{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.hspa5","code":"thing-q18027351","url":"https://ver.cy/models/thing/q18027351/","name":"HSPA5","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"HSPA5 commonly denotes the gene encoding BiP/GRP78, an ATP-dependent Hsp70-family molecular chaperone that primarily resides in the endoplasmic reticulum lumen and supports protein folding, protein quality control and regulation of the unfolded protein response.","purpose":"Enable an agent to identify HSPA5, distinguish its gene and protein referents, and assess evidence about the BiP chaperone's molecular state, location and experimentally supported functions.","scope":{"in":["Species-qualified HSPA5 protein identity, aliases and encoding-gene relationship","Native and engineered protein forms, sequence boundaries and targeting features","Compartment-specific abundance and localization evidence","Nucleotide-dependent chaperone activity and client interactions","HSPA5-specific perturbations, assay interpretation and evidence limitations"],"out":["Complete HSPA5 genomic locus, promoter and transcript models","Other HSP70-family proteins and their independent functions","The entire unfolded protein response or endoplasmic-reticulum quality-control system","Disease entities and patient-level diagnostic or treatment decisions","Antibodies, inhibitors and expression vectors as independently managed reagent objects"],"boundaries":[]},"distinguishingFeatures":["Resolve a protein sequence or accession to species-qualified HSPA5; the label HSP70 alone is insufficient.","Distinguish the encoding gene, its RNA and its protein by identifier namespace and the material actually measured.","For a proposed native BiP form, inspect endoplasmic-reticulum targeting and retention features alongside sequence identity; localization alone does not establish identity.","Require HSPA5-discriminating peptides, epitopes or genetic controls when distinguishing it from related HSP70 proteins.","Treat a surface-associated HSPA5 observation as a localization claim requiring evidence, not as proof of a separate protein identity."],"structure":{"bundles":[{"id":"hspa5-identity","name":"HSPA5 identity and referent","description":"Resolve what the registry name denotes before attaching molecular observations.","layers":[{"id":"gene-protein-boundary","name":"Gene-protein boundary","description":"Separate related molecular entities without creating an unsupported registry split.","findings":[{"id":"identifier-qualified-referent","name":"Identifier-qualified referent","description":"The human anchors are NCBI Gene 3309 for HSPA5 and UniProt P11021 for its protein product; these identifiers describe related entities rather than interchangeable measurement targets. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/3309/) [UniProt](https://www.uniprot.org/uniprotkb/P11021)","questions":[{"text":"Does vr.tr.hspa5 denote the protein, the gene or a deliberately combined concept?","id":"identifier-qualified-referent-q01","kind":"boundary"},{"text":"Which original registry identifier or import record establishes that interpretation?","id":"identifier-qualified-referent-q02","kind":"provenance"}]}]},{"id":"species-and-sequence","name":"Species and sequence","description":"Bind HSPA5 observations to a biological reference.","findings":[{"id":"reference-matched-identity","name":"Reference-matched identity","description":"Record species, accession and sequence version before transferring a feature or experimental result between HSPA5 records.","questions":[{"text":"Which species and protein sequence define the HSPA5 entity under observation?","id":"reference-matched-identity-q01","kind":"definition"},{"text":"Does the identity evidence distinguish HSPA5 from other HSP70-family proteins?","id":"reference-matched-identity-q02","kind":"measurement"}]}]}]},{"id":"protein-form-and-localization","name":"Protein form and localization","description":"Describe the molecular form and the compartment in which it is observed.","layers":[{"id":"sequence-integrity","name":"Sequence integrity","description":"Inspect sequence boundaries, modifications and engineered features.","findings":[{"id":"construct-feature-preservation","name":"Construct feature preservation","description":"Record whether a tested form preserves targeting, retention and functional regions rather than assuming a tagged or truncated construct behaves like native HSPA5.","questions":[{"text":"What residues, tags, substitutions and terminal changes distinguish the tested form from its reference?","id":"construct-feature-preservation-q01","kind":"definition"},{"text":"What evidence shows that the form retains the localization and activity required by the experiment?","id":"construct-feature-preservation-q02","kind":"measurement"}]}]},{"id":"compartment-evidence","name":"Compartment evidence","description":"Evaluate localization at the resolution supported by the assay.","findings":[{"id":"er-and-alternative-pools","name":"ER and alternative pools","description":"BiP is an endoplasmic-reticulum chaperone; proposed alternative pools need compartment-specific evidence and controls for sample contamination or membrane damage. [UniProt](https://www.uniprot.org/uniprotkb/P11021)","questions":[{"text":"Which assay establishes ER-luminal, surface or extracellular localization in this sample?","id":"er-and-alternative-pools-q01","kind":"measurement"},{"text":"Which controls exclude ER contamination, cell leakage or unintended antibody access?","id":"er-and-alternative-pools-q02","kind":"provenance"}]}]}]},{"id":"chaperone-cycle","name":"Chaperone cycle","description":"Represent nucleotide handling and client-binding behavior.","layers":[{"id":"nucleotide-dependent-activity","name":"Nucleotide-dependent activity","description":"Keep catalytic measurements tied to biochemical conditions.","findings":[{"id":"atpase-assay-context","name":"ATPase assay context","description":"HSPA5 activity assessment should distinguish nucleotide occupancy, ATP turnover and client-handling outcomes rather than treating them as one endpoint.","questions":[{"text":"What nucleotide concentrations, temperature, cofactors and HSPA5 concentration define the assay?","id":"atpase-assay-context-q01","kind":"measurement"},{"text":"Is the reported endpoint ATP hydrolysis, nucleotide exchange, client release or another specified event?","id":"atpase-assay-context-q02","kind":"definition"}]}]},{"id":"client-and-cofactor-coupling","name":"Client and cofactor coupling","description":"Identify which molecular partners shape the measured behavior.","findings":[{"id":"partner-dependent-function","name":"Partner-dependent function","description":"Record the client and cofactor composition of each experiment so that a result from isolated HSPA5 is not silently extended to a cellular complex.","questions":[{"text":"Which client proteins and co-chaperones were present, and at what concentrations or ratios?","id":"partner-dependent-function-q01","kind":"measurement"},{"text":"Does the evidence establish direct binding, co-complex membership or only functional dependence?","id":"partner-dependent-function-q02","kind":"boundary"}]}]}]},{"id":"er-quality-control-context","name":"ER quality-control context","description":"Connect HSPA5 observations to folding and stress responses without absorbing the entire pathway.","layers":[{"id":"client-fate","name":"Client fate","description":"Describe consequences for an identified client.","findings":[{"id":"binding-versus-folding-outcome","name":"Binding versus folding outcome","description":"BiP participates in ER protein folding and quality control, but a particular binding observation must be distinguished from demonstrated folding, retention or disposal of that client. [UniProt](https://www.uniprot.org/uniprotkb/P11021)","questions":[{"text":"Which client-specific endpoint demonstrates the proposed folding or quality-control outcome?","id":"binding-versus-folding-outcome-q01","kind":"measurement"},{"text":"What intervention connects that outcome specifically to HSPA5?","id":"binding-versus-folding-outcome-q02","kind":"provenance"}]}]},{"id":"stress-response-interpretation","name":"Stress-response interpretation","description":"Separate HSPA5 measurements from pathway-level conclusions.","findings":[{"id":"abundance-is-not-pathway-state","name":"Abundance and pathway state","description":"Record HSPA5 RNA, HSPA5 protein and stress-pathway readouts separately, with their timing and experimental conditions.","questions":[{"text":"Was the reported change measured in HSPA5 transcript, total protein or a particular protein pool?","id":"abundance-is-not-pathway-state-q01","kind":"measurement"},{"text":"Which independent readouts support the claimed ER-stress or unfolded-protein-response state?","id":"abundance-is-not-pathway-state-q02","kind":"provenance"}]}]}]},{"id":"assays-and-perturbations","name":"Assays and perturbations","description":"Determine which HSPA5 conclusions and experimental next steps the evidence supports.","layers":[{"id":"detection-specificity","name":"Detection specificity","description":"Assess whether a signal identifies the intended HSPA5 pool.","findings":[{"id":"hspa5-discriminating-signal","name":"HSPA5-discriminating signal","description":"Require assay-specific identity evidence, such as discriminating peptides or validated antibody controls, before assigning a signal to HSPA5.","questions":[{"text":"Which peptide, epitope or other recognition feature makes the signal attributable to HSPA5?","id":"hspa5-discriminating-signal-q01","kind":"definition"},{"text":"What controls assess cross-reactivity, background and loss of signal after HSPA5 depletion?","id":"hspa5-discriminating-signal-q02","kind":"provenance"}]}]},{"id":"causal-action-boundaries","name":"Causal action boundaries","description":"Qualify conclusions from depletion, overexpression or chemical perturbation.","findings":[{"id":"target-engagement-and-rescue","name":"Target engagement and rescue","description":"Record target engagement, exposure, viability and orthogonal or rescue evidence before attributing a perturbation phenotype to HSPA5.","questions":[{"text":"What evidence confirms the intervention changed the intended HSPA5 abundance or activity?","id":"target-engagement-and-rescue-q01","kind":"measurement"},{"text":"Which rescue or independent perturbation would resolve the main alternative explanation?","id":"target-engagement-and-rescue-q02","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of HSPA5 this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of HSPA5 this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of HSPA5 this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of HSPA5 this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of HSPA5 this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of HSPA5 this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe HSPA5 and the BiP chaperone it encodes from curated gene and protein databases.","Summarize published evidence on its role in endoplasmic reticulum stress, with sources."],"mustNot":["Present research findings on HSPA5 as an approved diagnostic or treatment target.","Share a person's sequence data about the gene without consent.","Confuse the gene with the protein or with other Hsp70 family members in a report.","Invent assay results or citations to support a claim."],"requiresHuman":["Reporting a gene finding back to a patient or study participant."]},"ethics":{"considerations":["Overstated claims about stress-response genes can mislead patients seeking cancer or disease treatments.","Genetic data identifies a person and their relatives."],"affectedParties":["Patients","Research participants","Researchers relying on the record"]},"owners":{"steward":"Nobody owns the gene; curated gene databases keep its reference record.","roles":[],"masterSystems":["HGNC gene symbol registry","Reference sequence databases"]},"relations":[{"target":"Q20747295","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.hspa5","Wikidata: Q18027351 (https://www.wikidata.org/wiki/Q18027351)"]},"properties":{"applicability":"required","items":["Biological referent: gene; transcript; protein; unresolved","Species and reference identity: Taxonomy identifier, protein accession and sequence version","Protein form: native precursor; processed protein; sequence variant; tagged construct; fragment","Observed compartment: ER lumen; cell surface; extracellular; other specified compartment; unresolved","HSPA5 abundance: mol/L, molecules/cell or explicitly normalized relative protein abundance","Nucleotide occupancy: ATP-bound; ADP-bound; nucleotide-free; mixed; unmeasured","ATP turnover: s^-1 under stated assay conditions","Client or cofactor association: Partner identity, interaction type, assay conditions and supporting evidence","Perturbation response: Endpoint-specific change with dose, duration, comparator and uncertainty"]},"recognition":{"applicability":"not-applicable","items":[]},"capabilities":{"applicability":"required","items":["Resolve an HSPA5, BiP or GRP78 label to a species-qualified molecular entity.","Assess whether a construct preserves the features needed for the claimed localization and activity.","Compare HSPA5 abundance or ATPase measurements under compatible conditions.","Evaluate whether an assay distinguishes HSPA5 from related proteins and distinguishes RNA from protein.","Link client interactions and perturbation outcomes to their experimental context.","Identify which additional controls are needed before making a localization or functional claim."]},"hazards":{"applicability":"required","items":["Mislabelled samples or misannotated sequences propagate errors into later studies.","Confusing gene, transcript and protein claims leads to wrong conclusions."]},"interfaces":{"applicability":"required","items":["HGNC guidelines for human gene nomenclature, HUGO Gene Nomenclature Committee."]},"context":{"applicability":"required","items":["HSPA5 is encountered in human genetics, gene expression studies and research on protein folding and cellular stress.","Its gene records help researchers connect DNA sequence and expression evidence with the functions of its encoded endoplasmic reticulum chaperone.","Clear identification is needed when distinguishing observations about the gene from measurements of its protein product."]}},"sources":[{"title":"Wikidata item Q18027351: HSPA5","url":"https://www.wikidata.org/wiki/Q18027351","note":"identity and sense of the item"},{"title":"Wikipedia: Binding immunoglobulin protein","url":"https://en.wikipedia.org/wiki/Binding_immunoglobulin_protein","note":"general description of the item"}],"openQuestions":["Does the registry's original source identify a human gene, a human protein or a species-independent HSPA5 concept?","Does an existing Vercy model already own this concept, requiring a registry link instead of a new publication?","Which reference sequence, processed forms and variants should define the entry's molecular boundary?","Which reported non-ER localizations and modifications have sufficient primary evidence to include as established HSPA5 states?","Which assays and perturbation reagents have independently demonstrated HSPA5 specificity, and in which species and sample contexts?"],"resources":{"spec":"/models/things/publications/thing-q18027351/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q18027351/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T10:19:51Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"not-applicable","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:27+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.recognition":"HSPA5 has no distinctive visual appearance and requires sequence-based or other validated molecular identification."},"score":1.0}}