Metadata Concepts
Quick Reference Table
| Concept | Description |
|---|---|
| User | Learn more about the metadata of your user account and its authentication |
| Project | Information about a projects metadata such as contact, funding and objective |
| Terminology | Find out more about the ontology terms employed within experiments and samples |
| Experiment | Everything related to the metadata within an experimental design |
| Sample | Detailed information concerning the metadata of sample and batches |
| Measurement | Everything related to NGS and PxP measurement metadata |
| Raw Data | Find out more about the metadata surrounding Data Upload and Download |
User
Check our documentation to find out how to register and edit your account.
The following concepts are associated with an user account.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Full name | John Doe | ✅ | Text, divided by a singular space into first and last name |
First and last name of the user View Description |
| Oidc id | 0009-0006- 0929-9338 |
✅ | Text, dependent on the oidc issuer (e.g. ORCID) | |
| Oidc issuer | https://www.orcid.org | ✅ | Link, dependent on the oidc issuer (e.g. ORCID) | |
| Registration date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the account was created within the system View Description |
| User email | John.Doe@ example.mail |
✅ | Text, validated against RFC5322 format specification |
Email address associated with the account View Description |
| User name | JohnDoe | ✅ | Text | Unique name specified for the account View Description |
Personal Access Token
Warning
Personal access token are used as app credentials. They are connected to the user that created them and must not be shared.
Check out our documentation to find out how to register and edit your personal access tokens.
Project
Visit the documentation
to find out how to register
and edit a project.
Additionally, it outlines how to grant or revoke access to your
project to other users.
The following concepts are associated with a project
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Id | Q2ABCD | ✅ | Text, always starts with 'Q2' and has a total length of 6. |
Human Readable unique project identifier of the project View Description |
| Modification date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the project was last modified View Description |
| Objective | Investigating the substance of interest with XXX to determine YYY |
✅ | Text, with a maximum length of 2000 characters | Objective detailing the purpose and goal of the project View Description |
| Principal investigator full name | John Doe | ✅ | Text, divided by a singular space into first and last name |
Full name of the principal investigator handling the project View Description |
| Principal investigator email address | John.Doe@ example.mail |
✅ | Text, validated against RFC5322 format specification |
Email address of the principal investigator handling the project View Description |
| Project manager full name | Jane Doe | ✅ | Text, divided by a singular space into first and last name |
Full name of the project manager handling the project View Description |
| Project manager email address | Jane.Doe@ example.mail |
✅ | Text, validated against RFC5322 format specification |
Email address of the project manager handling the project View Description |
| Title | Analysis of the transcriptome of liver cancer sample |
✅ | Text | Clear and concise title of the project View Description |
| Grant name | DFG | ❌ | Text | Name of the grant funding the project View Description |
| Grant id | 213896434 | ❌ | Text | Unique Id identifying the grant funding the project View Description |
| Responsible person full name | Max Mustermann | ❌ | Text, divided by a singular space into first and last name |
Full name of the person responsible for the project View Description |
| Responsible person email address | Max.Mustermann@ example.mail |
❌ | Text, validated against RFC5322 format specification |
Email address of the person responsible for the project View Description |
Offer
Visit the documentation to find out how to register and edit your offer file.
The following concepts are associated with an offer file
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Name | Q2ABCD_Offer.pdf | ✅ | Text | Filename of the uploaded offer View Description |
| Signed | yes/no | ✅ | Boolean | Uploaded Offer was signed by the customer View Description |
Experiment
Visit our documentation to find out how to register and edit an experiment.
The following concepts are associated with an experiment.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Analytes | BAO:0000270 | ✅ | List of Identifier, validated against the W3C format specification |
One or more substances or compounds of interest, whose expression changes are of interest within the experiment View Description |
| Biological replicates | 20 | ✅ | Number | Number of biologically distinct samples subjected to the same treatment during the experiment View Description |
| Experimental groups | control, treatment_cohort_1 | ✅ | List of Experimental Groups | Group of subjects exposed to a unique combination (condition) of experimental variables View Description |
| Experimental variables | temperature, time | ✅ | List of Experimental Variables | An Experimental factor defined to observe its effect on the subjects of an experiment. View Description |
| Modification date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the experiment was last modified View Description |
| Name | Pilot Experiment | ✅ | Text | Unique name of the experiment View Description |
| Specimen | NCIT:C12392 | ✅ | List of Identifier, validated against the W3C format specification |
One or more specific parts of the species from which the analytes are collected. View Description |
| Species | NCBITaxon:9606 | ✅ | List of Identifier, validated against the W3C format specification |
One ore more Organisms from which the samples were collected View Description |
| Confounding variables | Varies See here for more information |
❌ | List of Confounding Variables | A variable possibly influencing independent and dependent experimental variables. View Description |
Experimental Variables
Visit our documentation to find out how to register and edit your experimental variables.
The following concepts are associated with an experiment variable
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Levels | 0, 10, 100 | ✅ | List of Texts | One or more specific expression settings to which the variable can be set. View Description |
| Name | Temperature | ✅ | Text | Unique name of the experimental variable View Description |
| Unit | °C | ❌ | Text | Measurement Unit representing the specific setting of the variable View Description |
Experimental Groups
Visit our documentation to find out how to register and edit your experimental variables.
The following concepts are associated with an experiment group
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Biological replicates | 20 | ✅ | Number | Number of biologically distinct samples subjected to the same treatment during the experiment View Description |
| Condition | control, treatment_cohort_1 |
✅ | List of Experimental Variables | Unique combination of experimental variables View Description |
Confounding Variables
Visit our documentation to find out how to register and edit your experimental variables.
Values for confounding variables can be provided per sample and are defined in the experiment.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Name | Time | ✅ | Text | Unique name of the experimental variable View Description |
| Values | [6pm, 8pm] | ❌ | List | Possible values of the confounding variables. View Description |
Terminology
Visit our documentation to find out how to search for your terminology of interest.
The following concepts are associated with the terminology terms.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Class IRI | http://purl.obolibrary.org/obo/NCIT_C105979 | ✅ | Identifier | Unique resource identifier for the term View Description |
| Description | A protein complex that plays a role in neurotransmitter-gated ion transport |
✅ | Text | Description providing explanation for the term View Description |
| Label | 5-HT3 Receptor | ✅ | Text | Common human-readable label of the term View Description |
| Name | NCIT:C105979 | ✅ | Identifier, structured as prefix:reference as seen in the W3C format specification |
The OBO-style identifier, usually in the form PREFIX:ID View Description |
| Terminology term IRI | http://purl.obolibrary.org/obo/ncbitaxon.owl | ✅ | Identifier | Unique resource identifier for the ontology providing the term View Description |
| Terminology term version | http://purl.obolibrary.org/obo/ncbitaxon/2023-09-19/ncbitaxon.owl | ✅ | Identifier | Specific Version of the ontology providing the term View Description |
For more information check the documentation of the ontology service API
Sample
Visit our documentation to find out how to register and edit your batches and samples.
The following concepts are associated with a sample.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Analysis method | PROTEOMICS | ✅ | Enumeration | The test performed on samples for the purpose of finding and measuring chemical substances. View Description |
| Analyte | BAO:0000270 | ✅ | Identifier, structured as prefix:reference as seen in the W3C format specification |
The chemical substance extracted from the biological material that is identified and measured. Selection from the ones defined within the experiment View Description |
| Condition | Temperature: 0°C; Time: 100s; |
✅ | Number of the Experimental Group in Question | Condition to which the sample was subjected to. Selectable from the experimental groups within the experiment with each variable seperated by a semicolon. View Description |
| Label | Lab_Id_01 | ✅ | Text | Common human-readable name of the sample. Can also be internal lab identifier View Description |
| Sample id | Q2ABCD001AA | ✅ | Text, beginning with the project id followed by the running number of samples within the project and ending with randomly generated unique letters |
Human readable unique sample id, automatically assigned by the Data Manager View Description |
| Species | NCBITaxon:9606 | ✅ | Identifier, structured as prefix:reference as seen in the W3C format specification |
Scientific name of the organism(s) from which the biological material is derived. Selection from the ones defined within the experiment View Description |
| Specimen | NCIT:C12392 | ✅ | Identifier, structured as prefix:reference as seen in the W3C format specification |
Name of the biological material from which the analytes would be extracted. Selection from the ones defined within the experiment View Description |
| Biological replicate | Mouse_WT_1 | ❌ | Text | Specify if the samples belong to the same biological source within your experiment. View Description |
| Comment | Redone QC | ❌ | Text | Free Text, can contain any notes related to a specific sample in question View Description |
| Confounding Variables | color: red, location: labA | ❌ | List of key-value pairs | Confounding variables are a good way to annotate measured variables that are suspected to have an influence on your depending variable. View Description |
Additional information can be found in the Property Information tab within the sample registration template sheet.
Batch
Info
A batch can be defined as a group of samples processed together under the same
experimental conditions.
This is done to document and minimize technical variation.
The following concepts are associated with a sample batch.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Modification date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the batch was last modified View Description |
| Name | Pxp_Analysis_Trial_1 | ✅ | Text | Common human-readable label of the batch View Description |
| Registration date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the batch was created within the Data Manager View Description |
| Sample count | 20 | ✅ | Number | Number of samples contained within the batch, automatically determined by the Data Manager from the number of samples provided during registration View Description |
Measurement
For detailed information visit our measurement documentation
Genomics
Visit our documentation to find out how to register or edit your proteomics measurement
The following concepts are associated with a genomic measurement.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Facility | Quantitative Biology Center | ✅ | Text | The facilities name within the organisation (group name, etc.) View Description |
| Index I5 | NEBNext UDI UMI Set 1 B12 S579 | ✅ for pooled measurements | Text | Index used for multiplexing. View Description |
| Index I7 | NEBNext UDI UMI Set 1 B12 S789 | ✅ for pooled measurements | Text | Index used for multiplexing. View Description |
| Instrument | OBI:0002750 | ✅ | Identifier, structured as prefix:reference as seen in the W3C format specification |
Ontology Identifier of the instrument that has been used for the measurement, usually in the form PREFIX:REFERENCE View Description |
| Measurement id | NGSQ2ABCD001AA- 118569093700875 |
✅ | Text, beginning with the domain(NGS) prefix followed by the sample id, seperated by a hyphen with its unique creation timestamp |
Human readable unique measurement id, automatically assigned by the Data Manager, usually in the form "NGS"SAMPLEID"-"Timestamp" View Description |
| Organization IRI | https://ror.org/03a1kwz48 | ✅ | Identifier, validated according to the structure defined by the RoR |
Research organization registry identifier(RoR Id) of the organisation where the measurement has been conducted View Description |
| Organization label | University Tuebingen | ✅ | Text | Human Readable Name of the organization, automatically received from the RoR by the Organization IRI View Description |
| Read type | paired-end | ✅ | Enumeration | The sequencing read type used to generate the sequence data. View Description |
| Registration date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the batch was created within the Data Manager View Description |
| Comment | Repeated Measurement after Bad QC |
❌ | Text | Free Text, can contain any notes related to a measurement in question with up to 500 characters View Description |
| Flow cell | S4 | ❌ | Text | The flow cell type used for sequencing. View Description |
| Library kit | NEBNext Ultra II Directional RNA mRNA UMI | ❌ | Text | The library kit employed during sequencing processing View Description |
| Measurement name | Lab_Id_01 | ❌ | Text | Common human-readable name of the measurement. Can also be the internal lab identifier View Description |
| Run protocol | 104+19+10+104 | ❌ | Text | Information on how many cycles were used for each read and index during sequencing View Description |
Additional information can be found in the property information tab within the genomic measurement registration template sheet
Proteomics
Visit our documentation to find out how to register or edit your proteomics measurement
The following concepts are associated with a proteomics measurement.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| Digestion enzyme | Trypsin | ✅ | Text | Information about the enzymes used for the proteolytic step. View Description |
| Digestion method | in gel | ✅ | Enumeration | Method that has been used to break proteins into peptides, Selectable from the methods "in gel", "in solution", "iST proteomics kit", "on beads" View Description |
| Facility | "Quantitative Biology Center" | ✅ | Text | The facilities name within the organisation (group name, etc.) View Description |
| Instrument | BAO:0002733 | ✅ | Identifier, structured as prefix:reference as seen in the W3C format specification |
Ontology Identifier of the instrument that has been used for the measurement View Description |
| Lc column | ProteoSil_100-C18 | ✅ | Text | The type of column that has been used. View Description |
| Measurement id | MSQ2ABCD001AA- 118569093700875 |
✅ | Text, beginning with the domain(MS) prefix followed by the sample id, seperated by a hyphen with its unique creation timestamp |
Human readable unique measurement id, automatically assigned by the Data Manager, usually in the form "MS"SAMPLEID"-"Timestamp" View Description |
| Organization IRI | https://ror.org/03a1kwz48 | ✅ | Identifier, validated according to the structure defined by the RoR |
Research organization registry identifier(RoR Id) of the organisation where the measurement has been conducted View Description |
| Organization label | University Tuebingen | ✅ | Text | Human Readable Name of the organization, automatically received from the RoR by the Organization IRI View Description |
| Registration date | 2025-04-28 08:24:25.000000 |
✅ | Date | Timestamp when the batch was created within the Data Manager View Description |
| Comment | Repeated Measurement after Bad QC |
❌ | Text | Free Text, can contain any notes related to a measurement in question with up to 500 characters View Description |
| Enrichment method | Phosphopeptide Enrichment | ❌ | Text | Enrichment of proteins or peptides of different characteristics. View Description |
| Fraction name | Fraction01 | ❌ | Text | If the sample was fractionated this label can be used to indicate which fraction was measured. View Description |
| Injection volume | 10 | ❌ | Number | The sample volume injected into the LC column in microliter(µl). View Description |
| Label | Heavy | ❌ | Text | The label value for the label type that has been used. View Description |
| Label type | SILAC | ❌ | Text | The label type that has been used to label the sample for measurement. View Description |
| Measurement name | Lab_Id_01 | ❌ | Text | Common human-readable name of the measurement. Can also be the internal lab identifier View Description |
| LCMS method | APCI | ❌ | Text | Laboratory specific methods that have been used for LCMS measurement. View Description |
| Replicate name | Replicate_1 | ❌ | Text | Label to distinguish between technical replicates for repeated measurements of the same sample. View Description |
Additional information can be found the property information tab within the proteomics measurement registration template sheet.
Raw Data
Visit our documentation to find out how to upload or download your raw data.
The following concepts are associated with a raw data dataset.
| Concept | Example | Mandatory | Type | Description |
|---|---|---|---|---|
| File count | 20 | ✅ | Number | Number of Files contained within the raw data upload, automatically determined by the Data Manager View Description |
| File size | 2000Mb | ✅ | Text | Size of all Files within the raw data upload, automatically determined by the Data Manager View Description |
| File suffixes | fastq, tar, txt | ✅ | List of Text | List of File suffixes for all files within a raw data upload, automatically determined by the Data Manager View Description |
| Registration date | 2025-04-28 08:24:25.000000@ |
✅ | Date | Timestamp when the raw data was uploaded within the Data Manager View Description |