Immunoglobulin-like domain superfamily
Enable an agent to assess protein membership in the immunoglobulin superfamily, describe supporting domain architecture and constrain functional inferences to available evidence.
Bundle → Layer → Finding → Questions Filled
6 bundles · 11 layers · 17 findings · 27 questions
Superfamily identity and boundaries Establish what the registered superfamily denotes and how neighboring classifications relate to it.
Classification anchor
Resolve the registry name to an authoritative domain-superfamily concept.
Registry-to-classification mapping
Record the evidence connecting this registry entry to an external classification without assuming name equality proves equivalence.
- Does the registry's originating record explicitly identify InterPro IPR036179 or another classification? provenance
- What membership definition and release establish the intended superfamily? definition
Neighboring domain concepts
Distinguish domain, fold, subtype, and whole-protein concepts.
Classification overlap
Represent broader, narrower, and overlapping classifications explicitly.
- How does the selected superfamily relate to IPR007110 and IPR013783 in the cited release? boundary
- Which uses of 'immunoglobulin superfamily' refer to whole proteins rather than this domain-level concept? boundary
Domain detection and delimitation Establish which residues form a candidate member and how strongly the evidence supports that assignment.
Sequence intervals
Locate each domain occurrence on a specific protein sequence.
Domain boundary evidence
Record proposed residue boundaries and distinguish missing sequence from genuine domain variation.
- Which accession, isoform, sequence version, and residue interval identify this occurrence? provenance
- Do sequence and structure evidence support the same boundaries, particularly between tandem domains? boundary
Membership support
Assess computational and structural support for classification.
Assignment strength and conflicts
Keep evidence strength and conflicting assignments visible rather than reducing them to a binary label.
- Which signatures, database releases, scores, coverage values, and acceptance thresholds support membership? measurement
- What additional evidence is needed when sequence and structural classifications disagree? action
Fold topology and variation Describe the domain's structural core and supported departures from representative architectures.
Beta-sandwich core
Assess sheet organization, strand connectivity, and core packing.
Topological compatibility
Record structural observations needed to compare a candidate with classified representatives.
- Which strands form each sheet, and what connectivity supports an immunoglobulin-like topology? measurement
- Which structural observations distinguish this candidate from other beta-sandwich folds? boundary
Subtype and local variation
Describe subtype evidence, loop differences, insertions, and stabilizing features.
Supported structural subtype
Treat subtype labels as evidence-based refinements rather than universal requirements.
- Which strand and sequence features justify a V-set, C1-set, C2-set, I-set, or other source-defined assignment? definition
- Which loops, insertions, core residues, and disulfide connections are observed, predicted, or unresolved? measurement
Protein architecture and interactions Place the domain within its host protein and evaluate domain-specific contributions.
Host and repeat context
Describe neighboring domains, linkers, and biological placement.
Domain context
Identify the occurrence within a multidomain protein and record context without inheriting unsupported properties.
- What is this domain's ordinal position, and which domains and linkers flank it? definition
- What evidence establishes its cellular location and whether the studied construct preserves native domain neighbors? provenance
Interaction attribution
Separate tested domain interactions from functions inferred from the host protein.
Domain-specific functional evidence
Connect interaction claims to tested interfaces, constructs, and conditions.
- Which experiments attribute binding or a structural role to this domain rather than to the complete protein? provenance
- What partner, interface residues, affinity measurements, and assay conditions support the attributed interaction? measurement
Structural state and inference limits Assess the reliability of a domain representation and determine which downstream uses its evidence supports.
Representation and folding state
Distinguish native sequence, experimental constructs, predicted structures, and observed folding states.
Domain integrity
Track truncations, substitutions, unresolved regions, and evidence of structural disruption.
- Which sequence changes or missing residues affect the proposed core, loops, or interdomain junctions? measurement
- Does the evidence establish an intact fold, a disrupted state, or only an uncertain structural prediction? boundary
Permitted inferences
Constrain annotation transfer and prioritize validation.
Evidence-bounded use
Determine whether the occurrence supports membership annotation, subtype assignment, interface comparison, or a functional hypothesis.
- Which claims can be transferred from classified relatives, and which require direct evidence for this domain? action
- Would boundary refinement, structural validation, or a domain-specific interaction assay resolve the most consequential uncertainty? action
Evidence and external alignment What the world already says about this thing, gathered so the model can be checked against it.
Reported evidence
Findings from the breadth pass, kept separate from the structural claims.
Check these first
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these check these first hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Kinds and varieties
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these kinds and varieties hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Identifiers and schemes
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these identifiers and schemes hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Real-world use
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these real-world use hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Typical measurements
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these typical measurements hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Failure modes and hazards
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these failure modes and hazards hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Neighbouring kinds and how to tell them apart
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these neighbouring kinds and how to tell them apart hold for the sense of Immunoglobulin-like domain superfamily this model covers, and on what evidence? provenance
Classifiers Filled
- Family
- Thing Registry
- Category
- Physical world and living systems
- Entry kind
- thing
- Plane
- PHY
- Domain
- PHY.MAT
What it is Filled
The immunoglobulin superfamily is a large superfamily of cell-surface and soluble proteins containing one or more immunoglobulin-like domains, with members involved in immune functions, cell recognition, adhesion and other biological roles.
In scope
- Superfamily identity concerns proteins rather than isolated domain occurrences.
- Membership assessment uses evidence about protein identity and immunoglobulin-like domain architecture.
- Domain structure, subtype and repetition support descriptions of member proteins.
- Members include cell-surface and soluble proteins with diverse biological roles.
- Functional interpretation distinguishes protein-specific evidence from shared structural features.
Out of scope
- Standalone classification of immunoglobulin-like domains as the primary referent is outside scope.
- Complete models of antibody isotypes and immune repertoires are outside scope.
- Gene regulation, organism physiology and immune-system models are outside scope.
- Purified protein products, formulation, purity and manufacturing are outside scope.
- Proteins lacking evidence of membership are outside scope even if they contain a superficially similar beta-sandwich structure.
Why it exists Filled
Enable an agent to assess protein membership in the immunoglobulin superfamily, describe supporting domain architecture and constrain functional inferences to available evidence.
Distinguishing features Filled
- Membership is assigned to a protein, with its immunoglobulin-like domains providing supporting evidence.
- Member proteins contain one or more immunoglobulin-like domains, typically formed from opposing antiparallel beta sheets.
- A domain database assignment must be distinguished from a curated protein-superfamily assignment.
- An immune-system role is neither sufficient nor required to establish membership.
- Shared domain architecture does not establish identical biological functions across member proteins.
What robots and AI may and may not do Filled
Must not
- Present a domain prediction as confirmed structure without evidence.
- Claim that a member protein is a drug target or disease cause beyond the evidence.
- Help design proteins or antibodies for harming people.
Only with a human decision
- Publishing structure or function claims that inform clinical decisions.
May
- Describe the immunoglobulin protein superfamily and its members from structural biology sources.
- Assess protein-superfamily membership using recognized databases and domain annotations with stated confidence.
Moral aspects Filled
- Errors in protein annotation spread through databases and research.
- Antibody and receptor research has dual-use and clinical stakes.
Who is affected
- Researchers and database users
- Patients in clinical research
Owners Filled
Steward
Nobody owns the concept; curated protein databases maintain its classification.
Master systems
- Protein family and structure databases
Links to other meta-models Filled
parent
- Q8054 - registry parent class
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- Vercy registry: vr.tr.immunoglobulin-like-domain-superfamily
- Wikidata: Q41797304 (https://www.wikidata.org/wiki/Q41797304)
Direct properties required Filled
- Classification anchor: Database accession, entry type, release, and exact/broader/narrower/overlapping mapping
- Domain interval: Start and end residue positions, numbering convention, host accession, and sequence version
- Assignment status: Supported, provisional, conflicting, rejected, or unassessed
- Sequence-match support: Method-specific score, E-value where applicable, coverage percentage, and signature release
- Strand topology: Observed strand labels, sheet membership, connectivity, and unresolved segments
- Domain subtype: V-set, C1-set, C2-set, I-set, another source-defined subtype, or unresolved
- Core and disulfide integrity: Observed, predicted, disrupted, absent, or unresolved, with residue-level evidence
- Host-protein architecture: Host protein, domain ordinal, neighboring domains, linker intervals, and localization evidence
- Domain-attributed binding: Partner identity; Kd in mol/L where measured; assay, construct, and conditions
Recognition required Filled
- Molecular structure representations may show immunoglobulin-like beta-sandwich domains within a member protein, but appearance alone does not establish protein-superfamily membership.
Capabilities and actions required Filled
- Evaluate candidate sequence intervals against a versioned superfamily classification.
- Compare observed or predicted strand topology with supported domain representatives.
- Map repeated domain occurrences and their boundaries within a host protein.
- Identify domain assignments needing structural inspection or experimental validation.
- Assess whether interaction or variant evidence supports a domain-specific claim.
- Revise membership and subtype annotations when classification evidence changes.
Hazards and failure modes required Filled
- Over-broad annotation can mislabel unrelated proteins.
Standards and interfaces not applicable Not applicable
Not applicable
No universally applicable formal standard, law or official classification governs membership in this structural superfamily.
Context of use required Filled
- The immunoglobulin-like domain superfamily is encountered in protein structure analysis, sequence annotation and studies of immune recognition and cell adhesion.
- Its classification helps compare domains across antibodies, receptors and other proteins, but membership alone does not establish a particular biological function.
Sources Filled
- Wikidata item Q41797304: Immunoglobulin-like domain superfamily - identity and sense of the item
- Wikipedia: Immunoglobulin superfamily - general description of the item
Open questions
- Does registry provenance establish exact equivalence to InterPro IPR036179, or does the name denote a broader grouping?
- Which domain families lie within the intended superfamily boundary, particularly where structural classifications disagree?
- Which subtype vocabulary covers the intended membership without forcing atypical domains into antibody-derived categories?
- What evidence thresholds should govern acceptance of remote, partial, or structure-only domain assignments?
- Should PHY / PHY.MAT be retained for this classification of molecular domains, or reviewed separately as a registry placement issue?
Machine files
Provenance
thing registry research (pass 2) · unreviewed
Built from: models/things/publications/thing-q41797304/spec.json