NF Research Tools Central Schema

Data model for the NF Research Tools Central registry — 9 resource types, supporting entities, and controlled vocabularies for NF research.

v2.0.0 · LinkML

Class Hierarchy

Inheritance & Mixin Diagram

Tool

<<abstract>>

resourceId

resourceName

rrid

resourceType

description

howToAcquire

dateAdded

dateModified

HasGeneticDisorder

<<mixin>>

geneticDisorder

manifestation

HasTumorType

<<mixin>>

tumorType

HasPassageNumber

<<mixin>>

passageNumber

AnimalModel

donor : Donor

transplantationDonor : Donor

transplantationType

backgroundStrain

backgroundSubstrain

strainNomenclature

animalState

generation

CellLine

donor : Donor

organ

tissue

cellLineCategory

originYear

cultureMedia

Antibody

targetAntigen

clonality

reactiveSpecies

conjugate

hostOrganism

GeneticReagent

insertName

insertSpecies

vectorType

cloningMethod

hazardous

Biobank

biobankName

biobankURL

specimenType

specimenFormat

ComputationalTool

softwareName

softwareType

programmingLanguage

sourceRepository

licenseType

OrganoidProtocol

modelType

derivationSource

cellTypes

cultureSystem

PatientDerivedModel

modelSystemType

patientDiagnosis

hostStrain

engraftmentSite

ClinicalAssessmentTool

assessmentName

assessmentType

targetPopulation

numberOfItems

Entity Relationships

How entities connect

donor

transplantationDonor

donor

animalModelId

cellLineId

mutationDetailsId

resourceId

investigatorId

publicationId

funderId

resourceId

publicationId

resourceId

vendorId

resourceId

publicationId

AnimalModel

string

backgroundStrain

string

strainNomenclature

Donor

string

donorId

PK

enum

species

enum

sex

CellLine

enum

organ

enum

tissue

Mutation

string

mutationId

PK

string

mutationDetailsId

FK

string

animalModelId

FK

string

cellLineId

FK

MutationDetails

string

mutationDetailsId

PK

string

affectedGeneSymbol

enum

mutationType

DevelopmentRecord

string

resourceId

FK

string

investigatorId

FK

string

publicationId

FK

string

funderId

FK

Tool

string

resourceId

PK

string

resourceName

string

rrid

enum

resourceType

date

dateAdded

Investigator

string

investigatorId

PK

string

investigatorName

string

orcid

Publication

string

publicationId

PK

string

publicationTitle

string

doi

Funder

string

funderId

PK

string

funderName

Usage

string

usageId

PK

string

resourceId

FK

string

publicationId

FK

VendorItem

string

vendorItemId

PK

string

resourceId

FK

string

catalogNumber

Vendor

string

vendorId

PK

string

vendorName

Observation

string

observationId

PK

string

resourceId

FK

enum

observationType

Tool Types

All types inherit from the abstract Tool base class: resourceId, rrid, resourceName, synonyms, resourceType, description, aiSummary, usageRequirements, howToAcquire, dateAdded, dateModified. Related entities (vendors, observations, mutations, development records, usage publications) are in separate tables linked by FK.

AnimalModel

Animal models used in NF research — xenografts, transgenic, and knockout models.

HasGeneticDisorder
donor transplantationDonor transplantationType animalState backgroundStrain backgroundSubstrain strainNomenclature generation

CellLine

Cell cultures derived from homogeneous tissue sources for NF research.

HasGeneticDisorder
donor organ tissue cellLineCategory originYear strProfile populationDoublingTime resistance cultureMedia

Antibody

Antibody reagents for detecting NF-related antigens.

targetAntigen clonality cloneId reactiveSpecies conjugate hostOrganism uniprotId

GeneticReagent

Plasmids, viral vectors, CRISPR constructs, and other molecular tools.

insertName insertSpecies insertSize cloningMethod vectorType vectorBackbone promoter bacterialResistance selectableMarker hazardous +13 more

Biobank

Collections of biological specimens and data for NF research.

HasTumorType HasGeneticDisorder
biobankName biobankURL contact specimenType specimenTissueType specimenPreparationMethod specimenFormat

ComputationalTool

Software, pipelines, and analysis tools for NF research.

softwareName softwareType softwareVersion programmingLanguage sourceRepository documentation licenseType containerized dependencies lastUpdate maintainer

OrganoidProtocol

Organoids, assembloids, spheroids, and other 3D culture systems.

HasPassageNumber
modelType derivationSource cellTypes organoidType matrixType cultureSystem maturationTime characterizationMethods cryopreservationProtocol qualityControlMetrics

PatientDerivedModel

PDX, humanized mice, patient-derived organoids and cell lines.

HasTumorType HasPassageNumber
modelSystemType patientDiagnosis hostStrain engraftmentSite establishmentRate molecularCharacterization clinicalData validationMethods

ClinicalAssessmentTool

Questionnaires, scales, and patient-reported outcome measures.

assessmentName assessmentType targetPopulation diseaseSpecific numberOfItems scoringMethod validatedLanguages availabilityStatus licensingRequirements digitalVersion

Mixins

Cross-cutting concerns shared across tool types via mixin inheritance.

HasGeneticDisorder

NF-related genetic disorders. Used by: AnimalModel, CellLine, Biobank

geneticDisorder manifestation

HasTumorType

Tumor type classification. Used by: Biobank, PatientDerivedModel

tumorType

HasPassageNumber

Passage tracking. Used by: OrganoidProtocol, PatientDerivedModel

passageNumber

Supporting Entities

Donor

Biological donor from which a resource was derived.

donorId parentDonorId species sex age race

MutationDetails

Genetic mutation characterization, aligned with MGI vocabulary.

mutationDetailsId affectedGeneSymbol mutationType mutationMethod sequenceVariation +7 more

Publication

Publications associated with resource development or usage.

publicationId publicationTitle authors doi pmid citation

Investigator

Researchers who developed the resource.

investigatorId investigatorName orcid institution

Funder

Organizations funding resource development.

funderId funderName

Vendor / VendorItem

Vendors and their catalog listings for resources.

vendorName vendorUrl catalogNumber catalogNumberURL

Observation

User-submitted observations, ratings, and comments about resources.

observationText observationType reliabilityRating easeOfUseRating observationPhase

ResourceApplication

Applications and uses for a resource (e.g. Western Blot, ELISA).

applicationSource applicationTypes applicationLinks

DevelopmentRecord

Junction table linking tools to investigators, publications, and funders.

resourceId investigatorId publicationId funderId

Mutation

Junction table linking AnimalModel/CellLine to MutationDetails.

mutationId mutationDetailsId animalModelId cellLineId

Usage

Junction table linking tools to publications that cite their use.

usageId resourceId publicationId

Enumerations

53 controlled vocabularies. Click to expand values.