SampleTypes

Sample type representing the old BioSample model available to SysMO and VirtualLiver

Sample ID or name (String) *, Cell culture name (String) *, Cell culture lab identifier (String) , Cell culture start date (Date) , Cell culture growth type (Controlled Vocabulary) , Cell culture comment (Text) , Cell culture provider name (String) , Cell culture provider identifier (String) , Cell culture strain (SEEK Strain) *, Sample lab identifier (String) *, Sampling date (Date) , Age at sampling (Integer) ( s ) , Sample provider name (String) , Sample provider identifier (String) , Sample comment (Text) , Sample organism part (Controlled Vocabulary)

Not specified

SAMPLE TYPE to describe samples of CEN.PK-113-7D yeast strain upon metabolic perturbation of the steady state culture by glucose pulse

SEEK ID (Integer) *, STRAIN (SEEK Strain) , Genotype (String) , Cell culture ID (String) , Cell culture start date (Date) , Glucose pulse (concentration) (Integer) ( g/L ) , Sampling date (Date) , Time after glucose pulse (Integer) ( s ) , Cell part (Controlled Vocabulary) , Age at sampling (Integer) ( h ) *

yeast, genotype, chemostat, glucose pulse, Metabolomics

chemostat_yeast_anaerobic

Sample ID (String) *, time relative to glucose pulse time point (Real number) ( s ) , dilution_rate (Real number) ( h-1 ) , gas_flow (Real number) ( L/min ) , Strain in SEEK (SEEK Strain) , Genotype (String) , Phenotype (String) , Comments (String) , Treatment: glucose pulse (Real number) ( g/L ) , organism/cell part (Controlled Vocabulary) , Culture description (String) , Culture_start_date (Date time) , Date_at_sampling (Date time) , Age_at_sampling_hours (Real number) ( h ) , Description (String)

Not specified

test for SysMetEx1

seekid (String) *, strain 1 org 1 (SEEK Strain) , strain2 org 2 (SEEK Strain) , strain3 org 3 (String) , parent sample id (SEEK Sample - YEAST_chemostat_steady_state_culture)

Not specified

Sample type for continuous and batch cultures with up to 3 Organisms

Cell_Culture_ID (String) *, Culture_Start_Date (Date time) , Culture_End_Date (Date time) , Origin (String) , SOP (Web link) , Comments (Text) , Type of Culture (Controlled Vocabulary) , Organism1 (SEEK Strain) , Inoculum1 (Real number) , AddDate1 (Date time) , Organism2 (SEEK Strain) , Inoculum2 (Real number) , AddDate2 (Date time) , Organism3 (SEEK Strain) , Inoculum3 (Real number) , AddDate3 (Date time)

Not specified

Based on standard description of Pseudomonas putida strain from Pseudomonas Gene DB http://www.pseudomonas.com/

Organism/Strain Name (String) *, Species (String) *, Strain (String) *, Subspecific Genetic Lineage (String) , Description/Title (String) *, Scaffolds (String) , Contigs (String) , Contig (String) , Assembly Level (String) , Percent GC (Integer) ( % ) , Number of Annotated Genes (Integer) , References (String) , Partial Genes (String) , Provider Name (String) , Provider email (String) , Date Collected (Date) *, NCBI ID (Web link) , Genotype (String) , Phenotype (String)

Not specified

STRAIN EPP

STRAIN description (String) *, EPP (Empower putida) Code (String) *, Name (String) *, Previous Strain (NCBI ID) (String) *, Modification Made (description (String) , Genotype : gene name (String) , Genotype : modification (String) , Original Strain (String) *, Methods of Verification of Modification (String) , Function of the Strain (Phenotype) (String) , Date of Creation (Date) *, Created by (String) *, Contact to ask from (String) , Publication it was used (String) , Comment (String)

Not specified

PATIENT Description

Patient Provider ID (String) *, Sex (Controlled Vocabulary) *, Age (Integer) ( yr ) *, Body height (Integer) *, BMI (body mass index) (Integer) , Diagnosis (String) , Side diagnosis (String) , Provider contact (Email address)

Not specified

Sample_geo_accession

Sample_accession (String) *, Sample_title (String) *, Sample_organism_ch1 (String) *, Sample_characteristics_ch1 (String) *

Not specified

Library preparation

Library ID (SEEK Sample - Samples for dCod) *

Not specified

No description specified

Fastq ID (SEEK Sample - Library) *

Not specified

No description specified

Fastq ID (SEEK Sample - Library) *, Fastq position (Web link) *

Not specified

No description specified

ID (String) *, Name (String) *

Not specified

No description specified

Library ID (String) *, Sample ID (SEEK Sample - Samples for dCod)

Not specified

No description specified

Library ID (SEEK Sample - Library) *, FASTQ ID (String) , FASTQ file (Web link) , Original Sample ID (SEEK Sample - Samples for dCod)

Not specified

No description specified

LabPlasmidID (String) *, PartentStrain (String) , Reporter (String) , Resistance (String)

Not specified

No description specified

LabStrainID (String) *, Organism (String) *, Genotype (String) *, Plasmid (SEEK Sample - Plasmid) , GenotypeResistance (String) *, Parentstrain (String) , ProviderName (String)

Not specified

No description specified

ContainerName (String) *, Volume (String) ( ┬ÁL ) *, LabID (String) *, GasingType (String) *, pHControlMode (String) *, description (Text)

Not specified

No description specified

MeasurmentTypeID (String) *, LabID (String) *, DeviceName (String) *, Experimenter (Email address) *, MeasurmentMode (String) *

Not specified

No description specified

CellCultureID (String) *, Container (SEEK Sample - Container) *, CultivaitonMode (String) *, Temperatur (Integer) *, StartOD (Real number) , Ecoli_strain_des (SEEK Sample - Ecoli_strain_des) , Experimenter (Email address)

Not specified

No description specified

SampleID (String) *, CellCulture (SEEK Sample - CellCulture) *, Time (Date time) *, Dilution (Real number) *, MeasurmentTypeID (SEEK Sample - MeasurmentType) *

Not specified

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