Category 5: Economics Modules

Status: DONE (15/15)

15 economics modules in src/scidex_substrate/economics/:

Module	Purpose
wallets	Actor wallet creation/management
token_ledger	Double-entry token tracking
wallet_reconciler	Consistency checks
pricing	Price computation
compute_cost	Resource cost accounting
write_metering	Per-verb write debiting
demurrage	Token decay over time
credit_contributions	Reward attribution
discovery_dividends	Discovery reward distribution
backprop_dividend	Citation-graph dividend propagation
reputation_rollup	Aggregate reputation scoring
performance_scoring	Bayesian Beta-Binomial scoring
signed_wallet_outflows	Signed authorization for transfers
contributions_to_token_ledger_adapter	Bridge contribution records to ledger
cleanup_idempotency	Idempotent cleanup of economic events

Plus 50+ economics-related verbs (balance, transfer, market_, budget_, dividend_*, faucet, etc.).

Category 6: Tool Runtimes

Status: 12 DONE, 0 MISSING

Runtime	Status	Evidence
in_process	DONE	src/scidex_substrate/skill/tool_runtimes/in_process.py
bwrap	DONE	src/scidex_substrate/skill/tool_runtimes/bwrap.py
docker	DONE	src/scidex_substrate/skill/tool_runtimes/docker.py
kernel_execute	DONE	src/scidex_substrate/skill/tool_runtimes/kernel_execute.py
batch	DONE	src/scidex_substrate/skill/tool_runtimes/batch.py
http_post	DONE	src/scidex_substrate/skill/tool_runtimes/http_post.py
skill_call	DONE	src/scidex_substrate/skill/tool_runtimes/skill_call.py
causal_dowhy	DONE	src/scidex_substrate/skill/tool_runtimes/causal_dowhy.py
causal_llm	DONE	src/scidex_substrate/skill/tool_runtimes/causal_llm.py
mcp_server	DONE	src/scidex_substrate/skill/tool_runtimes/mcp_server.py
k8s sandbox	DONE	src/scidex_substrate/tool/runtimes/sandbox/k8s.py (task:55e0cdc8)
RemoteVM isolation	DONE	src/scidex_substrate/skill/tool_runtimes/remote_vm.py (task:280dd5f6)

Category 7: Forge Science Tools

Status: DONE (170/170)

Note: M15–M39 expanded beyond v1 parity targets; all 128 additions below are NEW capabilities, not v1 backfill. forge.reactome_pathways is now credited via task:5477f265, closing the long-running task:f697afee exclusion. forge.lovd_variants added via task:da412dcd. forge.oma_orthologs added via task:76c100b6.

All 170 Forge science tool verbs implemented:

Verb	Status
forge.pubmed.search	DONE
forge.semantic_scholar.search	DONE
forge.crossref.lookup	DONE
forge.uniprot.lookup	DONE
forge.pdb.lookup	DONE
forge.ensembl_xref	DONE
forge.interpro.domains	DONE
forge.allen_brain.expression	DONE
forge.alphafold.structure	DONE
forge.clinical_trials.search	DONE
forge.drug_indications	DONE
forge.gnomad_variant	DONE
forge.gtex_expression	DONE
forge.opentargets	DONE
forge.kegg_pathways	DONE (task:f634eac2)
forge.reactome_pathways	DONE (task:5477f265; closes task:f697afee) — Reactome ContentService pathway lookup; gene symbol(s) → curated R-HSA pathway IDs, species, top-level pathway hierarchy, matched genes, and Reactome URLs; supports lower-level pathway detail toggle
forge.go_term_enrichment	DONE (task:dc890a1a) — QuickGO EBI API; gene symbols → GO BP/MF/CC annotations with aspect + evidence-code filtering
forge.chembl_compound	DONE (task:2da4b7b3)
forge.hpo_phenotype	DONE (task:df02e6e8) — EBI OLS4 + Monarch Initiative; HPO term lookup, name search, gene→phenotype associations
forge.pharos_target	DONE (task:26617431) — Pharos/TCRD GraphQL API; gene symbol → TDL (Tdark/Tbio/Tchem/Tclin), disease associations, drug activities; critical for dark kinome hypothesis generation
forge.clinvar_variant	DONE (task:3463b61d) — NCBI ClinVar; clinical significance (Pathogenic/VUS/Benign), ACMG review stars (0–4), conditions, submitter count
forge.gwas_catalog	DONE (task:b7d5aa35) — NHGRI-EBI GWAS Catalog REST API; gene symbols/trait → genome-wide-significant variant-trait associations; rsID, p-value, odds ratio, effect allele, study accession, PubMed ID
forge.string_ppi	DONE (task:c0394d83, 82362255 #1778) — STRING DB protein-protein interaction lookup; gene symbol → interaction_partners endpoint; StringInteraction records with per-channel evidence scores (neighborhood, coexpression, experimental, database, textmining, combined); species-aware; limit+sort ordering; M35 rewrite
forge.biogrid_interactions	DONE (task:2fbb48aa) — BioGRID curated protein interaction lookup; gene symbol → BioGRID interaction records with experimental system, throughput, and PubMed evidence
forge.disgenet	DONE (task:59b8c3a5) — DisGeNET gene–disease associations; gene symbol → disease records with score, evidence index, source databases (CURATED/INFERRED)
forge.omim_disease	DONE (task:7d64606a) — OMIM Mendelian disease lookup; gene symbol → OMIM disease entries with MIM numbers, inheritance patterns, clinical synopsis
forge.power_calc	DONE (task:83e2843c) — statistical power calculation; test type, effect size, alpha, power → required sample size; supports t-test, ANOVA, proportion test, correlation
forge.rate_limits	DONE (task:83e2843c) — external API rate limit advisor; API name → rate limit tier, retry strategy, burst allowance recommendations
forge.resource_predictor	DONE (task:83e2843c) — compute resource prediction; job type, dataset size → estimated CPU/GPU/memory/runtime requirements
forge.msigdb_genesets	DONE (task:78f3dd39) — MSigDB gene set lookup via Enrichr; gene symbols → pathway/gene set enrichment from Hallmark, KEGG, Reactome, GO collections
forge.pharmgkb	DONE (task:3887741a) — PharmGKB pharmacogenomics gene-drug-variant associations; gene symbol → drug-gene relationships, variant annotations, clinical action levels
forge.human_protein_atlas	DONE (task:dd03d707) — HPA tissue and subcellular protein expression; gene symbol → per-tissue expression levels (Not detected/Low/Medium/High) with antibody reliability scores, subcellular compartments, protein class, cancer pathology
forge.europepmc	DONE (task:b84a0b91) — Europe PMC full-text literature search; query → papers from MEDLINE, PubMed Central, and preprints (bioRxiv/medRxiv/ChemRxiv) with source filtering, date range, and full-text availability filter
forge.cosmic_mutations	DONE (task:0e176703, e3ed379d #1499) — COSMIC somatic mutation catalog; gene symbols → COSV/COSM mutation IDs, amino acid changes (e.g. p.V600E), cancer types, sample counts, COSMIC tier (1=hallmark/2=candidate), Census driver gene flag; optional COSMIC_API_KEY for higher rate limits
forge.pubchem_compound	DONE (task:a6c38059, 01009ec1 #1506) — PubChem chemical compound and bioassay lookup; compound name/SMILES/CID → compound records with molecular formula, MW, canonical SMILES, InChIKey, XLogP, H-bond counts, active bioassay count; complements forge.chembl_compound
forge.tcga_genomics	DONE (task:53cc7967, 898d62e5 #1508) — TCGA/GDC cancer genomics lookup; gene symbols → somatic mutation statistics (count, frequency, top amino-acid changes) across 33 TCGA cancer types; complements forge.clinvar_variant (germline) and forge.gnomad_variant (population AF)
forge.encode_epigenomics	DONE (task:fe1be75d, 6f933ef7 #1511) — ENCODE Project epigenomics dataset lookup; gene target/assay type/biosample type/cell line → ENCODE experiments with accession IDs, assay details (ChIP-seq, ATAC-seq, Hi-C, RNA-seq), biosample info, file counts, lab attribution
forge.geo_expression	DONE (task:8993311d, 9d89182c #1496) — NCBI GEO gene expression dataset search; gene symbol/condition/organism → GEO datasets with accession, title, summary, organism, sample count, platform, submission date, linked PubMed IDs; unblocks transcriptomics-driven hypothesis generation
forge.ebi_expression_atlas	DONE (task:addb4bdc) — EMBL-EBI Expression Atlas cross-species gene expression; baseline/differential/single-cell RNA-seq and proteomics; gene_symbol, species (default: Homo sapiens), experiment_type filter, limit; per-factor expression values; 17 unit tests
forge.ncbi_gene	DONE (task:ad19a31e) — NCBI Gene E-utilities esearch+efetch; gene symbol → gene_id, full_name, chromosome, location, gene_type, organism, summary (≤1000 chars), aliases, RefSeq mRNA accession, OMIM IDs, Ensembl ID; NCBI_API_KEY → 10 rps
forge.uniprot_protein	DONE (task:816b17b8, #1534) — UniProt protein function, sequence, and domain lookup; gene symbol/UniProt accession → protein record with function description, sequence length, domains, GO terms, subcellular localization, active sites; complements forge.uniprot.lookup
forge.drugcentral_lookup	DONE (task:9629816e, #1541) — DrugCentral drug-target-indication database; drug names → DrugCentral records including dc_id, target bioactivity (Ki/IC50/EC50), approved indications, DOID codes; open API, no auth required; complements forge.chembl_compound
forge.monarch_initiative	DONE (task:7dc121d6, #1555) — Monarch Initiative disease-gene-phenotype association lookup; gene symbol/disease ID → gene-disease and gene-phenotype associations with evidence codes, sources (OMIM/Orphanet/MGI/Monarch), and HPO/MP phenotype terms
forge.cellxgene_expression	DONE (task:1110a12f, #1548) — CellxGene Census WMG v2 single-cell expression; gene symbols → per-cell-type expression summaries (mean expression, fraction expressing) across tissues and datasets from the CellxGene Census
forge.pride_proteomics	DONE (task:0295e1d8, #1560) — EMBL-EBI PRIDE proteomics experiment lookup; gene symbols → PRIDE experiments with project accessions, title, organism, instrument, sample size, publication info; complements forge.ebi_expression_atlas at protein level
forge.chebi_compound	DONE (task:981e9def, #1552) — ChEBI chemical entity and ontology lookup; compound name/ChEBI ID → chemical entity records with formula, charge, mass, SMILES, InChI, ontology roles (drug/metabolite/cofactor), synonyms, related ontology terms
forge.cbioportal_mutations	DONE (task:8b19a62d, #1551) — cBioPortal cancer genomics mutation lookup; gene symbols → somatic mutation records across TCGA/GENIE studies with amino acid changes, mutation types, study IDs, sample counts; complements forge.tcga_genomics with cross-study detail
forge.sider_side_effects	DONE (task:3ff2dcc4, #1570) — SIDER drug adverse event and side effect lookup; drug names → MedDRA-coded adverse events with frequency data from drug label text; fills pharmacovigilance gap not covered by forge.chembl_compound or forge.drugcentral_lookup
forge.intact_interactions	DONE (task:d75fa586, #1572) — IntAct EMBL-EBI molecular interaction lookup; gene symbols → molecular interaction records with interaction type, detection method, experimental role, publication evidence; complements forge.string_ppi and forge.biogrid_interactions with curated IntAct-specific data
forge.civic_variants	DONE (task:0397cef4, #1573) — CIViC clinical variant interpretations for precision oncology; gene symbols → cancer-specific clinical evidence records with drug associations, evidence strength, variant name, disease, evidence level (A–E); community-curated knowledgebase for clinical actionability
forge.signor_signaling	DONE (task:91b26ee1, #1576) — SIGNOR causal signaling network lookup; gene symbols → directed causal interaction records (activation/inhibition) with mechanism, effect, stimulus, context, and PubMed evidence; enables pathway-level hypothesis generation
forge.orphanet_disease	DONE (task:7795b00d, #1579) — Orphanet rare disease lookup via OLS4/ORDO; disease name/ORPHA code → structured disease entities with ORPHA codes, synonyms, inheritance patterns, prevalence, linked genes, and cross-references to OMIM/ICD/MeSH
forge.wikip_pathways	DONE (task:9bad15da, #1580) — WikiPathways community biological pathway lookup; gene symbols/keywords → pathway records with WPID, title, organism, gene members, data-node counts, and linked publications; complements forge.kegg_pathways with community-curated pathway content
forge.quickgo_annotations	DONE (task:57b73a9e, 510235ee #1581) — QuickGO GO term annotation lookup by gene or protein; EBI QuickGO single-entity lookup with annotation provenance fields (reference, qualifier, assigned_by) and aspects summary; complements forge.go_term_enrichment (multi-gene enrichment) with per-gene annotation detail
forge.dgidb_interactions	DONE (task:efbe2eb5, 195ee822 #1585) — DGIdb drug-gene interaction lookup; Drug Gene Interaction Database v2 REST API; drug names/gene symbols → interaction records with interaction type, score, directionality, source databases, and PubMed evidence; complements forge.chembl_compound and forge.pharmgkb
forge.clingen_gene_validity	DONE (task:3771258c, b56e21e8 #1586) — ClinGen gene-disease clinical validity; expert-panel curated classifications (Definitive/Strong/Moderate/Limited/No Known Disease Relationship/Disputed/Refuted); MOI, OMIM, MONDO cross-refs; authoritative for clinical interpretation of gene-disease relationships
forge.corum_complexes	DONE (task:d0d4cadc, fce66031 #1588) — CORUM human protein complex membership lookup via OmniPath REST API; gene symbols → complex records with CORUM ID, complex name, subunit gene list, GO annotations, PubMed evidence; gold standard for mammalian protein complex analysis
forge.mygene_info	DONE (task:2ab83011, 46db46dd #1594) — MyGene.info aggregated gene annotation; cross-database reconciliation of Entrez/Ensembl/UniProt/UCSC/RefSeq/GO/KEGG; gene symbols → aliases, summary, genomic location, GO terms, pathways, homologs; single call replaces multiple single-source lookups
forge.hgnc_gene_lookup	DONE (task:414c0e5d, 101cd658 #1595) — HGNC authoritative gene nomenclature; HGNC REST API; gene symbol/name → approved symbol, full name, HGNC ID, alias symbols, previous symbols, locus type, chromosome location, Ensembl/OMIM/NCBI cross-references
forge.hmdb_metabolites	DONE (task:3a2983dc, 1ec2d011 #1596) — HMDB Human Metabolome Database lookup; 217K+ metabolites; name/HMDB ID → chemical formula, MW, SMILES, InChI, biofluid locations, disease associations, protein interactions, metabolic pathways; gold standard for metabolomics
forge.gtex_eqtl	DONE (task:e0470074, 8e78a996 #1603) — GTEx v10 tissue-specific eQTL variant-to-gene associations; gene symbol/variant → eQTL records per tissue with p-value, slope, slope_se, FDR, minor allele frequency; 54 GTEx tissues; unblocks tissue-specific regulatory hypothesis generation
forge.depmap_gene_effect	DONE (task:b9ad2681, d37f7cfd #1604) — DepMap CRISPR gene effect scores; Broad Institute DepMap portal; gene symbols → per-cell-line gene effect scores (< -0.5 = likely essential) across 1000+ cancer cell lines; cancer type, lineage; complements forge.tcga_genomics with functional dependency data
forge.ensembl_vep	DONE (task:7f721ac2, 12f8bc15 #1605) — Ensembl VEP variant effect predictions; HGVS/rsID/chr:pos:ref/alt input → consequence annotations with biotype, impact (HIGH/MODERATE/LOW/MODIFIER), SIFT/PolyPhen2 scores, gene context; completes the variant annotation stack alongside ClinVar, gnomAD, dbSNP
forge.mirbase_mirna	DONE (task:13e25cb4, e592be5d #1607) — miRBase microRNA gene annotation lookup; miRNA ID (hsa-miR-21-5p) or stem-loop name → mature sequences, arm classification (5p/3p), stem-loop coordinates, Rfam IDs, species; primary resource for miRNA regulatory hypothesis generation
forge.ncbi_datasets	DONE (task:be286b82, 08efbbcd #1614) — NCBI Datasets v2 gene summary and RefSeq transcript lookup; gene symbol/ID → structured gene summary, chromosome, chromosome_location, full_name, RefSeq mRNA accessions (NM_), protein accessions (NP_); richer than legacy Entrez efetch; complements forge.ncbi_gene
forge.dbsnp	DONE (task:427e9b1c, 828f7a78 #1615) — NCBI dbSNP canonical variant reference lookup; rsID list → variant records with ref/alt alleles, GRCh38 position, gene context (exonic/intronic/UTR), multi-population allele frequencies (gnomAD/1000G/TOPMED/ESP), ClinVar clinical significance, merge history; completes variant annotation stack alongside ClinVar, gnomAD, VEP
forge.jaspar_tfbs	DONE (task:6213a120, 74167bac #1624) — JASPAR 2024 TF binding site profiles; gene symbol (TF name) or JASPAR matrix ID → TF binding site matrix records with PWM, information content, consensus sequence, taxonomic scope, data type (ChIP-seq/SELEX), PubMed evidence; gold standard for transcription factor binding site analysis
forge.phewas_catalog	DONE (task:d79137a2, 64ecc610 #1627) — PheWAS Catalog variant-phenotype cross-phenome associations; rsID/gene → all phenotypic associations from cross-phenome GWAS analyses with p-value, OR, phenotype category, study cohort; complements single-trait GWAS Catalog with cross-phenotype pleiotropy mapping
forge.regulome_db	DONE (task:807c3590, 6f0e9523 #1628) — ENCODE RegulomeDB variant regulatory element annotations; rsID or chr:pos variants → regulatory score (1a–7), score category (functional/likely_functional/not_functional), TF ChIP-seq peaks, DNase-seq accessibility, eQTL gene overlaps, nearby genes; mechanistic bridge between variant identification (dbSNP, gnomAD) and chromatin/TF interpretation
forge.mgi_mouse_gene	DONE (task:6007130f, 67a82f0c #1630) — MGI Mouse Genome Informatics; mouse/human gene symbols → MGI accession, mouse gene symbol, human ortholog, chromosomal location, KO phenotypes (Mammalian Phenotype ontology terms with allele type), human disease associations; auto-maps human gene symbols (e.g. TP53) to mouse orthologs (Trp53); authoritative for translational hypothesis generation; complements forge.monarch_initiative
forge.wormbase_gene	DONE (task:9563b815, 9cccb3f3 #1637) — WormBase C. elegans gene phenotype and disease lookup; C. elegans gene symbols (or human orthologs, auto-mapped) → WBGene accession, worm symbol, human ortholog, WormBase Phenotype terms from RNAi/mutant allele experiments (wbbt_id, term, allele_type), human disease associations with evidence codes; completes invertebrate model organism suite alongside MGI (mouse) and FlyBase (fly)
forge.flybase_gene	DONE (task:2bb38c01, c85c4b38 #1639) — FlyBase Drosophila melanogaster gene KO phenotype and disease lookup; Drosophila gene symbols (or human orthologs, auto-mapped) → FBgn ID, fly symbol, full name, human ortholog, chromosome, mutant phenotype descriptions from allele experiments, human disease models with DOID/OMIM and FlyBase URLs; complements forge.mgi_mouse_gene (mouse) and forge.wormbase_gene (worm)
forge.sgd_yeast	DONE (task:14c23bd3, 3389d3d6 #1640) — SGD Saccharomyces cerevisiae gene phenotype and pathway lookup; yeast gene symbols (or human orthologs, auto-mapped) → SGD accession, systematic name, human ortholog, deletion/overexpression phenotypes (experiment_type, mutant_type, phenotype_term, qualifier), GO annotations (MF/BP/CC with evidence codes); classic model for TOR signaling, DNA repair, autophagy; completes the four-species model organism forge suite
forge.zfin_gene	DONE (task:f2ec932f, c849988c #1648) — ZFIN Zebrafish gene phenotype and anatomy lookup; Alliance Genome Resource API; zebrafish gene symbols (or human orthologs, auto-mapped) → ZDB gene ID, zfin symbol, human ortholog, mutant phenotype terms (anatomy ontology), anatomical expression data from ZFIN allele experiments; extends model organism suite to five species (mouse/worm/fly/yeast/zebrafish)
forge.enrichr	DONE (task:e9997747, d6785ed2 #1646) — Enrichr gene set enrichment analysis; Enrichr API; gene symbols → enrichment results ranked by combined score from curated libraries (GO, KEGG, Reactome, MSigDB Hallmarks, GWAS traits, TF targets); broader library coverage than forge.msigdb_genesets including GWAS and TF-target collections
forge.lincs_l1000	DONE (task:bf5b5f55, a419dde0 #1647) — LINCS L1000 drug perturbation transcriptomic signatures; LINCS SigCom metadata API; drug/perturbagen/gene → L1000 expression profiles across ~978 landmark genes and multiple cell lines; enables perturbation-driven hypothesis generation about drug mechanism of action and gene regulatory networks
forge.openfda_adverse_events	DONE (task:e395d2b8, 615c758a #1651) — OpenFDA FAERS drug adverse event lookup; FDA Adverse Event Reporting System via OpenFDA API; drug names → aggregated MedDRA reaction counts and proportions from post-market safety surveillance; real-world pharmacovigilance signal data; complements forge.sider_side_effects
forge.nsides_offsides	DONE (task:55f49a12, f9cc2e5b) — nSIDES OFFSIDES/TWOSIDES post-marketing adverse drug event signals; OFFSIDES (single-drug) and TWOSIDES (drug-drug interaction) with PRR and reporting odds ratio statistical enrichment scores from FAERS; distinct from SIDER (drug label frequencies) and OpenFDA (raw report counts) by providing statistical enrichment metrics and the unique TWOSIDES drug-drug interaction signals; public API at nsides.io/api, no auth required
forge.bindingdb_affinity	DONE (task:a5c8acf4, 1f4f3736 #1652) — BindingDB protein-ligand binding affinity lookup; BindingDB REST API; UniProt accession → experimentally measured affinities (Kd, Ki, IC50, EC50) with ligand structure, assay conditions, and PubMed evidence; gold standard for target-ligand binding data in drug discovery; complements forge.chembl_compound
forge.iuphar_pharmacology	DONE (task:faa7c075, 4453297b #1656) — IUPHAR/BPS Guide to Pharmacology drug target lookup; GtoPdb REST API; target name → authoritative receptor/channel/transporter classification, approved ligand lists, selectivity data; gold standard for GPCR, ion channel, nuclear receptor, and transporter pharmacology
forge.gnomad_constraint	DONE (task:5f158409, d8069b05 #1658) — gnomAD per-gene constraint metrics; gnomAD GraphQL API; gene symbol → pLI, LOEUF, o/e ratios for missense/synonymous/LoF variants; quantifies selective pressure; complements forge.gnomad_variant (variant-level AFs) with gene-level intolerance scores for pathogenicity prioritization
forge.cadd_scores	DONE (task:50a4925a, 43ab97ac #1659) — CADD variant pathogenicity scoring; CADD REST API; variant coordinates → phred-scaled scores integrating >60 annotation features (conservation, regulatory, functional); applicable to any human genome variant; complements clinical databases (ClinVar, gnomAD) with a computational pathogenicity estimate
forge.rnacentral	DONE (task:8654e851, 72552af3 #1662) — RNAcentral non-coding RNA sequence lookup; RNAcentral REST API v1; description keyword/RNA class/species → URS identifiers, RNA class (lncRNA, snoRNA, miRNA, tRNA, rRNA, piRNA), sequence length, member-database cross-references; integrates 50+ databases (GENCODE, Ensembl, RefSeq, miRBase, Rfam); stable URS accessions across releases; complements forge.mirbase_mirna with broader ncRNA class coverage beyond microRNAs
forge.rfam_families	DONE (task:1581c0b8) — Rfam RNA family lookup; Rfam REST API (rfam.org); Rfam accession (RF00001) or keyword → RNA family records with rfam_acc, rfam_id, description, RNA type classification (Gene; rRNA, Gene; snRNA; snoRNA; CD-box, Cis-reg; riboswitch), clan accession/ID, num_seed, num_full, average_length, comment, consensus secondary structure (ss_cons); authoritative source for ncRNA family annotation; complements forge.rnacentral with Rfam-specific family metadata and clan structure
forge.cellosaurus	DONE (task:42940b24, a5712380 #1660) — ExPASy Cellosaurus cell line identity and metadata; ExPASy Cellosaurus REST API (api.cellosaurus.org); cell line name or CVCL accession → accession, name, synonyms, cell_line_type, species, tissue_of_origin, disease, sex_of_cell, problematic flag + note, derived_from, cross_references, pubmed_ids; authoritative for authenticating cancer and primary cell lines in biological experiments; covers HeLa (CVCL_0030), MCF-7, and 140K+ other cell lines
forge.panther_orthologs	DONE (task:29a54973, 9ffee040 #1671) — PANTHER orthology and family lookup; PANTHER DB matchortho + geneinfo endpoints (pantherdb.org); gene symbol/ID → panther_family, panther_subfamily, ortholog records (target_gene_id, target_organism, target_taxon_id, ortholog_type); ortholog_type filter (LDO/O/P/X/LDX, default LDO); 14 PANTHER genomes covered; asyncio.gather for concurrent matchortho+geneinfo calls; complements forge.mgi_mouse_gene, forge.wormbase_gene, forge.flybase_gene with pan-genome orthology inference across all PANTHER-supported species
forge.metabolights_study	DONE (task:9f37f050, 56a28395 #1675) — EBI MetaboLights metabolomics study metadata; MetaboLights REST API; keyword/MTBLS accession → study records with status, organism, assay types, factors, metabolite count, curator notes; metabolomics equivalent of GEO
forge.disease_ontology	DONE (task:b9a3d434, aa471460 #1676) — OBO Disease Ontology via EBI OLS4; disease name/DOID → DO term records with hierarchy, synonyms, OMIM/ICD/MeSH/SNOMEDCT cross-references; complements forge.hpo_phenotype with disease-level (not phenotype-level) ontology
forge.ncbi_taxonomy	DONE (task:98f34ce3, 7ffc3134 #1677) — NCBI Taxonomy species resolution and lineage; E-utilities esearch+esummary (JSON); common or scientific name or numeric taxon ID → taxon_id, scientific_name, common_name, rank, lineage (ordered list of NCBITaxonLineageNode), division, is_model_organism; numeric queries use [uid] qualifier for direct taxon-ID lookup; 15 model organism IDs flagged (human, mouse, zebrafish, fly, worm, yeast…); complements forge.ncbi_gene and forge.ncbi_datasets with species-level taxonomy resolution
forge.mesh_lookup	DONE (task:bcae5fa4, f18f46c0 #1678) — NCBI MeSH medical subject headings term lookup; NCBI MeSH API; term/query → descriptor records with tree numbers, scope notes, entry terms (synonyms), descriptor class; authoritative for biomedical literature indexing and controlled vocabulary
forge.paxdb_abundance	DONE (task:f28830a7, 228c8ddc #1680) — PAXdb protein tissue abundance lookup; PAXdb REST API; gene symbol + species → integrated abundance scores (ppm) across tissues/cell lines with data source and confidence; MS-based quantitative complement to forge.human_protein_atlas
forge.chea3	DONE (task:e1089b6a, 699b6d74 #1681) — ChEA3 transcription factor enrichment analysis; MaayanLab ChEA3 API; gene symbols → TF enrichment rankings across 6 libraries (ARCHS4/ENCODE/ReMap/GTEx/ENCODE ChIP-seq/Literature) with integrated rank score; identifies likely transcriptional regulators of a co-expressed gene set
forge.bioproject	DONE (task:3fd077bc, e04af9c8 #1684) — NCBI BioProject sequencing study metadata; NCBI E-utilities; keyword/organism/PRJNA accession → project records with accession, title, description, organism, project type, linked SRA run counts; unblocks raw-data retrieval for forge.sra_run
forge.oncokb	DONE (task:12c9d214, 6fea22f7 #1685) — OncoKB precision oncology biomarker annotations; MSK OncoKB API; gene symbol → mutation oncogenicity classifications, level-of-evidence tiers (Level 1–4B), FDA-approved therapeutic associations; authoritative clinical actionability knowledgebase
forge.eqtl_catalogue	DONE (task:e0033969, e719ef20 #1686) — EBI eQTL Catalogue multi-tissue eQTL lookup; EBI eQTL Catalogue REST API v2; gene symbol/rsID → eQTL records across 100+ datasets (GTEx, BLUEPRINT, DICE, HipSci, CEDAR, etc.) with p-value, beta, tissue/cell type; extends forge.gtex_eqtl beyond GTEx to non-GTEx datasets
forge.sra_run	DONE (task:6c79395e, 47558a11 #1687) — NCBI SRA sequencing run metadata; NCBI E-utilities; accession/bioproject/organism query → SRA run records with experiment type, platform, instrument model, run accession, base count, spot count; >50M runs across Illumina/PacBio/Nanopore platforms
forge.proteomicsdb_expression	DONE (task:e42cdef3, 3088c65a #1690) — ProteomicsDB quantitative proteomics atlas; ProteomicsDB REST API; gene symbol → protein expression records across tissues and cell lines with spectral count, iBAQ score, MaxQuant razor count; MS-based quantitative complement to RNA-level expression verbs
forge.ensembl_regulatory	DONE (task:b49f698e, 5a4e77ea #1694) — Ensembl Regulatory Build chromatin features; Ensembl REST API; gene symbol/genomic region → regulatory feature records (promoters, enhancers, open chromatin, CTCF binding sites) with biotype and epigenome activity score; bridges variant-to-regulatory-element interpretation gaps
forge.omnipath_interactions	DONE (task:0ab05d58, 134f8c58 #1696) — OmniPath multi-database signaling network; OmniPath REST API; gene symbols → curated signaling interactions aggregated from 100+ source databases (SIGNOR, IntAct, PathwayCommons, KEGG, etc.) with consensus direction and stimulation/inhibition effect; complements forge.signor_signaling with broader multi-source coverage
forge.repurposing_hub	DONE (task:938af8a5, 52bc5b73 #1699) — Broad Drug Repurposing Hub compound-target data; Broad Institute clue.io Repurposing Hub download; compound name → target records with clinical phase, mechanism of action, disease indication, SMILES/InChIKey; curated from FDA-approved and investigational drugs for repurposing hypothesis generation
forge.ncbi_protein	DONE (task:63065eb7, 7eff9d49 #1695) — NCBI Protein sequence and annotation lookup; NCBI E-utilities efetch GBSeq XML; RefSeq accession (NP_/XP_/YP_) or gene/protein name with optional organism filter → accession, GI, organism, sequence length, sequence, DB cross-references; NCBI_API_KEY → 10 rps; complements forge.ncbi_gene with protein-level sequence data
forge.brenda_enzyme	DONE (task:85a13d09, e0e7433d #1702) — BRENDA enzyme kinetics and substrate data; BRENDA SOAP API; EC number or enzyme name → Km, kcat, Vmax values with organism and substrate context, substrate/inhibitor/activator lists; auth via BRENDA_EMAIL + BRENDA_PASSWORD; gold standard for enzyme kinetics data
forge.open_gwas	DONE (task:ccf418f1, 5121838e #1707) — IEU OpenGWAS summary statistics lookup; IEU OpenGWAS REST API; GWAS study ID / trait keyword / variant list → GWAS dataset metadata, top hits, per-variant associations with p-value, beta, SE, effect allele; 100+ GWAS datasets including UK Biobank; complements forge.gwas_catalog with full summary statistics access
forge.alliance_genome	DONE (task:2bab4f98, f58e09b9 #1705) — Alliance of Genome Resources cross-species gene lookup; Alliance API (alliancegenome.org/api); gene symbol or Alliance cross-species ID → unified gene record with symbol, species, chromosome, synopsis, phenotype annotations (HPO/MP/WBPhenotype/FBbt/APO terms), disease associations (Disease Ontology + evidence codes), and expression summary; aggregates data from SGD, WormBase, FlyBase, ZFIN, MGI, RGD, and HGNC into a single call
forge.mirtarbase	DONE (task:a963ad0c, 5e871e26 #1709) — miRTarBase validated miRNA–target interactions; manually curated experimentally validated miRNA-target gene interactions; mature miRNA ID (hsa-miR-21-5p) or target gene symbol → interaction records with mirna_id, target_gene, species, experiments (Luciferase reporter / Western blot / CLIP-seq), support_type (Functional MTI / Non-Functional MTI), and supporting PubMed reference count; complements forge.mirbase_mirna with functional validated target evidence
forge.genemania	DONE (task:3cb05e81, 2b57134b #1711) — GeneMANIA gene functional association network; Bayesian integration framework across co-expression, genetic interaction, pathway co-membership, protein domain similarity, physical interaction, predicted, and co-localization evidence channels; gene symbols + organism → ranked functional partner genes with network contribution scores and network type breakdown; distinct from forge.string_ppi (edge-centric PPI) by weighting evidence channels per query and surfacing co-expression and pathway context
forge.cancermine	DONE (task:0bfc9724, 0fe0ccd1 #1712) — CancerMine text-mined cancer gene roles; literature-mined database from PubMed abstracts using ML text mining; gene symbol → oncogene/tumor_suppressor/driver role records per cancer type with citation count and publication year range; role filter support; complements forge.cosmic_mutations (mutation frequency), forge.cbioportal_mutations (mutation profiles), and forge.oncokb (clinical actionability) with literature-based role classification
forge.iedb_epitope	DONE (task:9b8dde84, 9f070465 #1714) — IEDB immune epitope database lookup; world’s largest curated repository of experimentally validated immune epitopes; antigen name/pathogen → T-cell and B-cell epitope records with epitope_sequence, epitope_type, mhc_allele (HLA restriction), host_organism, assay_type, qualitative_outcome (Positive/Negative), and supporting reference count; epitope_type and host_organism filters; essential for vaccine design and immunogenicity hypothesis generation
forge.ot_genetics	DONE (task:a2999a7f, d3cc8861 #1715) — Open Targets Genetics variant-to-gene fine-mapping; OT Genetics GraphQL API (api.genetics.opentargets.org); rsID/positional variant ID → ranked gene list with V2G scores (0..1 composite of QTL colocalisation, functional annotation, distance-to-TSS); gene symbol → GWAS loci where gene is top causal candidate with L2G scores; study accession → top Manhattan loci; adds Bayesian posterior inclusion probabilities (PIP) from credible sets; distinct from forge.opentargets (OT Platform disease-to-target) and forge.open_gwas (summary statistics)
forge.ncbi_biosample	DONE (task:7af5d34d, dc400c1d #1713) — NCBI BioSample per-sample metadata lookup; NCBI E-utilities esearch+efetch XML; SAMN*/SAME*/SAMD* accession, keyword, or BioProject accession → sample records with title, organism, taxonomy_id, attributes dict (tissue/disease/sex/treatment), and SRA run count; complements forge.bioproject (project-level) and forge.sra_run (run-level) with biological and clinical sample context
forge.genecards	DONE (task:ed7257cb, 69aeba84 #1719) — GeneCards synthesized multi-DB gene summaries; GeneCards REST API; gene symbol → synthesized narrative summary (up to 2000 chars), aliases, chromosomal location, expression profile, disease associations, drug count, and GO terms; aggregates 150+ databases (UniProt, NCBI Gene, Ensembl, OMIM, GO, GTEx, HPO, DrugBank); complements forge.ncbi_gene, forge.mygene_info, and forge.human_protein_atlas with a single authoritative synthesized view
forge.pharmvar	DONE (task:ff1d5f9f, ad24f670 #1721) — PharmVar pharmacogenomics star-allele definitions; Pharmacogene Variation Consortium (pharmvar.org) public API; gene symbol → star-allele records with allele_name (e.g. CYP2D6*4), haplotype_id, functional_status, defining_variants (HGVS), and rsIDs; supports allele_name and functional_status filters; complements forge.pharmgkb (clinical guidelines) with allele-level haplotype-to-function mapping
forge.bgee	DONE (task:b4f11bf2, 10e60678 #1722) — Bgee comparative gene expression across species; bgee.org free API; gene symbol/Ensembl ID + optional taxon filter → expression records with condition (anatomy+stage via Uberon ontology), expression score, call type (Expressed/Not Expressed), and rank score; integrates RNA-seq, Affymetrix, in situ hybridisation, and EST data across 30+ animal species; ortholog-aware cross-species comparison; complements forge.gtex_expression (human eQTL) and forge.cellxgene_expression (single-cell RNA-seq)
forge.encode_screen_ccres	DONE (task:f9acec14, 7abcba34 #1726) — ENCODE SCREEN cis-regulatory element lookup; ENCODE SCREEN API v0; gene symbol or genomic region → cCRE records with accession, element type (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), GRCh38 coordinates, H3K4me3/H3K27ac/ATAC-seq/CTCF Z-scores, and nearest protein-coding gene; 1M+ classified regulatory loci; complements forge.encode_epigenomics (raw experiment metadata) and forge.ensembl_regulatory (activity states per tissue)
forge.mirdb_mirna_targets	DONE (task:b81618b3, df944b02 #1727) — miRDB computational miRNA-target predictions; mirdb.org free API; mature miRNA name or gene symbol → interaction records with target_score (0–100; ≥80 = high-confidence), target_gene, genbank_accession, and species; 37k+ miRNA sequences across 5 species (Human/Mouse/Rat/Dog/Chicken); ML-predicted targets; complements forge.mirtarbase (experimentally validated) and forge.mirbase_mirna (miRNA gene annotations)
forge.ndex_networks	DONE (task:bf16b98a, 33d56a5d #1729) — NDEx biological network retrieval; NDEx REST API v2; two modes: network search (ranked list of published networks with metadata: uuid, name, node/edge counts, owner) and neighborhood query (subgraph of query terms within a specific network by uuid); community-curated pathway models including NCI-PID, SIGNOR networks, and disease interactomes; complements forge.string_ppi (PPI scoring) and forge.signor_signaling (causal-signaling relations)
forge.zinc_compounds	DONE (task:45038485, b788a023 #1731) — ZINC15 purchasable small molecule lookup; zinc15.docking.org REST API; SMILES similarity search (Tanimoto threshold), InChIKey exact lookup, or compound name text search → records with purchasable status, vendor availability, and physico-chemical properties (MW, LogP, TPSA, HBD, HBA, rotatable bonds); 1.5B+ substances; complements forge.pubchem_compound (all compounds, no purchasability) and forge.chembl_compound (bioactivity-annotated)
forge.ebi_complex_portal	DONE (task:294a2cbc, d35e76d9 #1735) — EBI Complex Portal macromolecular complex lookup; EBI Complex Portal REST API; gene symbol/complex name/CPX accession → curated complex entries with subunit composition (gene + UniProt AC), stoichiometry, GO annotations, organism; cross-species coverage; complements forge.corum_complexes (mammalian purified complexes) and forge.intact_interactions (binary PPI)
forge.iptmnet_ptm	DONE (task:d2fbc73b, 4f810934 #1736) — iPTMnet post-translational modification lookup; integrates 10+ sources (PhosphoSitePlus, PhosphoELM, HPRD, SIGNOR, RLIMS-P, UniProt, neXtProt, BioGRID); gene symbol/UniProt AC → PTM sites (position, amino acid, modification type, enzyme, score) and enzyme-substrate relationships; covers phosphorylation, ubiquitination, acetylation, methylation, sumoylation; primary unified PTM resource for kinase signaling research
forge.stitch_interactions	DONE (task:a89b3b78, d08718d4 #1741) — STITCH chemical-protein interaction network; stitch.embl.de; 9.6M chemicals × 2031 organisms; chemical/protein identifier → interaction records with combined, experimental, textmining evidence scores (0–1000); bidirectional lookup (chemical→proteins or protein→chemicals); complements forge.string_ppi (protein-protein only) and forge.chembl_compound (bioactivity assay data)
forge.pharmacodb_sensitivity	DONE (task:1645615e, 9ef18ec4 #1744) — PharmacoDB quantitative drug sensitivity measurements; pharmacodb.ca; drug name → IC50, AAC, dose-response profiles across cancer cell lines from CCLE, GDSC1/2, CTRPv2, GRAY, FIMM, and 15+ pharmacogenomics studies; cross-study harmonized profiles; complements forge.depmap_gene_effect (genetic dependency) and forge.chembl_compound (binding assay data)
forge.phenodigm	DONE (task:df9a8342, 6fba3553 #1745) — EBI PhenoDigm phenotype similarity scoring; EBI PhenoDigm Solr API; mouse gene knockout → ranked human diseases by IC-weighted Jaccard similarity over HPO/MP phenotype term sets; IMPC/MGI model genotype descriptions; complements forge.mgi_mouse_gene (mouse KO phenotypes) and forge.monarch_initiative (disease-gene-phenotype)
forge.compartments	DONE (task:7cde2ffc, e11623a3 #1747) — COMPARTMENTS subcellular localization; compartments.jensenlab.org; gene symbol → confidence-scored localization evidence across five channels (knowledge/experiments/textmining/prediction/integrated); integrates UniProt, HPA, ProteomicsDB, PubMed; complements forge.quickgo_annotations (raw GO CC provenance) and forge.human_protein_atlas (antibody images)
forge.mgnify_microbiome	DONE (task:ecb0cefa, a3e51e82 #1750) — EBI MGnify microbiome study metadata; EBI MGnify REST API v1; keyword/biome/MGYS accession → study records with sample counts, biome classification, taxonomic/functional analysis availability; 700K+ samples, 70K+ studies spanning gut/soil/ocean/skin; fills first microbiome/metagenomics gap in forge suite
forge.kegg_compound	DONE (task:2e5ae66c, 57e67244 #1752) — KEGG COMPOUND small molecule database; KEGG REST API; compound ID (C00031) or name → chemical properties (formula, mass), KEGG metabolic context (pathways, EC numbers, reaction IDs); cross-species metabolic network reference with direct KEGG pathway/enzyme links; complements forge.hmdb_metabolites (human metabolome) and forge.chebi_compound (ontology)
forge.dorothea_regulons	DONE (task:eefcce6e, c06d077f #1753) — DoRothEA TF–target gene regulon database; OmniPath REST API; TF gene symbol → target genes with confidence tier A–E (A=ChIP-seq+motif+literature+coexpression); complements forge.jaspar_tfbs (binding-site motifs) and forge.chea3 (inverse enrichment)
forge.panglaodb_markers	DONE (task:534abcb1, 08d7ba2a #1754) — PanglaoDB single-cell cell type marker database; panglaodb.se; gene symbol → cell types expressing it as confirmed marker (with sensitivity/specificity), or cell type → all curated markers; 350+ cell types, 8000+ marker genes from 1300+ scRNA-seq datasets; fills cell-type annotation gap for scRNA-seq workflows
forge.genage_aging	DONE (task:edd37550, 01115a42 #1755) — GenAge human aging gene database; genomics.senescence.info/genes; gene symbol → aging gene record with pro-longevity/anti-longevity/unclear classification, senescence effect, lifespan effect, longevity influence, intervention data; ~307 human aging genes; fills first aging/senescence/longevity database gap
forge.rhea_reactions	DONE (task:e08c578e, 85bd5690 #1756) — Rhea biochemical reaction database; rhea-db.org; free-text query or RHEA:ID → stoichiometric reaction records with ChEBI small molecule participants, UniProt enzyme annotations, cross-references to MetaNetX and genome-scale metabolic models; 14,000+ curated reactions; complements forge.brenda_enzyme (kinetics) and forge.kegg_pathways (pathway-level)
forge.tair_plant	DONE (task:6ed2e974, 1fdf145b #1757) — TAIR Arabidopsis thaliana gene annotation; arabidopsis.org; gene symbol or AGI locus ID (AT1G65480) → gene record with GO terms (MF/BP/CC), mutant allele phenotypes, human ortholog; completes plant model organism coverage alongside SGD (yeast), WormBase (worm), FlyBase (fly), ZFIN (zebrafish), MGI (mouse)
forge.ctd_chemical_disease	DONE (task:de3eb18b, 9267062a #1759) — CTD Comparative Toxicogenomics Database chemical-gene-disease associations; ctdbase.org; chemical name → gene interaction records (interaction action, organism) and disease association records (direct/inferred evidence, MESH disease IDs); curated resource bridging environmental exposures to disease etiology
forge.syngo	DONE (task:e2ae65b3, 1de77e80 #1760) — SynGO synaptic gene ontology database; syngoportal.org; gene symbol → SynGO annotations with biological process and cellular component terms specific to synaptic biology; expert-curated resource for synapse research and neurological disease gene characterization
forge.unichem	DONE (task:541ad13e, 26790c44 #1761) — UniChem cross-reference resolver; ebi.ac.uk/unichem; InChIKey/compound name → cross-references across 40+ chemical databases (ChEMBL, PubChem, DrugBank, KEGG, ChEBI, BindingDB, etc.) with source compound IDs; authoritative compound identity resolver for multi-database chemical workflows
forge.fantom5_enhancers	DONE (task:3f8411c2, 8355ddec #1762) — FANTOM5 CAGE-based enhancer database; fantom.gsc.riken.jp; genomic region/gene symbol → enhancer records with CAGE signal coordinates, tissue/cell type activity, target gene associations, and phase-1/phase-2 classification; unique for cell-type-specific enhancer activity from CAGE sequencing
forge.proteomexchange	DONE (task:559b75c8, 3bd037ea #1767) — ProteomeXchange multi-repository proteomics dataset search; proteomexchange.org; keyword/gene symbol → dataset records across PRIDE, MassIVE, jPOST, iProX, and PanoramaPublic with dataset title, species, instrument, sample size, and PX accession; complements forge.pride_proteomics with cross-repository coverage
forge.lncbase	DONE (task:163721f0, a29f4ea4 #1720) — DIANA-LncBase v3 lncRNA-miRNA sponge interaction database; experimentally validated and computationally predicted ceRNA interactions; lncRNA ID/gene symbol or miRNA → interaction records with experiment type, tissue specificity, prediction score; fills regulatory RNA/ceRNA research gap; complements forge.mirbase_mirna and forge.mirtarbase
forge.lncipedia_lncrna	DONE (task:04dd096d) — LNCipedia human lncRNA gene/transcript catalogue; lncipedia.org REST API; gene symbol/LNCipedia gene ID/transcript ID → gene records with genomic coordinates (GRCh38/GRCh37), strand, aliases, transcript count, transcript lengths, and exon counts; fills lncRNA gene-model gap; complements forge.lncbase (ceRNA interactions) and forge.rnacentral (cross-DB ncRNA IDs)
forge.cath_domains	DONE (task:9d90f7ce, 062612e5 #1764) — CATH protein structural domain classification; CATH REST API; gene symbol/UniProt accession → protein domain records with CATH class/architecture/topology/homologous superfamily hierarchy, domain boundaries, sequence coverage; gold standard for structure-based domain analysis; complements forge.interpro.domains with structure-based classification
forge.chembl_activity	DONE (task:ec5cebeb, 3606ba35 #1768) — ChEMBL bioactivity assay data; ChEMBL REST API; target gene symbol → bioactivity records with compound chembl_id, SMILES, activity type (Ki/IC50/EC50/Kd), value, units, assay type; 20M+ bioactivity records across 14K+ targets; complements forge.chembl_compound (compound lookup) with target-centric bioactivity data
forge.bigg_metabolites	DONE (task:47e62fd8, 260e3ee1 #1782) — BiGG Models genome-scale metabolic network lookup; UCSD BiGG REST API; metabolite name/BiGG ID or reaction query → curated network records with stoichiometry, gene-reaction associations, metabolite formula/charge, organism model membership; fills FBA and systems biology gap; complements forge.hmdb_metabolites and forge.rhea_reactions
forge.mondo_disease	DONE (task:c2211759, 7fd3d579 #1800) — MONDO integrated disease ontology; OLS4 EBI API; disease name/MONDO ID → disease records with MONDO accession, name, synonyms, definition, ontology hierarchy, cross-references to OMIM/DOID/Orphanet/MeSH/ICD; integrates 50+ disease ontology sources; complements forge.disease_ontology (DO) and forge.orphanet_disease (rare diseases)
forge.pubchem_bioassay	DONE (task:42b6491d, 36d5b8c9 #1803) — PubChem BioAssay high-throughput screening data; PubChem BioAssay is the world’s largest public HTS repository with 1M+ assays and 270M+ bioactivity outcomes; compound name/CID → bioactivity records with activity outcome, quantitative activity value, assay type, and target name; distinct from forge.pubchem_compound (chemical properties); complements forge.chembl_activity with broader HTS coverage
forge.impc_phenotypes	DONE (task:af7971e0, 1f651d7d #1792) — IMPC international mouse phenotyping data; IMPC REST API; gene symbol → systematic knockout phenotype records across 10,000+ gene knockouts with procedure, parameter, p-value, effect size, and phenotype ontology terms; most comprehensive source of mammalian gene function data from systematic screens; complements forge.mgi_mouse_gene (MGI-curated) with IMPC systematic screen data
forge.openfda_recalls	DONE (task:eebe1903, e63d36a8 #1787) — FDA drug/device enforcement and recall data; OpenFDA enforcement/recall API; drug/device name → recall records with enforcement type, voluntary/mandatory classification, product description, recalling firm, distribution pattern, status, recall number; covers both drug enforcement (FDA drug/enforcement) and device recalls (FDA device/recall); distinct from forge.openfda_adverse_events (post-market FAERS safety reports)
forge.clingen_dosage	DONE (task:00261e39, ced8baf9 #1788) — ClinGen Dosage Sensitivity Map lookup; ClinGen API; gene symbol → haploinsufficiency (HI) and triplosensitivity (TS) scores (0–3 scale) for 3,000+ curated human genes; critical for CNV interpretation, gene essentiality scoring, and pathogenicity assessment; distinct from forge.clingen_gene_validity (disease classification) with complementary dosage sensitivity scores
forge.array_express	DONE (task:31e2cf80, eef85732 #1793) — ArrayExpress/BioStudies experiment search; EBI BioStudies REST API; keyword/accession → functional genomics study records with title, organism, assay type (microarray/RNA-seq/ChIP-seq/methylation), sample count, submitter; EBI counterpart to NCBI GEO with 100K+ studies not duplicated in GEO; complements forge.geo_expression with EBI-hosted studies
forge.cell_ontology	DONE (task:fa99f03c, 36d08d64 #1795) — Cell Ontology (CL) cell type lookup; EBI OLS4 v2 API; cell type name or CL identifier → standardized CL:0000000-format records with term label, definition, synonyms, ontology hierarchy (parents/children), cross-references; used by HCA, CellxGene, BGEE, and all major scRNA-seq pipelines for cell type annotation standardization
forge.efo_ontology	DONE (task:085c1bde, 785d7294 #1797) — Experimental Factor Ontology (EFO) trait lookup; EBI OLS4 API; disease/trait/condition name or EFO ID → standardized EFO records with term label, definition, synonyms, ontology hierarchy, cross-references to GWAS Catalog, MeSH, HP, MONDO; used by GWAS Catalog, GTEx, ArrayExpress, and all major EBI databases; 17,000+ terms covering quantitative traits, molecular measurements, and experimental conditions
forge.chembl_target	DONE (task:a9e44482, b209ba46 #1798) — ChEMBL target search by gene name or UniProt ID; ChEMBL REST API; gene symbol/UniProt accession → target records with ChEMBL target ID, name, organism, target class, and associated compound count; 15,000+ targets with structural annotations linking to 2M+ bioactive compounds; distinct from forge.chembl_compound (compound-centric) and forge.chembl_activity (bioactivity assay data) with target-centric lookup
forge.rxnorm	DONE (task:d832f3df, 267be565 #1799) — NLM RxNorm drug name standardization; NLM RxNorm API; drug name → primary RxCUI, canonical name, drug concepts with term types (IN/BN/MIN/SBD/SCD), related ingredients, brand names; 750K+ concepts used by FDA, CMS, and EHR systems; stable RxCUI identifiers enable cross-system drug name harmonization
forge.gtex_splice_qtl	DONE (task:5ad68051, 0342b293 #1801) — GTEx tissue-specific splice QTL (sQTL) associations; GTEx Portal REST API; gene symbol → sQTL records per tissue with variant ID, phenotype ID (intron), p-value, slope, FDR across 54 GTEx tissues; maps genetic variants to alternative splicing events (intron excision); distinct from forge.gtex_eqtl (expression QTL) by targeting splicing regulation
forge.human_cell_atlas	DONE (task:d75d7d12, 3321c1c3 #1848) — Human Cell Atlas single-cell expression lookup; HCA REST API; gene symbol/cell type/tissue → cell type expression summaries with mean expression, fraction expressing, and tissue specificity from HCA Atlas data; complements forge.cellxgene_expression (Census) and forge.gtex_expression (GTEx bulk)
forge.phosphositeplus	DONE (task:dc7d87c7, b85f4e82 #1852) — PhosphoSitePlus PTM site database lookup; PhosphoSitePlus REST API; gene symbol/UniProt accession → PTM site records (phosphorylation, acetylation, ubiquitination, methylation, etc.) with modification type, position, residue, flanking sequence, and clinical relevance; gold standard for post-translational modification site annotation
forge.pathway_commons	DONE (task:a16ba8c8, a16ba8c8 #1855) — Pathway Commons multi-pathway database aggregator; Pathway Commons REST API v13; gene symbol → curated pathway memberships across Reactome, KEGG, NCI-Nature PID, Humancyc, EcoCyc, SMPDB, and 30+ source databases; pathway member count, pathway name, and data source; complements forge.reactome_pathways with broader multi-database coverage
forge.drugbank_interactions	DONE (task:f2664498, f2664498 #1857) — DrugBank drug-target interaction lookup; DrugBank REST API; drug name → interaction records with drug name, brand names, mechanism of action, drug groups (approved/experimental/investigational), and target gene symbols; 12,700+ drugs; complements forge.chembl_compound and forge.drugcentral_lookup
forge.targetscan_mirna	DONE (task:d416d5c9, d416d5c9 #1858) — TargetScan miRNA target site prediction; TargetScan REST API; mature miRNA name (hsa-miR-21-5p) or gene symbol → predicted miRNA target sites with context score, weighted context score, weighted conservation score, and seed match type (8mer/7mer-m8/7mer-1A); distinguishes conserved/non-conserved sites; complements forge.mirbase_mirna and forge.mirtarbase
forge.nci_thesaurus	DONE (task:f3877e5e, f3877e5e #1862) — NCI Thesaurus cancer terminology lookup; NLM/NCI REST API; disease/treatment/cancer-related term → NCI Thesaurus concepts with concept code (C12345), definitions, synonyms, and semantic type; 70,000+ concepts; authoritative for cancer-related terminology standardization
forge.cptac_proteomics	DONE (task:4f43ae8b, 4f43ae8b #1863) — CPTAC cancer proteomics dataset lookup; CPTAC REST API; gene symbol → proteomics dataset records with dataset accession, cancer type (breast, colorectal, ovarian, clear cell renal, endometrial, lung adenocarcinoma), data type (protein/phosphoproteome/glycoproteome), and associated publication; complements forge.tcga_genomics and forge.pride_proteomics
forge.pfam_domains	DONE (task:3a13d49e, eb9f212f #1872) — Pfam protein domain family lookup; InterPro Pfam-specific endpoint; UniProt accession → Pfam domain records with accession, name, description, start/end residue positions, e-value, and optional clan accession/name; Pfam-specific companion to forge.interpro.domains surfacing Pfam metadata not available from the broad InterPro aggregator
forge.gencode_transcripts	DONE (task:9cff655c, 1a96a975 #1877) — GENCODE/Ensembl transcript isoform lookup; Ensembl REST API; gene symbol or Ensembl gene ID → all GENCODE transcript isoforms with biotype, transcript support level (TSL), APPRIS principal designation, exon count, and CDS coordinates; authoritative for isoform-aware hypothesis generation and splice-variant interpretation
forge.rgd_rat	DONE (task:77604540, e55b0d0d #1890) — RGD Rat Genome Database gene and QTL lookup; gene symbol/RGD ID → rat gene records with RGD ID, symbol, name, chromosome, aliases, gene type, associated QTLs (qtl_id, symbol, trait name), and human ortholog mapping; complements forge.mgi_mouse_gene (mouse) with rat-specific QTL trait data for comparative genetics
forge.immport_immunology	DONE (task:77604540, e55b0d0d #1890) — ImmPort autoimmune/immunology gene expression lookup; gene symbol → ImmPort study records with study accession, title, organisms, cell type, condition, experiment type (RNA-seq/microarray/qPCR), sample count, and publication; fills immunology research gap not covered by general expression databases
forge.kegg_drug	DONE (task:77604540, e55b0d0d #1890) — KEGG DRUG drug database lookup; KEGG REST API; drug name/KEGG drug ID (D...) → drug records with brand names, structural properties (mol weight, formula, SMILES), drug class, efficacy classification, target pathway, and associated disease indication; complements forge.chembl_compound (bioactivity-centric) with FDA-approved drug-centric coverage
forge.smpdb_pathways	DONE (task:77604540, e55b0d0d #1890) — SMPDB human metabolic pathway database lookup; SMPDB REST API; gene symbol/pathway name → SMPDB pathway records with pathway name, description, pathway type (metabolic/signaling/protein), member metabolites and proteins, disease association, and linked publications; small molecule pathway reference distinct from KEGG and Reactome
forge.metacyc_pathways	DONE (task:19cf9d01, 04b54e9e #1892) — MetaCyc metabolic pathway database lookup; BioCyc REST API; gene symbol/metabolite name → MetaCyc pathway records with pathway name, organism, metabolic class, reaction list (substrates/products), enzymes, and gene associations; complements forge.kegg_pathways with curated non-KEGG metabolic pathways and organism-specific coverage
forge.gdc_genomics	DONE (task:19cf9d01, 04b54e9e #1892) — GDC TCGA genomic variant lookup; GDC Genomics API; gene symbol → GDC genomic records with variant type (SNP/Mutation/CNV), chromosome position, reference/alternate allele, germline/somatic classification, cancer type (TCGA project), validation status, and affected protein change; complements forge.tcga_genomics (mutation frequency) with individual variant-level detail from GDC
forge.encode_chipseq_experiments	DONE (task:19cf9d01, 04b54e9e #1892) — ENCODE ChIP-seq experiment lookup; ENCODE REST API; gene symbol/TF name/assay → ENCODE ChIP-seq experiment records with experiment accession, target antigen (TF/chromatin mark), biosample, lab, replicate count, read depth, peak calls (BED format), and processing pipeline; complements forge.encode_epigenomics with dedicated ChIP-seq coverage
forge.rgd_quantitative_traits	DONE (task:19cf9d01, 04b54e9e #1892) — RGD Quantitative Trait Locus database; gene symbol/qtl_id → RGD QTL records with qtl_id, symbol, chromosome, peak marker, flanking markers, trait name (phenotype), LOD score, effect size, population strain, and associated publications; complements forge.rgd_rat with quantitative trait mapping data beyond simple gene lookup
forge.elm_motifs	DONE (task:9b051d90) — ELM eukaryotic linear motif lookup; elm.eu.org instances.json REST API; UniProt accession → predicted/annotated SLiMs with ELM class identifier, start/end positions, peptide sequence, instance logic (true/false positive), and experimental annotation status; covers CLV_, DEG_, DOC_, LIG_, MOD_, TRG_ motif classes
forge.lovd_variants	DONE (task:da412dcd) — LOVD3 shared variant records lookup; LOVD3 shared REST API (databases.lovd.nl/shared/api/rest.php); gene symbol → unique variant records with HGVS DNA/protein notation per transcript, genomic positions (hg19/hg38), LOVD DBID, times reported, submitter info; community-curated clinical genetics variant database; complements forge.clinvar_variant (NCBI clinical significance) and forge.gnomad_variant (population AF)
forge.oma_orthologs	DONE (task:76c100b6) — OMA Browser ortholog lookup; OMA REST API; UniProt accession/OMA ID/canonical protein ID → ortholog records with OMA ID, canonical ID, species/taxon, rel_type, score, distance, HOG/group, and locus metadata; optional rel_type filter; complements forge.panther_orthologs with OMA pairwise orthology evidence
forge.modomics_modifications	DONE (task:748f7e6c) — MODOMICS RNA modification catalog; genesilico.pl/modomics/api/modifications/; modification symbol/type/nucleotide keyword → modification records with short_name (m6A, m1A, psi), full IUPAC name, molecular formula, modification_type (methylation/pseudouridylation/…), moiety_class (A/C/G/U), KEGG/PubChem/ChEBI cross-references, and biosynthetic enzymes; 18 mocked unit tests; fills first dedicated RNA modification chemical catalog gap
forge.eggnog_annotations	DONE (task:070c62e4) — eggNOG 6 orthologous group (OG) membership and functional annotation; eggNOG 6 REST API; gene/protein query → OG IDs, COG functional category codes, descriptions, GO terms, KEGG KO links, and per-level taxonomic scope; supports optional taxonomic_scope filter (Bacteria/Eukaryota/Archaea or NCBI taxon IDs); graceful not_found flag; 16 mocked unit tests
forge.nextprot_entry	DONE (task:e729d78d) — neXtProt curated human protein entry lookup; neXtProt REST API; UniProt or NX accession → protein names, gene names, isoform count, and annotation type summary; neXtProt deeply curates PTMs, isoforms, and expression for human proteins; graceful not_found on absent entries
forge.thermomutdb_stability	DONE (task:bb0a4f21) — ThermoMutDB protein thermal stability lookup; ThermoMutDB REST API (biosig.lab.uq.edu.au/thermomutdb); UniProt accession or PDB entry ID → experimentally measured ΔΔG (kcal/mol) and ΔTm (°C) per point mutation with pH, temperature, experimental method (DSC/CD/fluorescence), and PubMed ID; 14,000+ mutations across 1,600+ proteins from peer-reviewed literature; essential for protein engineering and stability-guided drug design; complements forge.alphafold_structure (3-D coordinates) with measured thermodynamic effect of each mutation

Category 8: Auth

Status: 5 DONE

Feature	Status	Notes
Dev login (email)	DONE	/auth/dev/login + JWT cookie
Logout + revocation	DONE	/auth/logout + JTI revocation in DB
Google OAuth	DONE	/auth/oauth/google/start + callback
API key auth	DONE	ApiKeyAuthMiddleware for /v1/* write gate
DID-based agent auth	DONE	did:key resolution local (no network); PoP JWT exchange via /v1/auth/jwt; JTI replay protection; 7 integration tests in tests/integration/test_did_auth.py; runbook at docs/runbooks/did-auth-verification.md (verified 2026-05-16, task 5c51c319)

Category 9: HTML Page Parity (Prism Frontend)

Per SPEC-003 tier list. Prism has 190+ +page.svelte files but many render shells with empty data. Substrate-side readiness is tracked here.

Tier 1 — Must Ship (18 routes)

Page	Substrate Ready	Prism Status	Notes
/ (landing)	DONE	Shell	scidex.landing.snapshot verb exists
/search	DONE	Shell	scidex.search verb + /v1/search route
/atlas	DONE	Shell	scidex.landscape.* verbs
/graph	DONE	Shell	scidex.graph.* verbs
/wiki	DONE	Shell	scidex.list(type='wiki_page')
/wiki/[slug]	DONE	Shell	scidex.get by slug
/papers	DONE	Shell	scidex.paper.search verb
/paper/[id]	DONE	Shell	scidex.get
/hypothesis/[id]	DONE	Shell	scidex.get
/analysis/[id]	DONE	Shell	scidex.get
/debate/[session_id]	DONE	Shell	Debate verbs + SSE stream
/debate/[id]/replay	DONE	Shell	scidex.debate.argument_map verb fixed: accepts Ref-dict input, returns Prism-shaped nodes/rounds (task:b1157de9)
/agora	DONE	Shell	Pantheon debate verbs
/exchange	DONE	Shell	Market/collider verbs
/senate	DONE	Shell	Senate proposal/gate verbs
/actor/[id]	DONE	Shell	Actor profile verb
/login	DONE	Done	JWT auth wired
/join	DONE	Missing	POST /auth/register route added (#1398, task:3993f748); Prism form pending

Tier 2 — Should Ship (~18 routes)

Page	Status	Notes
Quest/missions	DONE	scidex.mission.* verbs
Forge tools	DONE	16 forge verbs (incl. KEGG pathways task:f634eac2, ChEMBL compound task:2da4b7b3)
Benchmarks	DONE	scidex.benchmark.* verbs
Notebooks	DONE	scidex.notebook.* verbs
Exchange arbitrage/bids	DONE	Market/collider verbs
Senate sub-dashboards	DONE	Senate gate/quality/cost verbs
Leaderboard	DONE	scidex.leaderboard + many *_leaderboard verbs
Compare	DONE	scidex.agent.compare + scidex.artifact.compare
Missions	DONE	scidex.mission.* verbs
Challenges	DONE	scidex.bounty_challenge.* verbs
Arenas	DONE	scidex.arena.* verbs
Expert review	DONE	scidex.review.* verbs
Relationship graph	DONE	scidex.graph.neighborhood + graph.path
Working groups	DONE	scidex.working_group.* (via REST routes)
Wallet	DONE	scidex.wallet.* verbs
Portfolio	DONE	scidex.portfolio verb
QF rounds	DONE	scidex.qf.* verbs
Squads	DONE	scidex.squad.* verbs

Tier 3 — Nice to Have (~40 routes)

Full audit completed 2026-05-17 (task:d0e5c26f). All 40 Tier 3 pages enumerated below. DONE: 38, DEGRADED: 2, MISSING: 0 (3 retired pages counted in DONE total).

Senate Advanced Dashboards (9 pages)

Page	Status	Notes
/senate/persona-drift	DONE	GET /v1/senate/persona-drift + scidex.senate.persona_drift verb (task:b88fcd74)
/senate/prompt-evolution	DONE	GET /v1/senate/prompt-evolution + scidex.senate.prompt_evolution verb (task:b88fcd74)
/senate/sandbox-audit	DONE	GET /v1/senate/sandbox-audit + scidex.senate.sandbox_audit verb (task:b88fcd74)
/senate/drift-reviews	DONE	ProposalType Literal extended through migration 0140 (agent_review 0116, agent_dispute_escalation 0123, governance_term_renewal 0140); regression test test_proposal_type_literal_matches_db_check pins Literal == DB CHECK; parity gap closed (task:100da4d4)
/senate/gates	DONE	quality_gate artifact type + senate_gate_list/senate_gate_enforce/senate_gate_history/senate_gate_define verbs; Prism page uses per-gate evaluation with dry_run fallback
/senate/proposals	DONE	/v1/proposals REST route (api/routes/senate.py); senate_proposal_* verbs; Prism page with status-tab + offset pagination
/senate/proposals/[id]	DONE	Proposal detail view; same route group
/senate/proposal/new	DONE	senate_proposal_create verb; Prism creation form
/senate/[slug]	DONE	Composite executive sub-dashboard; 10 named slugs with 4-panel layout using existing verbs only; degrades gracefully for unknown slugs (no new verbs needed per Prism code)

Forge Sub-Pages (7 pages)

Page	Status	Notes
/forge/landscape	DONE	scidex.tool.calls verb + Prism server loader (forge/landscape/+page.server.ts); previously DEGRADED as “Prism page absent” — page now exists with latency histogram and per-tool analytics
/forge/runs	DONE	scidex.tool.calls verb; Prism full tool-invocation deep view with tool/actor/status filters
/forge/tools	DONE	scidex.verbs catalog verb (verbs_intro.py) with name_prefix='scidex.forge.'; auto-discovers all registered forge verbs
/forge/tools/[name]	DONE	Verb detail page sourced from scidex.verbs response
/forge/power-calc	DONE	scidex.forge.power_calc verb + tests (task:83e2843c)
/forge/rate-limits	DONE	scidex.forge.rate_limits verb + tests (task:83e2843c)
/forge/resource-predictor	DONE	scidex.forge.resource_predictor verb + tests (task:83e2843c)

Workspace Pages (5 pages)

Page	Status	Notes
/workspace	DONE	scidex.list + scidex.activity verbs; Prism dashboard pulls theses, hypotheses, analyses, debates, quests per actor
/workspace/thesis/[id]	DONE	workspace_thesis_list/workspace_thesis_create/workspace_thesis_update verbs (workspace_thesis_*.py)
/workspace/timeline	DONE	scidex.workspace.timeline verb (workspace_timeline.py); actor-scoped chronological event feed
/workspace/collaborators	DONE	scidex.workspace.collaborators verb (workspace_collaborators.py); persona-advisors + human co-debaters
/workspace/library	DEGRADED	Prism page reads localStorage (scidex.saved.artifacts) for saved items; substrate scidex.list(type='signal', filter={kind:'saved'}) wiring deferred to SPEC-066 P2

Agent Detail Pages (5 pages)

Page	Status	Notes
/agent/[did]	DONE	GET /v1/agents/{did} (api/routes/agents.py); returns profile + bundle version list
/agent/[did]/drift	DONE	scidex.senate.persona_drift verb filtered by agent DID; Prism drift timeline
/agent/[did]/memory	DONE	GET /v1/agents/registry/{did}/memory/episodic (api/routes/agent_memory.py); memory sub-pages (procedural/semantic/social) backed by agent_semantic_memory.py / agent_social_memory.py routes
/agent/[did]/messages	DONE	api/routes/agent_messages.py REST router; Prism message timeline page
/agent/[did]/reflection-runs	DONE	GET /v1/agents/registry/{did}/reflection-runs (api/routes/reflection_runs.py); reflection list + detail view

A2A Federation Pages (2 pages)

Page	Status	Notes
/a2a/tasks	DONE	scidex.a2a.* verbs (a2a.py); AT Protocol federation layer (verified task:aac7845e)
/a2a/tasks/[id]	DONE	A2A task detail view; same verb/route group

Educational / Onboarding Pages (9 pages)

Page	Status	Notes
/demo	DONE	Static 5-step guided tour linking to live pages; no substrate API beyond what Tier 1/2 pages use
/vision	DONE	Static explainer page; no substrate API required
/how	DONE	Static mechanics guide (debate flow, vocabulary, self-evolution loop)
/welcome	DONE	Onboarding CTA page linking to /colliders, /gaps, /debates, /agora
/showcase	DONE	scidex.leaderboard + scidex.graph.neighborhood verbs; Prism KG entity showcase with graph visualization
/intro	DONE	client.domains verb for live field listing + FEATURED_DISEASES fallback; Prism page with server loader
/intro/[field]	DONE	Per-field onboarding; uses domains verb
/learn	DONE	client.domains verb for learning path listing; mirrors /intro
/learn/[field]	DONE	Per-field guided learning path; uses domains verb

Retired / Out of Scope (3 pages — counted in DONE total)

Page	Status	Notes
/walkthrough	RETIRED	No Prism route; static onboarding flow fully covered by /demo and /welcome; no substrate API gap
/badge/learning-path/[id]	RETIRED	No Prism route; gamification/badge features deprioritized per SPEC-015 §3.1; no substrate implementation needed
/quiz/[id]	RETIRED	No Prism route; interactive quiz features deprioritized; /learn/[field] covers domain-based learning

Tier 4 — Sunset / Evaluate

No substrate action needed. v1 mobile swipe, attribution, and promotional pages are intentionally retired per SPEC-015 §3.1.

Category 10: Corpus Migration (ETL)

Status: 6 DONE, 0 CODE_ONLY, 0 MISSING

Per SPEC-015 §3.8, the v1 PG database holds:

Content	v1 Count	v2 Target	Status	Notes
wiki_pages	17,790	wiki_page artifacts	DONE	Live scidex_v2: 17,790 wiki_pages rows, 15,135 enriched (mermaid_diagrams set), 18,969 wiki_page artifacts; GET /v1/wiki/pages returns total=17790; 5 slugs spot-checked 2026-05-16
hypotheses	2,369	hypothesis artifacts	DONE	Live scidex_v2: 6,916 hypothesis artifacts, 5,584 hypotheses rows verified 2026-05-16
papers	29,566	paper artifacts	DONE	Live scidex_v2: 30,455 paper artifacts, 29,566 papers rows verified 2026-05-16
knowledge_edges	710,066	KG link rows	DONE	Live scidex_v2.edges: 710,066 kind='knowledge' rows verified 2026-05-16
analyses	479	analysis artifacts	DONE	analysis_bundle_ingest verb verified
canonical_entities	49,342	Entity-typed wiki backbone	DONE	48,929 kg_entity artifacts in v2 (413 skipped — IDs collide with existing hypothesis/experiment artifacts); BRCA1 gene and Alzheimer disease entities verified 2026-05-16
predicate_vocab	—	KG predicate canonicalization table	DONE	Migration 0225 creates predicate_vocab table and seeds 210 canonical forms (RO, SIO, BioLink, SciDEX v1); idempotent ON CONFLICT; unblocks KG canonicalization pass 2 (task b0139464) — 2026-05-16

Verified 2026-05-16: Papers, hypotheses, knowledge edges, canonical entities, and wiki pages now meet the corpus bulk import thresholds from the parity blocker tasks. Canonical entities backfill completed 2026-05-16: 48,929 kg_entity artifacts written via scripts/backfill/canonical_entities_from_v1.py (49,342 source rows; 413 skipped due to ID collisions with existing hypothesis/experiment artifacts). BRCA1 gene (ent-gene-b806fb43) and Alzheimer disease entities confirmed present. Wiki pages were marked DONE in 41c93eff after backfill verification. predicate_vocab table seeded 2026-05-16 with 210 canonical predicate forms via migration 0225 (scripts/etl/seed_predicate_vocab.py); KG canonicalization pass 2 (task b0139464) is now unblocked.

Category 11: Live Agent Population

Status: 59 DONE, 0 CODE_ONLY, 0 MISSING

Per SPEC-020:

Wave	Count	Status	Notes
10 founding personas	10	DONE	seed_personas.py + seed_skills.py in 01dcfd26
Wave 1 named scientists	12	DONE	Activated by PR #1405 (task af013c0c): migration 0224
Wave 2 Allen/AI2 scientists	17	DONE	Activated by migration 0225 (task 7dd4b17e)
Wave 2 founding + role agents	4	DONE	bootstrap-statistician, historian, bountyhunter, replicator-role (migration 0225)
Wave 3 historical scientists	20	DONE	Activated by migration 0225 (task 7dd4b17e): Cajal, Crick, Sherrington, Hebb, Penfield, McClintock, Franklin, Sanger, Brenner, Mendel, Watson, Avery, Pauling, Salk, Fisher, Bayes, Neyman, Box, Darwin, Mayr
Wave 3 role agent	1	DONE	Admin (migration 0225)
Wave 4-5 remaining personas	17	DONE	data/wave4-personas/ (17 configs), mimeo bundles + agent configs (task 1dbdb64f); Wallace added to v1-personas.yaml; seed_v1_personas default waves updated to {1,2,3,4}
System agents (3)	3	DONE	Orchestra, Senate, Forge agents registered
Role agents (7)	7	DONE	Janitor, Curator, Onboarder, Historian, Bountyhunter, Replicator, Admin

Verified 2026-05-17: 59-persona Pantheon complete. Wave 4-5 persona configs in data/wave4-personas/ (17 YAML files), mimeo bundles in seeds/mimeos/ (all 17 slugs), agent configs in seeds/agent_configs/. Wallace (missing from wave-5 72c04c72) added to v1-personas.yaml with wave: 4. seed_v1_personas.py default waves updated to {1,2,3,4}. 221 unit tests pass (task 1dbdb64f).

Category 12: Skills Bundles

Status: 23 DONE, 0 MISSING

Bundle	Status	Notes
participant_contrarian_bettor	DONE	Agent-owned skill moved to scidex-agents/skills/; substrate keeps market metadata/mechanisms
participant_diversifier	DONE	Agent-owned skill moved to scidex-agents/skills/; substrate keeps market metadata/mechanisms
participant_value_funder	DONE	Agent-owned skill moved to scidex-agents/skills/; substrate keeps market metadata/mechanisms
scidex (onboarding doc)	DONE	Original native skill
site_auditor	DONE	Original native skill
gap_analysis	DONE	Wave 1 port [task:61f0b8b1]
literature_review	DONE	Wave 1 port [task:61f0b8b1]
peer_review	DONE	Wave 1 port [task:61f0b8b1]
hypothesis_refiner	DONE	Wave 1 port [task:61f0b8b1]
statistical_analysis	DONE	Wave 1 port [task:61f0b8b1]
systematic_review	DONE	Wave 1 port [task:61f0b8b1]
meta_analysis	DONE	Wave 1 port [task:61f0b8b1]
data_extraction	DONE	Wave 1 port [task:61f0b8b1]
replication_protocol	DONE	Wave 1 port [task:61f0b8b1]
citation_manager	DONE + BUILT OUT	Wave 2 port [task:86bd0ccc]; iter-309 v0.1 → v0.2 judgement-driven rewrite (four named dimensions: citation_need / source_authority / recency_adequacy / coverage_completeness; anti-patterns section; corpus-tunable defaults — no hardcoded max_citations=5 / current_year - 10 staleness cut) + new src/scidex_substrate/scheduled_workers/citation_quality_worker/ that calls load_skill_body("citation_manager") and emits one calibration signal per artifact with dimension='citation_quality' (artifacts of types hypothesis / analysis / wiki_page / paper, freshness window 30 days). Promotes citation_manager from LEGACY-DOC-ONLY to LLM-WORKER-LOADED in docs/skill-orphan-audit.md.
confidence_calibrator	DONE + BUILT OUT	Wave 2 port [task:86bd0ccc]; iter-220 PR #2241 v0.1 → v0.2 judgement-driven rewrite (drops likelihood-ratio table + Beta-binomial conjugate; semantic calibration bands replace numeric formula); iter-310 ships src/scidex_substrate/scheduled_workers/confidence_calibrator_worker/ (per-hypothesis LLM-judged calibration; walks supported_by/contradicts edges, emits one calibration signal with dimension='probability' and a strong_shift_flag when the posterior shift exceeds the policy threshold — operationalising the skill body’s anti-pattern guard on un-defended large shifts).
debate_mediator	DONE	Wave 2 port [task:86bd0ccc]
discovery_scout	CONSOLIDATED	Wave 2 port [task:86bd0ccc]; iter-307 folded into proposal-authoring as its ## Discovery scouting / opportunity scoring section (4 signal dims: momentum/coverage/newness/conviction-asymmetry + 4 named patterns: cluster-formation/paper-avalanche/forgotten-gap/contrarian-opportunity + corpus-tunable thresholds + abstract-linkage rule) so a proposal author’s scouting read lives in-flow with the proposal authoring rather than as a separate hand-off step.
entity_resolver	CONSOLIDATED	Wave 2 port [task:86bd0ccc]; iter-304 folded into entity-linking as its ## NER & canonical resolution authorities section so artifact linking and entity recognition + canonical-ID resolution live as one skill rather than a hand-off chain.
evidence_synthesizer	DONE	Wave 2 port [task:86bd0ccc]
feasibility_assessor	CONSOLIDATED	Wave 2 port [task:86bd0ccc]; iter-303 folded into proposal-authoring as its ## Feasibility assessment section so authors apply feasibility in-flow rather than calling out to a separate skill.
knowledge_mapper	DONE	Wave 2 port [task:86bd0ccc]
novelty_detector	CONSOLIDATED	Wave 2 port [task:86bd0ccc]; iter-305 folded into claim-extraction as its fourth extraction-policy mode ## Mode 4 — Novelty assessment (NOVELTY) so per-claim novelty assessment lives alongside per-claim atomic-extraction / fallacy / relation modes rather than as a separate sister skill.

Category 13: Mimeo Policies

Status: 11 DONE, 0 DEGRADED

Mimeo	Status	Notes
Theorist debate persona	DONE	M3 delivery
Skeptic debate persona	DONE	M3 delivery
Domain Expert persona	DONE	M3 delivery
Synthesizer persona	DONE	M3 delivery
Quality scorer	DONE	M3 delivery
PMID validator	DONE	M3 delivery
Link checker	DONE	M3 delivery
KG extractor	DONE	M2+M3 delivery
Gap scanner	DONE	M3 delivery
Statistician mimeo	DONE	M9 delivery: schema added (statistical_review.json), policy parity harness passes (33 cassettes), subscriptions + artifact kind verified
Methodologist mimeo	DONE	M9 delivery: schema added (methodology_review.json), policy parity harness passes (33 cassettes), EQUATOR/ARRIVE validation confirmed

Category 14: Cross-Cutting Behaviors

Status: 11 DONE, 0 MISSING, 0 DEGRADED

Behavior	Status	Notes
Live search debounce	DONE	scidex.search + scidex.suggest + autocomplete
JWT cookie auth	DONE	Dev login + OAuth + revocation
Rate limiting	DONE	Two-tier token bucket (per-IP + per-actor)
SSE event stream	DONE	/api/scidex/subscribe + per-debate stream
x402 payment gate	DONE	Middleware + pricing rules
Monitoring + alerting	DONE	/healthz, /metrics, 5 alert surfaces
Mermaid wiki rendering	DONE	GET /v1/wiki/pages/{slug} now returns mermaid_diagrams array from wiki_pages.mermaid_diagrams JSONB column (migration 0154); Prism lazy-loads via import('mermaid') per spec-lazy-load-mermaid-cytoscape_spec.md
Post-merge guard	DONE	src/scidex_substrate/core/post_merge_guard.py added (#1399, task:1d1baec8); integration tests and v1-parity bug fixes landed in cb28f43a (#1421)
OAuth live round-trip	DONE	Google OAuth callback smoke test PASS (#1397, task:61d330cd); verified 2026-05-16
Federation peer sync	DONE	Full outbound + inbound pipeline confirmed via unit + integration tests; live round-trip smoke documented in runbook (#1395, task:aac7845e)
scidex.poll long-poll	DONE	Wired to SSE event stream (#1401); substrate-side complete; Prism poll.ts integration pending

Critical Blockers

These items must be resolved before the cutover script (SPEC-006 §3) will execute:

Resolved Blocker 1: Corpus ETL bulk data verified

• Evidence: Live scidex_v2 counts on 2026-05-16: 30,455 paper artifacts, 6,916 hypothesis artifacts, and 710,066 edges rows with kind='knowledge'.

• ETL state: Latest scidex.v1.etl.papers, scidex.v1.etl.hypotheses, and scidex.v1.etl.kg_edges audit rows are skipped_empty, indicating no pending source delta for the scheduled sync.

• Residual corpus work: All corpus ETL complete. wiki_pages (17,790 v1 rows) now verified DONE — GET /v1/wiki/pages returns total=17790 with all acceptance criteria met.

Resolved Blocker 2: /join registration route — CLOSED

• Resolution: POST /auth/register route added in PR #1398 (commit aec69305, task:3993f748, 2026-05-16). Substrate side DONE; Prism /join form is a separate Prism-side task.

Resolved Blocker 3: Live agent population — 59/59 DONE

• Resolution: All 59 personas activated. Wave 1 (12 scientists) activated by PR #1405 (task af013c0c). Wave 2-3 (42 personas: 17 Allen/AI2, 20 historical, 5 founding/role) activated by migration 0225 (task 7dd4b17e). Wave 4-5 (17 remaining) configs added in task 1dbdb64f: data/wave4-personas/ YAML files, mimeo bundles, agent configs, Wallace added to v1-personas.yaml.

• Impact: v2 has all 59 active agents. Full Pantheon persona coverage complete.

Resolved Blocker 4: OAuth live round-trip — CLOSED

• Resolution: Google OAuth live callback smoke test PASS in PR #1397 (commit 38925cd3, task:61d330cd, 2026-05-16). End-to-end round-trip confirmed with live Google endpoints.

Resolved Blocker 5: Federation live peer sync — CLOSED

• Resolution: AT Protocol federation end-to-end smoke test PASS in PR #1395 (commit a0685aca, task:aac7845e, 2026-05-16). Outbound + inbound sync verified between two substrate instances; runbook documented.

RC Gate Checklist Summary

Per docs/operations/v2-rc-checklist.md:

Section	Status	Notes
§1 Spec corpus (SPEC-173..187)	DONE	All 15 merged
§2 M1 foundation (14 items)	13/14 unchecked	Smoke test framework done; 13 items have code but not individually verified
§3 M2 implementation (8 items)	All unchecked	Code merged but not individually verified
§4 M3 mimeos (9 items)	All unchecked	Code merged
§5 M4 cross-cuts (12 items)	All unchecked	Code merged
§6 M5-M7 operational (16 items)	All unchecked	Code merged
§7 Audit finding closure	DONE	6/6 closed
§8 Integration smoke	3 items	Runner done; readiness scorer + merge prioritizer pending
§9 Production prerequisites	DONE	All 7 gates closed
Post-delta process gaps	1 open	Live restore drill (DID login wiring closed task:5c51c319; federation round-trip closed #1395)

Recommendations

1. Keep corpus ETL in monitor mode. Papers, hypotheses, knowledge edges, canonical entities, and wiki_pages are all verified DONE; future work should watch scheduled sync deltas rather than backfill a known gap.

2. Persona population complete (Blocker 3 resolved). All 59 personas activated including Wave 4-5 configs (task 1dbdb64f). No remaining activation work.

3. Wire Prism /join form (substrate DONE via #1398; Prism form still missing). Create a linked Prism task.

4. Live restore drill (last remaining post-delta process gap). DID login and federation round-trip are closed; only the live restore drill is outstanding.

5. Run RC checklist verification sweep. Sections 2-6 have code merged but 52 individual items remain unchecked. A systematic verification pass should flip these to checked.

Methodology

This document was produced by:

1. Reading SPEC-015 (docs/design/spec-015-v1-parity-tracking.md) for the v1 target surface definition.

2. Enumerating all 416 verb files in src/scidex_substrate/skill/verbs/ and extracting 276+ registered @verb names.

3. Enumerating 56 mounted FastAPI routers with ~190 REST routes.

4. Listing 104 artifact schemas, 221 migrations, 15 economics modules, 12 tool runtimes, 33 forge tools.

5. Cross-referencing SPEC-003 tier list for HTML page parity against Prism reconciliation (spec-003-reconciliation-2026-05-16.md).

6. Cross-referencing v1 persona list (data/v1-personas.yaml, 59 entries) against seeded personas.

7. Reviewing the RC checklist (docs/operations/v2-rc-checklist.md) for production gate status.

8. Reviewing the M-wave summary (docs/operations/m_wave_summary.md) for M1-M7 delivery evidence.

9. Verifying live corpus counts in scidex_v2 for papers, hypotheses, and knowledge edges on 2026-05-16.

Code counts taken against origin/main at commit 890b8c05 on 2026-05-16. Corpus ETL counts taken from live scidex_v2 on 2026-05-16. M10-M13 completions reflected: post-merge guard (#1399 + #1421), /auth/register (#1398), Google OAuth smoke (#1397), federation smoke (#1395), scidex.poll SSE wiring (#1401), DID auth verified (task:5c51c319), canonical entity backfill (#1402), remote_vm runtime (#1411), wiki_pages ETL verification (#1412), skill bundle port waves (#1408 + #1413), Senate analytics (#1416), MCP contract tests (#1418), A2A relay integration test (bb297cb9), Senate governance lifecycle test (#1423), mimeo policy restoration (#1424), mermaid diagram API surfacing (#1427), Wave 2-3 Pantheon activation (#1431), Wave 5 persona configs (#1433), and predicate_vocab seeding (#1437), and persona tick lifecycle coverage (#1438).

Category 7 forge verb count updated 2026-05-17 (task:c58adea3) against origin/main commit 52bc5b73. 16 M27–M28 adapters credited: cellosaurus (#1660), panther_orthologs (#1671), metabolights_study (#1675), disease_ontology (#1676), ncbi_taxonomy (#1677), mesh_lookup (#1678), paxdb_abundance (#1680), chea3 (#1681), bioproject (#1684), oncokb (#1685), eqtl_catalogue (#1686), sra_run (#1687), proteomicsdb_expression (#1690), ensembl_regulatory (#1694), omnipath_interactions (#1696), repurposing_hub (#1699). reactome_pathways later credited by task:5477f265, closing task:f697afee.

Category 7 forge verb count updated 2026-05-17 (task:3ba9915b) against origin/main commit cd063463. 6 M28–M29 adapters credited: alliance_genome (#1705, missed in prior refresh), mirtarbase (#1709), genemania (#1711), cancermine (#1712), iedb_epitope (#1714), ot_genetics (#1715). ncbi_biosample (task:7af5d34d) not yet merged to main; excluded from this count. 100→106 DONE.

Category 7 forge verb count updated 2026-05-17 (task:f15846ba) against origin/main commit 327502b4. 3 M30 adapters credited: ncbi_biosample (#1713, previously pending), genecards (#1719), pharmvar (#1721). reactome_pathways later credited by task:5477f265, closing task:f697afee. 106→109 DONE.

Category 7 forge verb count updated 2026-05-17 (task:9c0296a4) against origin/main commit b788a023. 5 M31 adapters credited: bgee (#1722), encode_screen_ccres (#1726), mirdb_mirna_targets (#1727), ndex_networks (#1729), zinc_compounds (#1731). reactome_pathways later credited by task:5477f265, closing task:f697afee. 109→114 DONE.

Category 7 forge verb count updated 2026-05-17 (task:dc3a0556) against origin/main commit 4f810934. 3 M32 adapters credited: ebi_complex_portal (#1735, task:294a2cbc — landed after M31 parity sweep), iptmnet_ptm (#1736, task:d2fbc73b), stitch_interactions (#1741, task:a89b3b78). reactome_pathways later credited by task:5477f265, closing task:f697afee. 114→117 DONE.

Category 7 forge verb count updated 2026-05-17 (task:3d491903) against origin/main commit 1fdf145b. 10 adapters credited: pharmacodb_sensitivity (#1744, task:1645615e), phenodigm (#1745, task:df9a8342), mgnify_microbiome (#1750, task:ecb0cefa), kegg_compound (#1752, task:2e5ae66c) — 4 inter-M32/M33 verbs; plus compartments (#1747, task:7cde2ffc), dorothea_regulons (#1753, task:eefcce6e), panglaodb_markers (#1754, task:534abcb1), genage_aging (#1755, task:edd37550), rhea_reactions (#1756, task:e08c578e), tair_plant (#1757, task:6ed2e974) — 6 M33 verbs. reactome_pathways later credited by task:5477f265, closing task:f697afee. 117→127 DONE.

Category 7 forge verb count updated 2026-05-17 (task:c775dade) against origin/main commit 2829b6da. 5 M34 adapters credited: ctd_chemical_disease (#1759, task:de3eb18b), syngo (#1760, task:e2ae65b3), unichem (#1761, task:541ad13e), fantom5_enhancers (#1762, task:3f8411c2), proteomexchange (#1767, task:559b75c8). reactome_pathways later credited by task:5477f265, closing task:f697afee. 127→132 DONE.

Category 7 forge verb count updated 2026-05-18 (task:7379ac58) against origin/main commit 7d218eff. 15 M35–M36 adapters credited: lncbase (#1720, task:163721f0), cath_domains (#1764, task:9d90f7ce), chembl_activity (#1768, task:ec5cebeb), bigg_metabolites (#1782, task:47e62fd8), mondo_disease (#1800, task:c2211759) — 5 M35 verbs previously in unmerged branch task:57d0ccb8; pubchem_bioassay (#1803, task:42b6491d), impc_phenotypes (#1792, task:af7971e0) — 2 M35 verbs deferred from prior sweep, now on main; openfda_recalls (#1787, task:eebe1903), clingen_dosage (#1788, task:00261e39), array_express (#1793, task:31e2cf80), cell_ontology (#1795, task:fa99f03c), efo_ontology (#1797, task:085c1bde), chembl_target (#1798, task:a9e44482), rxnorm (#1799, task:d832f3df), gtex_splice_qtl (#1801, task:5ad68051) — 8 M36 verbs. string_ppi task ref updated 8fccd5eb→c0394d83 (#1778, M35 gene-symbol rewrite). reactome_pathways later credited by task:5477f265, closing task:f697afee. 132→147 DONE.

Category 7 forge verb count updated 2026-05-18 (task:9609d28f) against origin/main commit 891205a9. 7 M37 adapters credited: human_cell_atlas (#1848, task:d75d7d12), phosphositeplus (#1852, task:dc7d87c7), pathway_commons (#1855, task:a16ba8c8), drugbank_interactions (#1857, task:f2664498), targetscan_mirna (#1858, task:d416d5c9), nci_thesaurus (#1862, task:f3877e5e), cptac_proteomics (#1863, task:4f43ae8b). reactome_pathways later credited by task:5477f265, closing task:f697afee. 147→154 DONE.

Category 7 forge verb count updated 2026-05-18 (task:84b8d172) against origin/main commit 84f41ef1. 2 M38 adapters credited: pfam_domains (#1872, task:3a13d49e), gencode_transcripts (#1877, task:9cff655c). reactome_pathways later credited by task:5477f265, closing task:f697afee. 154→156 DONE.

Category 7 forge verb count updated 2026-05-18 (task:5477f265) against task branch orchestra/task/5477f265-implement-scidex-forge-reactome-pathways: reactome_pathways credited as DONE via Reactome ContentService adapter with mocked unit coverage. Category 7 156→157 DONE; summary surface counts updated for the new verb, MCP tool, and forge science tool.

Category 7 forge verb count updated 2026-05-18 (task:e5c01b8c) against origin/main commit f0643343. 8 M39 adapters credited: batch A — rgd_rat (#1890, task:77604540), immport_immunology (#1890, task:77604540), kegg_drug (#1890, task:77604540), smpdb_pathways (#1890, task:77604540); batch B — metacyc_pathways (#1892, task:19cf9d01), gdc_genomics (#1892, task:19cf9d01), encode_chipseq_experiments (#1892, task:19cf9d01), rgd_quantitative_traits (#1892, task:19cf9d01). reactome_pathways already credited by task:5477f265 (PR #1891). 157→165 DONE.

Category 7 forge verb count updated 2026-05-18 (task:da412dcd) against task branch orchestra/task/da412dcd-add-scidex-forge-lovd-variants-lovd-shar: lovd_variants credited as DONE via LOVD3 shared REST API adapter with 8 mocked unit tests. Category 7 165→166 DONE; summary surface counts updated for the new verb, MCP tool, and forge science tool.

Category 7 forge verb count updated 2026-05-18 (task:76c100b6) against origin/main commit 33eaa624 plus task branch orchestra/task/76c100b6-add-scidex-forge-oma-orthologs-oma-brows: oma_orthologs credited as DONE via OMA Browser REST adapter with mocked unit and integration coverage, preserving the forge.elm_motifs and forge.lovd_variants rows already on main. Category 7 166→167 DONE.

Category 7 forge verb count updated 2026-05-18 (task:04dd096d). 1 adapter credited: lncipedia_lncrna (task:04dd096d) — LNCipedia lncRNA gene/transcript catalogue, GRCh38/GRCh37. 167→168 DONE.

Category 7 forge verb count updated 2026-05-18 (task:755704f9): circatlas_circrna credited as DONE — circAtlas 3.0 circular RNA adapter, gene_symbol/region query, 11 mocked unit tests, ruff+mypy clean. 168→169 DONE.

Category 7 forge verb count updated 2026-05-18 (task:748f7e6c). 1 adapter credited: modomics_modifications (task:748f7e6c) — MODOMICS RNA modification catalog; MODOMICS REST API; modification symbol/type/nucleotide keyword → modification records with short_name, IUPAC name, formula, modification_type, moiety_class, KEGG/PubChem/ChEBI cross-references, and enzymes. 169→170 DONE.

Category 7 forge verb count updated 2026-05-18 (task:bb0a4f21): thermomutdb_stability credited as DONE — ThermoMutDB experimental ΔΔG/Tm adapter, UniProt/PDB query, 10 mocked unit tests, ruff+mypy clean. 170→171 DONE.

Category 9 Status Update — 2026-05-17

/debate/[id]/replay (was DEGRADED) → DONE (substrate side)

Evidence: task:c44c4ce3 shipped the following to close the substrate gap:

• GET /v1/debates/{session_id}/rounds now returns 404 for non-existent debate IDs (previously returned 200 with empty list — silent failure hiding caller errors).

• offset query parameter added alongside existing limit support.

• _row_to_round bug fixed: created_at and JSON-parsed columns were omitted from the response envelope due to a missing out[col] = val assignment.

• 6 integration tests in tests/integration/test_debate_round_replay.py verify: happy path (3-round debate), score/confidence fields, empty-debate 200, nonexistent-debate 404, round ordering (ASC), and limit/offset pagination.

Prism UI wiring (replay view rendering) is tracked as a separate Prism task.

Category 12 (Tier 3 HTML) Status Update — 2026-05-17

Full 40-page audit completed (task:d0e5c26f): DONE=38, DEGRADED=2, MISSING=0

The parity doc previously listed only 10 Tier 3 “key gaps” with placeholder summary counts of DONE=10/MISSING=15/DEGRADED=15. This update enumerates all 40 pages, verifies substrate support for each, and resolves the counts.

Key findings:

• /forge/landscape upgraded DEGRADED→DONE: Prism page src/routes/forge/landscape/+page.server.ts now exists and calls scidex.tool.calls verb which exists in verbs/tool_calls.py.

• 22 pages newly documented as DONE: workspace (5), agent detail (5), A2A federation (2), senate governance (5), educational/onboarding (5) — all have backing substrate verbs or REST routes.

• 3 pages RETIRED: /walkthrough, /badge/learning-path/[id], /quiz/[id] — no Prism routes exist; covered by /demo+/welcome and /learn/[field] respectively; no substrate API gap.

Remaining DEGRADED items (1): (updated 2026-05-16; /senate/drift-reviews resolved by task:100da4d4)

1. /workspace/library — Prism page reads localStorage (scidex.saved.artifacts) rather than querying substrate scidex.list(type='signal', filter={kind:'saved'}); the substrate query would need SPEC-066 P2 to wire the saved-signal → workspace-library route properly.

The remaining DEGRADED item is a minor workaround (not a broken page) and does not block cutover.