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DraconiticBiochemistryBiomolecules · Catabolism · Biosynthesis · Metabolism
Data

Evidence methodology

A release-locked process for joining protein identity, experimental construct, molecular form, biochemical reaction, assay measurement and provenance.

Identity

Protein identity is modeled as a UniProt accession, taxon, sequence version or checksum, and canonical-versus-isoform state. PDB structures remain identified by PDB entry, polymer entity, and chain, then map through SIFTS with observed coverage, mutations, deletions, tags, and chimeric boundaries preserved.

Family membership uses the curated inclusion list plus supporting alpha-carbonic-anhydrase domain evidence. A name substring or shared reaction is not sufficient.

Sources

Release provenance records each build input's snapshot path, canonical request URL, parameters, release/version, retrieval timestamp, response hash, upstream IDs, and license context. The corpus producer retains those source snapshot files separately; they are not embedded in the served binary. Source-reported measurement fields remain intact in the downloadable corpus, and normalized additions carry separate transform provenance rather than overwriting them.

Inspect the current source ledger.

Normalization

  • ChEMBL target admission requires a direct SINGLE_PROTEIN target, matching taxon, and exact component accession.
  • Compounds use full stereochemical identity when relevant. Parent and salt forms remain distinct measurements.
  • Constructs keep mutations, truncations, fusions, tags, missing regions, and sequence coverage.
  • Raw measurement value, relation, and unit are preserved alongside distinct source-standardized fields.
  • Predicted structures remain a separate evidence class from experimental structures.

Comparison

The server checks required identity and numeric-value fields before any matching. It then evaluates target scope, taxon, construct, catalytic status, endpoint type, relation operator, unit, assay format, pH, temperature, substrate, buffer, tested molecular form, stereochemistry, duplicate dependence, reaction direction, evidence class, assay or matched-protocol group, and provenance completeness.

No Ki/Kd/IC50/Km/kcat conversion is inferred. Censored bounds remain bounds. Same-paper records are not automatically comparable.

TARGET_MISMATCH

The records do not map to the same versioned protein identity.

Select records for one exact accession, taxon and sequence identity.
TARGET_SCOPE_NOT_SINGLE_PROTEIN

At least one target is a family, complex, tissue, cell or phenotypic context.

Use direct SINGLE_PROTEIN target records.
TAXON_MISMATCH

The source organisms differ.

Use records with the same NCBI Taxonomy identifier.
VARIANT_OR_CONSTRUCT_MISMATCH

Variant, truncation, tag, fusion or construct state differs.

Match the complete experimental construct identity.
CATALYTIC_STATUS_MISMATCH

Curated catalytic-status classes differ.

Do not place catalytic and acatalytic-related proteins on one activity ranking.
PARAMETER_TYPE_MISMATCH

The endpoint types differ.

Compare like with like; do not convert between Ki, Kd, IC50, Km, kcat or related endpoints.
CENSORED_RELATION

At least one source value is bounded or approximate.

Preserve the relation operator and avoid point ranking.
UNSUPPORTED_UNIT

A unit is missing, unsupported or mismatched.

Use a supported common unit for the same endpoint.
ASSAY_FORMAT_MISMATCH

Assay formats differ.

Use records produced with the same assay format.
CONDITION_MISSING

A required identity or assay condition is absent.

Supply taxon, format, pH, temperature, substrate and buffer as applicable.
CONDITION_MISMATCH

Reported pH, temperature, substrate or buffer differs.

Use a reviewed matched protocol or present without ranking.
MOLECULE_FORM_AMBIGUOUS

Parent, salt or tested molecular form is unresolved or differs.

Resolve and match the exact tested form.
STEREOCHEMISTRY_AMBIGUOUS

Full stereochemical identity is incomplete.

Resolve stereochemistry for both records.
DUPLICATE_DEPENDENCE

Records share a duplicate or citation-derived cluster.

Treat them as dependent evidence or select independent measurements.
REACTION_DIRECTION_MISMATCH

The represented reaction directions differ.

Match explicit reaction direction before quantitative comparison.
PREDICTED_VS_EXPERIMENTAL

Predicted and experimental records are being treated as one evidence class.

View them side by side without a shared confidence ranking.
PROVENANCE_INCOMPLETE

Source, release, raw value or transform provenance is incomplete.

Complete the provenance chain for both records.
PROTOCOL_MISMATCH

Records are neither from one assay nor a reviewed matched-protocol group.

Use one assay ID or the same independently reviewed protocol group.

Reaction data

The map is a source-linked reaction hypergraph. The current map is drawn from 2,039 Reactome 97 events across 58 pathway modules (source data, manifest). The earlier audited edition spans 12 human metabolic domains and 49 pathway groups (download). The layout is computed once at build time.

The canonical model treats each Reactome event as a node with role-bearing input and output participants. Compound instances retain Reactome identity, ChEBI identity when supplied, formula, entity class, and compartment. Catalysts, Rhea cross-references, literature citations, pathway membership, and source URLs remain attached to the event rather than being inferred from visual proximity.

  • Domain and pathway membership preserve the source hierarchy without treating screen position as evidence.
  • Reaction records retain primary participants, stoichiometric context, cofactors, sets, complexes, source context, and citations.
  • Transport is marked only when source participants occupy different compartments; no membrane crossing is inferred from map geometry.
  • Collapsed objects retain their Reactome class and never receive an invented balanced equation.

The direction-aware traversal model follows the source’s input-to-output relationships. ATP, NAD(H), NADP(H), water, protons, phosphate, and free CoA remain present in reaction detail but are excluded as intermediate shortcuts so frequently reused compounds do not create nonsensical connections.

Oxalosuccinate is retained as charge-specific CHEBI:153066 inside the NADP-dependent IDH2 mechanism, paired with the human net event R-HSA-450984 and Rhea reaction RHEA:19630. It is not modeled as a freely accumulating pool.

Review

Every manual identity decision, matched-protocol group, correction and source update should record the reviewer, date, rationale and the state it replaces. Material changes enter the public changelog.

The evidence release passes its automated checks. The corpus, the family ontology and the catalytic-status presentation have not yet had an independent biochemical review; a review will be labelled here once it has happened.