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STRENDA DB

This page provides comprehensive information about the structure and components of the data model, including detailed descriptions of the types and their properties, information on enumerations, and an overview of the ontologies used and their associated prefixes. Below, you will find a graph that visually represents the overall structure of the data model.

Graph 
flowchart TB
    publication(Publication)
    author(Author)
    experiment(Experiment)
    proteindescription(ProteinDescription)
    proteinsource(ProteinSource)
    sequencemodifications(SequenceModifications)
    posttranslationalmodifications(PosttranslationalModifications)
    proteinreaction(ProteinReaction)
    dataset(Dataset)
    assayconditions(AssayConditions)
    smallassaycomponents(SmallAssayComponents)
    macromolecularcomponents(MacromolecularComponents)
    roleofcomponent(RoleOfComponent)
    compoundclassification(CompoundClassification)
    resultsset(ResultsSet)
    initialkineticsparameters(InitialKineticsParameters)
    activation(Activation)
    inhibition(Inhibition)
    publication(Publication) --> author(Author)
    publication(Publication) --> experiment(Experiment)
    experiment(Experiment) --> proteindescription(ProteinDescription)
    proteindescription(ProteinDescription) --> sequencemodifications(SequenceModifications)
    proteindescription(ProteinDescription) --> posttranslationalmodifications(PosttranslationalModifications)
    proteindescription(ProteinDescription) --> proteinsource(ProteinSource)
    proteindescription(ProteinDescription) --> proteinreaction(ProteinReaction)
    proteindescription(ProteinDescription) --> dataset(Dataset)
    dataset(Dataset) --> assayconditions(AssayConditions)
    dataset(Dataset) --> resultsset(ResultsSet)
    assayconditions(AssayConditions) --> smallassaycomponents(SmallAssayComponents)
    assayconditions(AssayConditions) --> macromolecularcomponents(MacromolecularComponents)
    macromolecularcomponents(MacromolecularComponents) --> roleofcomponent(RoleOfComponent)
    resultsset(ResultsSet) --> initialkineticsparameters(InitialKineticsParameters)
    resultsset(ResultsSet) --> activation(Activation)
    resultsset(ResultsSet) --> inhibition(Inhibition)

    click publication "#publication" "Go to Publication"
    click author "#author" "Go to Author"
    click experiment "#experiment" "Go to Experiment"
    click proteindescription "#proteindescription" "Go to ProteinDescription"
    click proteinsource "#proteinsource" "Go to ProteinSource"
    click sequencemodifications "#sequencemodifications" "Go to SequenceModifications"
    click posttranslationalmodifications "#posttranslationalmodifications" "Go to PosttranslationalModifications"
    click proteinreaction "#proteinreaction" "Go to ProteinReaction"
    click dataset "#dataset" "Go to Dataset"
    click assayconditions "#assayconditions" "Go to AssayConditions"
    click smallassaycomponents "#smallassaycomponents" "Go to SmallAssayComponents"
    click macromolecularcomponents "#macromolecularcomponents" "Go to MacromolecularComponents"
    click roleofcomponent "#roleofcomponent" "Go to RoleOfComponent"
    click compoundclassification "#compoundclassification" "Go to CompoundClassification"
    click resultsset "#resultsset" "Go to ResultsSet"
    click initialkineticsparameters "#initialkineticsparameters" "Go to InitialKineticsParameters"
    click activation "#activation" "Go to Activation"
    click inhibition "#inhibition" "Go to Inhibition"

Types

Publication

This is the publication that includes the experimental results of an enzyme kinetics characterization.

title* string

  • Title of the publication

doi string

  • identifier of the publication

pmid string

  • identifier of the publication as indexed in PubMed

author list[Author]

experiment list[Experiment]

Author

name* string

  • name of the author. Nomenclature: Family name initials first name

affiliation string

  • name of organizaton, department, city, country

email string

  • email address

orcid string

  • ORCID idenfier

Experiment

name_of_experiment string

  • name of the experiment, just for internal purposes

type_of_assay string

  • name of the assay

direction_of_the_assay string

definition_of_the_compound_monitored string

continuously_monitored string

  • selection of the stopping procedure

directly_monitored string

protein_assay ProteinDescription

ProteinDescription

uniprotkb_ac string

  • identifier obtained from UniProtKB

protein_name string

  • name of the protein as of UniProtKB

protein_sequence SequenceModifications

  • amino acid sequence as from UniProtKB

posttranslational_modifications PosttranslationalModifications

protein_source ProteinSource

reaction ProteinReaction

protein_characterization list[Dataset]

ProteinSource

expression_system string

  • Description of expression system if heterologously expressed

organism string

  • as in UniProtKB provided, name of organism

taxon_id string

  • ID as obtained from NCBI Taxonomy

strain string

  • name or identifier of the strain

cell_type string

  • determination of the cell in which the protein is expressed

tissue string

  • determination of the tissue, ideally BTO is used

localization string

  • determination of the localization (membran, cytosol, etc.)

SequenceModifications

sequence_modification string

  • modified amino acid sequence

specification_of_the_type_of_modification string

  • Description of the types of modifications

PosttranslationalModifications

determination_of_ptm string

  • Phosphorylation, Glycosylation, Acetylation, Hydroxylation, Methylation, Other

ProteinReaction

ec_number string

  • EC number obtained from ExplorEnz

reaction_as_in_explorenz string

  • reaction as described in ExplorEnz

comment string

  • comment on the protein reaction if not properly described in ExplorEnz

Dataset

name string

  • name of the dataset

assay_conditions list[AssayConditions]

results_set list[ResultsSet]

doi string

  • DOI of the dataset

AssayConditions

small_assay_components SmallAssayComponents

  • Description of the compound used in the assay

macromolecular_components MacromolecularComponents

  • Description of the macromolecular components

concentration_of_the_assayed_protein string

  • value with unit

description_of_concentration_measurement string

  • free text field

ph string

  • value and unit

pd string

  • value and unit

temperature string

  • value and unit, K and Celsius

SmallAssayComponents

role string

  • role in the assay, i.e. substrate, product, etc.

initial_concentration_fixed string

  • unit, value

initial_concentration_varied string

  • concentration range, value, unit

compound_name string

  • name as obtained from PubChem

inchi string

  • InChi string

iupac string

  • IUPAC name

chebi_id string

  • identifier

pubchem_cid string

  • identifier

MacromolecularComponents

role RoleOfComponent

  • role in the assay, i.e. substrate, product, etc.

initial_concentration_fixed string

  • unit, value

initial_concentration_varied string

  • concentration range, value, unit

classification string

  • protein, carbohydrate, DNA, RNA, etc.

compound_name string

  • name as obtained from PubChem

inchi string

  • InChi string

iupac string

  • IUPAC name

database_used string

  • name of the database

identifier string

  • identifier

RoleOfComponent

substrate string

  • substrate of chemical reaction

product string

  • production of chemical reaction

inhibitor string

  • component that inhibits the chemical reaction

activator string

  • component that activates/enhances the chemical reaction

CompoundClassification

protein string

carbohydrate string

dna string

rna string

lipid string

other string

ResultsSet

name string

  • Name of the results set

initial_kinetic_parameters InitialKineticsParameters

  • Km, kcat, V, kcat/Km, V/Km

activation Activation

inhibition Inhibition

InitialKineticsParameters

km string

  • Descriptor: value, SE, unit

kcat string

  • Descriptor: value, SE, unit

v string

  • Descriptor: value, SE, unit

kcat_over_km string

  • Descriptor: value, SE, unit

v_over_km string

  • Descriptor: value, SE, unit

Activation

affinity_constant string

  • Descriptor: value, SE, unit, true or apparent

velocity_no_activator string

  • velocity without activator

velocity_at_max_concentration string

  • velocity at maximum concentration of activator

saturation string

  • statement whether the concentration was saturating or not

incluence_no_activator string

  • Influence on MM kinetics. Schema: Value, SE, Unit, true/apparent

influence_at_maxconcentration string

  • Influence on MM kinetics. Schema: Value, SE, Unit, true/apparent

Inhibition

reversibility_yes string

  • inhbition type - competitive, uncompetitive, mixed, kic, SE, Unit, Math function

reversibility_no string

  • ki, SE, Unit, Comment