{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.d-mannose-1-phosphate","code":"thing-q258734","url":"https://ver.cy/models/thing/q258734/","name":"D-mannose 1-phosphate","alternateNames":["beta-D-glucose 1-phosphate","alpha-D-mannose 1-phosphate","alpha-L-galactose 1-phosphate"],"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.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"D-Mannose 1-phosphate is a phosphate monoester of D-mannose at its anomeric carbon, C1, whose α anomer is an intermediate in GDP-mannose biosynthesis.","purpose":"Enable an agent to recognise D-mannose 1-phosphate, assess the identity and condition of a sample, and determine its suitability for a specified analytical or biochemical use.","scope":{"in":["D-mannose stereochemistry, carbon-1 phosphate attachment and anomeric specification","Free-acid, ionic, salt and hydrated forms as qualified representations of the registered substance","Sample concentration, purity and discrimination from related sugar phosphates","Physical state, solution conditions and evidence of stability","Substrate suitability and experimentally supported metabolic relationships","Form-specific identifiers, handling evidence and permitted uses"],"out":["Independent models of D-mannose, D-mannose 6-phosphate and mannose bisphosphates","GDP-mannose and downstream glycans as independently registered substances","Enzyme structures, gene regulation and complete metabolic pathway models","Manufacturing equipment and complete synthesis procedures","Commercial formulations and supplier organisations","Clinical efficacy or dosing of D-mannose supplements"],"boundaries":[]},"distinguishingFeatures":["Require structural evidence for phosphate attachment at carbon 1; detecting a mannose monophosphate alone does not establish the positional assignment.","Require the D-mannose stereochemical pattern, rather than accepting another hexose phosphate with the same elemental composition.","Distinguish unspecified anomeric identity from an explicitly assigned alpha form; ChEBI treats alpha-D-mannose 1-phosphate as a narrower entity. [ChEBI hierarchy](https://www.ebi.ac.uk/chebi/CHEBI:35374)","Distinguish the sugar monophosphate from GDP-mannose, which is a separate participant in the guanylyltransferase reaction. [KEGG reaction R00885](https://www.kegg.jp/entry/R00885)","Check whether reported composition and mass describe the neutral parent, an ion or an isolated salt before matching a sample to a reference."],"structure":{"bundles":[{"id":"molecular-identity","name":"Molecular identity","description":"Establish the mannose configuration and phosphate position represented by this registry entry.","layers":[{"id":"connectivity-and-configuration","name":"Connectivity and configuration","description":"Resolve the structural features required for membership.","findings":[{"id":"carbon-one-phosphate-assignment","name":"Carbon-one phosphate assignment","description":"Record evidence that the structure is D-mannose with phosphate attached through oxygen at carbon 1. [ChEBI definition](https://www.ebi.ac.uk/chebi/CHEBI:35374)","questions":[{"text":"What structural evidence assigns the phosphate to carbon 1 rather than carbon 6?","id":"carbon-one-phosphate-assignment-q01","kind":"definition"},{"text":"What evidence establishes the D-mannose configuration rather than another hexose configuration?","id":"carbon-one-phosphate-assignment-q02","kind":"measurement"}]}]},{"id":"anomer-and-record-mapping","name":"Anomer and record mapping","description":"Preserve distinctions between the registered name and more specific external structures.","findings":[{"id":"anomer-qualified-equivalence","name":"Anomer-qualified equivalence","description":"Record whether a mapping is exact or narrower: KEGG C00636 lists both general and alpha names, whereas ChEBI distinguishes the parent entry from its alpha subtype. [KEGG C00636](https://www.kegg.jp/entry/C00636) [ChEBI hierarchy](https://www.ebi.ac.uk/chebi/CHEBI:35374)","questions":[{"text":"Is the sample's anomer assigned experimentally, specified by its source or unresolved?","id":"anomer-qualified-equivalence-q01","kind":"provenance"},{"text":"Does each external identifier describe the same anomeric scope as the registry entry?","id":"anomer-qualified-equivalence-q02","kind":"boundary"}]}]}]},{"id":"material-form-and-preparation","name":"Material form and preparation","description":"Relate the parent chemical identity to the material weighed or dissolved.","layers":[{"id":"isolated-composition","name":"Isolated composition","description":"Qualify the chemical form and mass basis of a sample.","findings":[{"id":"counterion-and-water-accounting","name":"Counterion and water accounting","description":"Require counterion stoichiometry, water content and assay basis before converting weighed mass to target amount.","questions":[{"text":"Which counterions, waters or residual solvents contribute to the measured sample mass?","id":"counterion-and-water-accounting-q01","kind":"measurement"},{"text":"Does the certificate report purity for the supplied material, dried material or parent-equivalent content?","id":"counterion-and-water-accounting-q02","kind":"provenance"}]}]},{"id":"dissolved-state","name":"Dissolved state","description":"Capture the conditions and amount of target in an experimental solution.","findings":[{"id":"usable-stock-composition","name":"Usable stock composition","description":"Express stock concentration on a declared mannose 1-phosphate basis with solvent, pH and temperature.","questions":[{"text":"What is the measured or calculated target concentration after purity and material-form corrections?","id":"usable-stock-composition-q01","kind":"measurement"},{"text":"Under the intended buffer and temperature conditions, is dissolution complete and is the stock suitable for use?","id":"usable-stock-composition-q02","kind":"action"}]}]}]},{"id":"analytical-identity-and-quality","name":"Analytical identity and quality","description":"Determine whether measurements establish identity and usable target content.","layers":[{"id":"selective-identification","name":"Selective identification","description":"Assess the resolving power of the identification method.","findings":[{"id":"isomer-discrimination","name":"Isomer discrimination","description":"Require evidence that the selected method distinguishes the target from plausible coexisting sugar phosphates.","questions":[{"text":"Does the method resolve mannose 1-phosphate from mannose 6-phosphate and relevant hexose 1-phosphates?","id":"isomer-discrimination-q01","kind":"measurement"},{"text":"Which authenticated standard or orthogonal structural measurement supports the assignment?","id":"isomer-discrimination-q02","kind":"provenance"}]}]},{"id":"quantitation-and-interference","name":"Quantitation and interference","description":"Determine target amount and impurities relevant to the intended assay.","findings":[{"id":"target-content-and-background","name":"Target content and background","description":"Separate target concentration from method response and assess potential interference from free phosphate, mannose and related compounds.","questions":[{"text":"What calibration, recovery and uncertainty support the reported target content?","id":"target-content-and-background-q01","kind":"measurement"},{"text":"Do detected impurities contribute to the intended assay signal or alter its reaction conditions?","id":"target-content-and-background-q02","kind":"action"}]}]}]},{"id":"biochemical-participation","name":"Biochemical participation","description":"Record reaction-specific substrate roles without treating the substance as an entire pathway.","layers":[{"id":"gdp-mannose-connection","name":"GDP-mannose connection","description":"Represent the supported relationship to nucleotide-sugar formation.","findings":[{"id":"guanylyltransferase-substrate-role","name":"Guanylyltransferase substrate role","description":"KEGG R00885 records GTP plus D-mannose 1-phosphate interconversion with diphosphate plus GDP-mannose and identifies the reaction as alpha-substrate specific in its name. [KEGG R00885](https://www.kegg.jp/entry/R00885)","questions":[{"text":"Does the enzyme preparation require alpha-D-mannose 1-phosphate, and is that form established for the sample?","id":"guanylyltransferase-substrate-role-q01","kind":"boundary"},{"text":"Which assay conditions and product measurements demonstrate conversion in the intended system?","id":"guanylyltransferase-substrate-role-q02","kind":"measurement"}]}]},{"id":"biological-context","name":"Biological context","description":"Qualify metabolite observations and reaction associations by biological system.","findings":[{"id":"occurrence-versus-function","name":"Occurrence versus function","description":"Keep measured occurrence, inferred pathway membership and demonstrated substrate turnover as distinct evidence states.","questions":[{"text":"In which organism, compartment and sample was mannose 1-phosphate identified, and how specific was that identification?","id":"occurrence-versus-function-q01","kind":"provenance"},{"text":"Does the evidence demonstrate a reaction role or only support a database or pathway association?","id":"occurrence-versus-function-q02","kind":"boundary"}]}]}]},{"id":"stability-and-use-constraints","name":"Stability and use constraints","description":"Determine whether a particular sample remains suitable for its intended handling and use.","layers":[{"id":"integrity-under-storage","name":"Integrity under storage","description":"Track target retention under documented solid and solution conditions.","findings":[{"id":"condition-dependent-retention","name":"Condition-dependent retention","description":"Base storage and retest decisions on measured target retention and impurity changes rather than an assumed universal shelf life.","questions":[{"text":"How do target content and impurity profile change with storage time, pH, temperature and freeze-thaw history?","id":"condition-dependent-retention-q01","kind":"measurement"},{"text":"What evidence determines whether this stock can be used, must be requalified or should be discarded?","id":"condition-dependent-retention-q02","kind":"action"}]}]},{"id":"form-specific-handling","name":"Form-specific handling","description":"Match handling and use decisions to the actual supplied material.","findings":[{"id":"documented-use-boundaries","name":"Documented use boundaries","description":"Attach safety and regulatory conclusions to a verified form and current documentation; retain unknown status where evidence is absent.","questions":[{"text":"Does the available SDS match this anomer, salt form and supplier material?","id":"documented-use-boundaries-q01","kind":"provenance"},{"text":"Which handling, disposal and intended-use constraints are supported for that material in the relevant jurisdiction?","id":"documented-use-boundaries-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 D-mannose 1-phosphate this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of D-mannose 1-phosphate this model covers, and on what evidence?","id":"evidence-kinds-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 D-mannose 1-phosphate 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 D-mannose 1-phosphate 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 D-mannose 1-phosphate 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 D-mannose 1-phosphate 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 D-mannose 1-phosphate this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe the compound and its role in GDP-mannose biosynthesis from scientific sources.","Record and track laboratory stocks the agent is authorized to manage."],"mustNot":["Present laboratory results as clinical findings for a person.","Recommend the compound as a supplement or treatment.","Mislabel samples or mix up the compound with other sugar phosphates.","Dispose of laboratory chemicals outside the lab's waste rules."],"requiresHuman":["Using research data on the compound for decisions about a patient with a glycosylation disorder."]},"ethics":{"considerations":["Research on sugar metabolism informs care of children with rare congenital disorders.","Laboratory records must be accurate for results to be trusted."],"affectedParties":["Patients with congenital disorders of glycosylation","Researchers","Laboratory staff"]},"owners":{"steward":"Nobody owns the compound; laboratories answer for their stocks.","roles":[],"masterSystems":["Chemical substance databases"]},"relations":[{"target":"Q11173","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.d-mannose-1-phosphate","Wikidata: Q258734 (https://www.wikidata.org/wiki/Q258734)"]},"properties":{"applicability":"required","items":["Phosphate attachment: Carbon-1 O-phosphate; other position; unresolved","Stereochemical assignment: D-mannose configuration; alpha, beta, mixture or unspecified anomer","Parent composition: Neutral parent formula C6H13O9P. [ChEBI composition](https://www.ebi.ac.uk/chebi/CHEBI:35374)","Material form: Protonation state, counterion identity and stoichiometry, hydrate or solvate content","Analyte concentration: mmol/L or mol/L, with analyte basis and uncertainty","Purity and related substances: Mass fraction, mole fraction or method-qualified peak-area percentage","Solution environment: Solvent, pH, temperature in degrees Celsius, buffer and ionic composition","Integrity over time: Target remaining as percentage versus elapsed time under specified conditions","Biochemical participation: Reaction, enzyme, organism, compartment and supporting evidence","Handling and regulatory identity: Form-specific identifier, SDS revision, jurisdiction and documented classification or unknown"]},"recognition":{"applicability":"required","items":["A reagent label specifying D-mannose 1-phosphate distinguishes the stated identity from mannose phosphates with substitution at other positions.","An anomer designation and any stated counterion distinguish labeled chemical forms, although visual inspection cannot confirm the sample's molecular identity."]},"capabilities":{"applicability":"required","items":["Resolve an external chemical record to this registry entry while retaining anomer and material-form qualifications.","Evaluate whether analytical evidence distinguishes the target from positional and stereochemical alternatives.","Calculate a preparation amount using verified target content, counterion stoichiometry and hydration.","Assess a sample for an anomer-specific enzyme assay using documented substrate requirements.","Track concentration and integrity during storage or experimental use.","Identify missing evidence that prevents a defensible identity, quality or handling decision."]},"hazards":{"applicability":"required","items":["Unstable in solution; degraded samples give misleading results.","Disturbed mannose phosphate metabolism underlies some inherited disorders of glycosylation."]},"interfaces":{"applicability":"required","items":["The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations Economic Commission for Europe, provides the framework for evaluating and communicating chemical hazards where implemented."]},"context":{"applicability":"required","items":["This compound is encountered in carbohydrate biochemistry and research on the formation of activated mannose donors.","Laboratory samples are used in enzyme studies and analytical work that require a specified anomer, chemical form and purity."]}},"sources":[{"title":"Wikidata item Q258734: D-mannose 1-phosphate","url":"https://www.wikidata.org/wiki/Q258734","note":"identity and sense of the item"},{"title":"Wikipedia: Mannose 1-phosphate","url":"https://en.wikipedia.org/wiki/Mannose_1-phosphate","note":"general description of the item"}],"openQuestions":["Which CAS, PubChem and EC identifiers match the registry's unspecified-anomer scope, and which instead identify particular anomers or salts?","Which analytical methods and reference materials adequately resolve anomers and positional isomers in the intended sample matrix?","What measured solubility, thermal behaviour and storage stability apply to each relevant isolated form and solution condition?","Which organism-specific reactions and enzyme preparations accept which anomer, and what kinetic evidence supports their use?","What form-specific GHS classification, exposure limits and handling documentation exist, and where are these unestablished?"],"resources":{"spec":"/models/things/publications/thing-q258734/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q258734/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T09:00:24Z","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":"filled","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 2026-10-07T10:10:29+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}