Guide to entering life sciences metadata
This guide is currently being compiled. Some of the information may be updated shortly.
Life Sciences Metadata
International recommendations are available on the European portal: https://rdmkit.elixir-europe.org/
Design Type
Based on the “Study Design Type” metadata from the ISA Model and Serialization Specifications.
Design types that are based on the overall experimental design. (Optional)
Note: That is a value-list controlled metadata, please see the list below.
| Case Control | Cas témoin |
| Cross Sectional | Transversal |
| Cohort Study | Étude de cohorte |
| Nested Case Control Design | Modèle de cas témoins hiérarchique |
| Not Specified | Non spécifié |
| Parallel Group Design | Conception de groupes parallèles |
| Perturbation Design | Conception de perturbations |
| Randomized Controlled Trial | Essai contrôlé randomisé |
| Technological Design | Conception technologique |
| Other | Autre |
Étude de cohorte
Other Design Type
Based on the “Study Design Type” metadata from the ISA Model and Serialization Specifications.
If Other was selected in Design Type, list any other design types that were used in this Dataset. (Optional)
Click on the (+) button to add another design type.
Genomic Diversity Panel
Factor Type
Based on the “Study FactorType” metadata from the ISA Model and Serialization Specifications.
Factor type used in the Dataset. (Optional)
Note: That is a value-list controlled metadata, please see the list below.
| Age | Age |
| Biomarkers | Biomarqueurs |
| Cell Surface Markers | Marqueurs de surface cellulaire |
| Cell Type/Cell Line | Type cellulaire / Lignée cellulaire |
| Developmental Stage | Etape de développement |
| Disease State | Etat de la maladie |
| Drug Susceptibility | Sensibilité aux médicaments |
| Extract Molecule | Extraction de molécule |
| Genetic Characteristics | Caractéristiques génétiques |
| Immunoprecipitation Antibody | Anticorps d’immunoprécipitation |
| Organism | Organisme |
| Passages | Passages |
| Platform | Platforme |
| Sex | Sexe |
| Strain | Souche |
| Time Point | Point temporel |
| Tissue Type | Type de tissu |
| Treatment Compound | Composé de traitement |
| Treatment Type | Type de traitement |
| Other | Autre |
Caractéristiques génétiques
Other Factor Type
Based on the “Study FactorType” metadata from the ISA Model and Serialization Specifications.
If Other was selected in Factor Type, list any other factor types that were used in this Dataset. (Optional)
Click on the (+) button to add another factor type.
Stress
Organism
Based on the NCBI taxonomy.
The taxonomic name of the organism used in the dataset or from which the starting biological material derives. (Optional)
Note 1: That is a value-list controlled metadata, please see the list below.
Note 2: We strongly advise to enter the studied organisms in the Keyword metadata ("Common metadata bloc") and add the corresponding URI to NCBI's taxonomy, Catalogue of Life or TaxRef.
- Arabidopsis thaliana
- Bos taurus
- Caenorhabditis elegans
- Chlamydomonas reinhardtii
- Danio rerio (zebrafish)
- Dictyostelium discoideum
- Drosophila melanogaster
- Escherichia coli
- Hepatitis C virus
- Homo sapiens
- Mus musculus
- Mycobacterium africanum
- Mycobacterium canetti
- Mycobacterium tuberculosis
- Mycoplasma pneumoniae
- Oryza sativa
- Plasmodium falciparum
- Pneumocystis carinii
- Rattus norvegicus
- Saccharomyces cerevisiae (brewer's yeast)
- Schizosaccharomyces pombe
- Takifugu rubripes
- Xenopus laevis
- Zea mays
- Other
Chlamydomonas reinhardtii
Other organism
If Other was selected in Organism, list any other organisms that were used in this Dataset. We strongly recommend to use the NCBI taxonomy. (Optional)
We strongly advise to enter the studied organisms in the Keyword metadata ("Common metadata bloc").
Note : The following references are recommended by the Thematic Reference Centre IFB as reliable sources to enter taxons:
Click on the (+) button to add another organism.
Triticum aestivum
Measurement Type
Based on the “Study Assay Measurement” metadata from the ISA Model and Serialization Specifications.
A term to qualify the endpoint, or what is being measured. (Optional)
Note: That is a value-list controlled metadata, please see the list below.
| Cell sorting | Tri cellulaire |
| Clinical chemistry analysis | Analyse de chimie clinique |
| Copy number variation profiling | Profilage de la variation du nombre de copies |
| DNA methylation profiling | Profilage de la méthylation de l'ADN |
| DNA methylation profiling (Bisulfite-Seq) | Profilage de la méthylation de l'ADN (Bisulfite-Seq) |
| DNA methylation profiling (MeDIP-Seq) | Profilage de la méthylation de l'ADN (MeDIP-Seq) |
| Drug susceptibility | Sensibilité aux médicaments |
| Environmental gene survey | Enquête en génomique environnementale |
| Genome sequencing | Séquençage du génome |
| Hematology | Hématologie |
| Histology | Histologie |
| Histone Modification (ChIP-Seq) | Modification des histones (ChIP-Seq) |
| Loss of heterozygosity profiling | Profilage de perte d'hétérozygotie |
| Metabolite profiling | Profilage des métabolites |
| Metagenome sequencing | Séquençage du métagénome |
| Protein expression profiling | Profilage de l'expression des protéines |
| Protein identification | Identification de protéine |
| Protein-DNA binding site identification | Identification du site de liaison protéine-ADN |
| Protein-protein interaction detection | Détection d'interaction protéine-protéine |
| Protein-RNA binding (RIP-Seq) | Liaison protéine-ARN (RIP-Seq) |
| SNP analysis | Analyse SNP |
| Targeted sequencing | Séquençage ciblé |
| Transcription factor binding (ChIP-Seq) | Liaison au facteur de transcription (ChIP-Seq) |
| Transcription factor binding site identification | Identification du site de liaison du facteur de transcription |
| Transcription profiling | Profilage de la transcription |
| Transcription profiling (Microarray) | Profilage de la transcription (Biopuce) |
| Transcription profiling (RNA-Seq) | Profilage de la transcription (RNA-Seq) |
| TRAP translational profiling | Profilage traductionnel TRAP |
| Other | Autre |
Profilage de la transcription (RNA-Seq)
Other Measurement Type
Based on the “Study Assay Measurement” metadata from the ISA Model and Serialization Specifications.
If Other was selected in Measurement Type, list any other measurement type that were used. (Optional)
We strongly advise to use terms from NCBO's Bioportal.
Click on the (+) button to add another measurement type.
High-Throughput Nucleotide Sequencing
Technology Type
Based on the “Study Assay Technology Type” metadata from the ISA Model and Serialization Specifications.
A term to identify the technology used to perform the measurement. (Optional)
Note: That is a value-list controlled metadata, please see the list below.
| Culture based drug susceptibility testing, single concentration | Test de sensibilité aux médicaments en culture, concentration unique |
| Culture based drug susceptibility testing, two concentrations | Test de sensibilité aux médicaments en culture, deux concentrations |
| Culture based drug susceptibility testing, three or more concentrations (minimium inhibitory concentration measurement) | Test de sensibilité aux médicaments en culture, trois concentrations ou plus (mesure de la concentration minimale inhibitoire) |
| DNA microarray | Puce à ADN |
| Flow cytometry | Cytométrie en flux |
| Gel electrophoresis | Electrophorèse en gel |
| Mass spectrometry | Spectrométrie de masse |
| NMR spectroscopy | Spectroscopie RMN |
| Nucleotide sequencing | Séquençage des nucléotides |
| Protein microarray | Biopuce de protéine |
| Real time PCR | PCR en temps réel |
| No technology required | Sans technologie requise |
| Other | Autre |
Spectrométrie de masse
Other Technology Type
Based on the “Study Assay Technology Type” metadata from the ISA Model and Serialization Specifications.
If Other was selected in Technology Type, list any other technology types that were used in this Dataset.
Click on the (+) button to add another technology type.
Crystallography
Technology Platform
Based on the “Study Assay Technology Platform” metadata from the ISA Model and Serialization Specifications.
The manufacturer and name of the technology platform used in the assay.
Note: That is a value-list controlled metadata
Illumina
Other Technology Platform
Based on the “Study Assay Technology Platform” metadata from the ISA Model and Serialization Specifications.
If Other was selected in Technology Platform, list any other technology platforms that were used in this Dataset. (Optional)
The Thematic Reference Centre IFB maintains a list of platforms on the CatOPIDoR.
Click on the (+) button to add another technology platform.
AVANCE (Bruker)
Cell Type
The name of the cell line from which the source or sample derives. (Optional)
Cell Types can be found using The Ontology Lookup Service (OLS).
Click on the (+) button to add a cell type.
HeLa Cells
- Fruit: PO_0030104
- Stem: PO_0009047
- Root: PO_0009005
- Leaf: PO_0025034
Sample Type
Sample description. (Optional)
Click on the (+) button to add a sample type.
Transcriptomic case study on the within-species diversity panel: RNA extracted from leaves, stems, roots and ears.
Protocol Type
Protocol type. (Optional)
Click on the (+) button to add a protocol type.
Spontaneous fermentation of the raw milks, then serial fermentations in sterile milk; pH monitoring during each fermentation and metabarcoding (16S V3-V4) on raw milks and after each fermentation
R scripts to process the analysis of variants and cultivars.