SampleTypes
This sample type is created to represent STRAINS as they were handled in SEEK for SySMO projects
Name (String) *, Provider's strain ID (String) , Provider name (String) , Synonym (String) , Comment (String) , Genotype (String) , Phenotype (String) , Organism (Web link)
Not specified
Sample type for March 2017 in vivo-1 exposure
Date (Date) *, Tank no. (Integer) , Exposure (String) , Fish ID (Integer) , Weight (g) (Real number) , Length (cm) (Real number) , Gender (String) , Liver (g) (Real number) , Gonads (g) (Real number) , Gross pathology (String) , k-faktor (Real number) , Liver index faktor (Real number) , Gonade somatic index (Real number)
Not specified
Date (Date) *, Cage (Integer) , Fish ID (Integer) , Weight (g) (Real number) , Length (cm) (Real number) , Gender (F/M) (String) , Liver weight (g) (Real number) , Gonade weight (g) (Real number) , k-faktor (Real number) , Liver index faktor (Real number) , Gonade index factor (GSI) (Real number) , Comments (String) , Severity of pathology (String)
Not specified
This sample type is based on standartised description of human cell cultures provided by ATCC (https://www.lgcstandards-atcc.org/)
Provider cell culture ID (String) *, Provider name (String) , Lab internal cell culture ID (String) , Organism (Controlled Vocabulary) , Gender (Controlled Vocabulary) , Tissue (String) , Morphology (String) , Disease/Diagnosis (String) , Age (String) , Ethnicity (Controlled Vocabulary) , Karyotype (String) , Basic Documentation File (Web link)
Not specified
Samples collected from harvested Salmon for subsequent investigations.
Experiment (String) *
Not specified
FASTQ Paired ID (String) *, Sample Origine ID (SEEK Sample - Samples for dCod) *, Library Origine ID (SEEK Sample - Library preparation) *, FASTQ R1 (String) *, FASTQ R2 (String) *
Not specified
Library ID (String) *, Sample Origine ID (SEEK Sample - Samples for dCod) *
Not specified
Count ID (String) *, Sample Origine ID (SEEK Sample - Samples for dCod) *, Bam Origine ID (SEEK Sample - BAM file) *
Not specified
Bam ID (String) *, Sample Origine ID (SEEK Sample - Samples for dCod) *, FASTQ Paired Origine ID (SEEK Sample - FASTQ Paired) *
Not specified
Sample ID (String) *, Sample name (String) , Date sampled (Date) , Treatment (String) , Fish# (sampling) (Integer) , Fish# (RNA-seq) (Integer) , Body wt in (g) (Integer) , Liver wt in (g) (Integer) , Sex (String) , Species (String) , Tissue (String)
Not specified
SampleID (String) *, CellCulture (SEEK Sample - CellCulture) *, Time (Real number) ( h ) *, Dilution (Real number) *, MeasurmentTypeID (SEEK Sample - MeasurmentType) *, Value (Real number) *
Not 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
MeasurmentTypeID (String) *, LabID (String) *, DeviceName (String) *, Experimenter (Email address) *, MeasurmentMode (String) *
Not specified
ContainerName (String) *, Volume (String) *, LabID (String) *, GasingType (String) *, pHControlMode (String) *, description (Text)
Not specified
LabStrainID (String) *, Organism (String) *, Genotype (String) *, Plasmid (SEEK Sample - Plasmid) , GenotypeResistance (String) *, Parentstrain (String) , ProviderName (String)
Not specified
LabPlasmidID (String) *, PartentStrain (String) , Reporter (String) , Resistance (String)
Not specified
PATIENT Description
Patient Provider ID (String) *, Sex (Controlled Vocabulary) *, Age (Integer) *, Body height (Integer) *, BMI (body mass index) (Integer) , Diagnosis (String) , Side diagnosis (String) , Provider contact (Email address)
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
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
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
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
chemostat_yeast_anaerobic
Sample ID (String) *, time relative to glucose pulse time point (Real number) , dilution_rate (Real number) , gas_flow (Real number) , Strain in SEEK (SEEK Strain) , Genotype (String) , Phenotype (String) , Comments (String) , Treatment: glucose pulse (Real number) , organism/cell part (Controlled Vocabulary) , Culture description (String) , Culture_start_date (Date time) , Date_at_sampling (Date time) , Age_at_sampling_hours (Real number) , Description (String)
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) , Sampling date (Date) , Time after glucose pulse (Integer) , Cell part (Controlled Vocabulary) , Age at sampling (Integer) *
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) , Sample provider name (String) , Sample provider identifier (String) , Sample comment (Text) , Sample organism part (Controlled Vocabulary)
Not specified
