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STRENDADB_light_20240722.md

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+# STRENDA DB
+
+## Administration
+
+## Data
+
+### Publication
+
+This is the publication that includes the experimental results of an enzyme kinetics characterization.
+
+* **Title**
+  * type: string
+  * description: title of the publication
+* DOI
+  * type: string
+  * description: identifier of the publication
+* PMID
+  * type: string
+  * description: identifier of the publication as indexed in PubMed
+* Author
+  * type: Author
+  * Multiple: true
+* Experiment
+  * type: Experiment
+  * Multiple: true
+
+### Author
+
+* **Name**
+  * type: string
+  * description: name of the author. Nomenclature: Family name initials first name
+* Affiliation
+  * type: string
+  * description: name of organizaton, department, city, country
+* Email
+  * type: string
+  * description: email address
+* ORCID
+  * type: string
+  * description: ORCID idenfier
+
+### Experiment
+
+* Name of Experiment
+  * type: string
+  * description: name of the experiment, just for internal purposes
+* Type of Assay
+  * type: string
+  * description: name of the assay
+* Direction of the Assay
+  * type: string
+  * description:
+* Definition of the compound monitored
+  * type: string
+  * description:
+* Continuously monitored
+  * type: string
+  * description: selection of the stopping procedure
+  * type: string
+  * description: other
+  * type: string
+* Directly monitored
+  * type: string
+* Protein Assay
+  * type: ProteinDescription
+  * Multiple: false
+
+### ProteinDescription
+
+* UniProtKB AC
+  * type: string
+  * description: identifier obtained from UniProtKB
+* Protein name
+  * type: string
+  * description: name of the protein as of UniProtKB
+* Protein Sequence
+  * type: SequenceModifications
+  * description: amino acid sequence as from UniProtKB
+* Modifications
+  * type: Modifications
+* Protein Source
+  * type: ProteinSource
+* Reaction
+  * type: ProteinReaction
+* Protein characterization
+  * type: Dataset
+  * Multiple: true
+
+### ProteinSource
+
+* Expression system
+  * type: string
+  * description: description of expression system if heterologously expressed
+* Organism
+  * type: string
+  * description: as in UniProtKB provided, name of organism
+* Taxon ID
+  * type: string
+  * description: ID as obtained from NCBI Taxonomy
+* Strain
+  * type: string
+  * description: name or identifier of the strain
+* Cell Type
+  * type: string
+  * description: determination of the cell in which the protein is expressed
+* Tissue
+  * type: string
+  * description: determination of the tissue, ideally BTO is used
+* Localization
+  * type: string
+  * description: determination of the localization (membran, cytosol, etc.)
+
+### SequenceModifications
+
+* Sequence modification
+  * type: string
+  * description: modified amino acid sequence
+* Specification of the type of modification
+  * type: string
+  * description: description of the types of modifications
+* Determination of PTM
+  * type: string
+  * description: Phosphorylation, Glycosylation, Acetylation, Hydroxylation, Methylation, Other
+
+### ProteinReaction
+
+* EC number
+  * type: string
+  * description: EC number obtained from ExplorEnz
+* Reaction as in ExplorEnz
+  * type: string
+  * description: reaction as described in ExplorEnz
+* Comment
+  * type: string
+  * description: comment on the protein reaction if not properly described in ExplorEnz
+
+### Dataset
+
+* Name
+  * type: string
+  * description: name of the dataset
+* Assay conditions
+  * type: AssayConditions
+  * Multiple: true
+* Results Set
+  * type: ResultsSet
+  * Multiple: true
+* DOI
+  * type: string
+  * description: DOI of the dataset
+
+### AssayConditions
+
+* Small Assay Components
+  * type: Small\_Assay\_Components
+  * description: description of the compound used in the assay
+* Macromolecular Components
+  * type: Macromolecular\_Components
+  * description: description of the macromolecular components
+* Concentration of the assayed protein
+  * type: string
+  * description: value with unit
+* Description of concentration measurement
+  * type: string
+  * description: free text field
+* pH
+  * type: string
+  * description: value and unit
+* pD
+  * type: string
+  * description: value and unit
+* Temperature
+  * type: string
+  * description: value and unit, K and Celsius
+
+### Small\_Assay\_Components
+
+* Role
+  * type: Role\_of\_Component
+  * description: role in the assay, i.e. substrate, product, etc.
+* Initial concentration - fixed
+  * type: string
+  * description: unit, value
+* Initial concentration - varied
+  * type: string
+  * description: concentration range, value, unit
+* Compound name
+  * type: string
+  * description: name as obtained from PubChem
+* InChi
+  * type: string
+  * description: InChi string
+* IUPAC
+  * type: string
+  * description: IUPAC name
+* ChEBI ID
+  * type: string
+  * description: identifier
+* PubChem CID
+  * type: string
+  * description: identifier
+
+### Macromolecular\_Components
+
+* Role
+  * type: Role\_of\_Component
+  * description: role in the assay, i.e. substrate, product, etc.
+* Initial concentration - fixed
+  * type: string
+  * description: unit, value
+* Initial concentration - varied
+  * type: string
+  * description: concentration range, value, unit
+* Class
+  * type: Class
+  * description: protein, carbohydrate, DNA, RNA, etc.
+* Compound name
+  * type: string
+  * description: name as obtained from PubChem
+* InChi
+  * type: string
+  * description: InChi string
+* IUPAC
+  * type: string
+  * description: IUPAC name
+* Database used
+  * type: string
+  * description: name of the database
+* Identifier
+  * type: string
+  * description: identifier
+
+### Role\_of\_Component
+
+* Substrate
+  * type: string
+  * description: substrate of chemical reaction
+* Product
+  * type: string
+  * description: production of chemical reaction
+* Inhibitor
+  * type: string
+  * description: component that inhibits the chemical reaction
+* Activator
+  * type: string
+  * description: component that activates/enhances the chemical reaction
+
+### Class
+
+* Protein
+  * type: string
+* Carbohydrate
+  * type: string
+* DNA
+  * type: string
+* RNA
+  * type: string
+* Lipid
+  * type: string
+* Other
+  * type: string
+
+### ResultsSet
+
+* Initial Kinetic Parameters
+  * type: Initial\_Kinetics\_Parameters
+  * description: Km, kcat, V, kcat/Km, V/Km
+* Activation
+  * type: Activation
+* Inhibition
+  * type: Inhibition
+  *
+
+### Initial\_Kinetics\_Parameters
+
+* Km
+  * type: string
+  * descriptor: value, SE, unit
+* kcat
+  * type: string
+  * descriptor: value, SE, unit
+* V
+  * type: string
+  * descriptor: value, SE, unit
+* kcat/Km
+  * type: string
+  * descriptor: value, SE, unit
+* V/Km
+  * type: string
+  * descriptor: value, SE, unit
+
+### Activation
+
+* Affinity constant
+  * type: string
+  * descriptor: value, SE, unit, true or apparent
+* Reaction velocity
+* no activator
+  * type: string
+  * description: velocity without activator
+* at max. concentration
+  * type: string
+  * description: velocity at maximum concentration of activator
+* Saturation
+  * type: string
+  * description: statement whether the concentration was saturating or not
+* Influence on substrate MM kinetics
+  * Km no activator
+    * type: string
+    * description: Value, SE, Unit, true/apparent
+  * at max. concentration
+    * type: string
+    * description: Value, SE, Unit, true/apparent
+
+### Inhibition
+
+* Reversibility\_yes
+  * type: string
+  * description: competitive, uncompetitive, mixed, kic, SE, Unit, Math function
+* Reversibility\_no
+  * type: string
+  * description: ki, SE, Unit, Comment