Minimum Metadata Guidelines for the SysMO SEEK

The more metadata you provide for your assets in the SEEK, the easier it is to find them and to compare them with other assets. If you provide assets with very little metadata, these will also be displayed (in accordance with access control policies set by you), but they may be hard to interpret for other people.

In addition to SEEK data sharing guidelines, some types of data have minimum metadata requirements for publication, for example, microarray data must be MIAME compliant. Following the guidelines for SEEK metadata should ensure that when you come to publish, you have already met these requirements.
These guidelines outline what we require for SEEK.

General SEEK Metadata

Name (of the data uploader). This is the person responsible for the data and responsible for setting sharing and dissemination policies. If more than one person was involved in the experiment, you can credit these people separately
SEEK ID – (Of the above person). This helps us identify each person within SEEK.
Project – The name of the project that the asset relates to. If your data is being uploaded by a JERM harvester, we will know which project it belongs to, but if you are uploading directly to SEEK and you are in more than one SysMO project, it is important to specify. Typically, an asset will belong to only one project.
Upload Date (yymmdd). This is the date of publication to SEEK rather than the date of the experiment. Depending on the system your project uses, we will try to automatically detect when changes are made to a file. Each upload will automatically receive its own timestamp when uploaded directly into SEEK
Experiment Date (yymmdd). This is the date the experiment was performed
Title – a unique name for your asset file. If you upload manually, you will receive an error message if the file title is not unique within your project. If your asset is uploaded via a JERM Harvester without a title, you will receive an email notification.
Version Number – If your file replaces an existing file, the version number will help us pick this up. Keep it simple, versions should go up by integers.
Names of other people involved – many experiments involve multiple steps and multiple people. This metadata field allows you to give credit and attribution to all those involved

ISA Infrastructure

Investigation

Title – described above. All assets should have a title
Description – free text describing the purpose of the investigation
Project – as described above. All assets should be associated with a project

Study

Title – as described above. All assets should have a title
Description – free text describing the purpose of the study
Person Responsible – the creator of the study description
Experimentalists – other scientists involved in any of the work in the study. If they are in SysMO, please give their SEEK ID, so we can link to their profiles in SEEK. If they are not in SEEK, their names will still be displayed, but not linked. People’s involvement can also be inferred from anyone named in included assays.
Project – as described above. All assets should be associated with a project
Investigation title – The name of the investigation the study belongs to.

Assay

Assay Title – The name of the assay that the asset links to.
Assay type – The controlled vocabulary term describing the assay classification
If you cannot find a suitable Assay Type term, please contact us or your PAL to update the vocabulary
Technology type – The controlled vocabulary term describing the technology used in the assay
If you cannot find a suitable Technology Type term, please contact us or your PAL to update the vocabulary
Study title – The name of the study the assay belongs to. An assay can belong to more than one study
Organism The name of the organism being studied with this asset. If uploading through SEEK, organism names are provided as a drop-down list
Strain The name of the particular strain being studied
WT/Mutant – Specifies whether this strain is wild-type or mutant
Genotype – a brief text description of the genotype
Phenotype – a brief text description of the phenotype
Culture Growth – This describes how the culture was grown for this assay. You can choose values from a drop-down list when adding new assays directly to SEEK
Data File Titles – the title of one or many data files produced during this assay
SOP Titles – the title of one or many SOPs used to execute this assay

SysMO Assets

Data

Title – as described above
Description – free text to describe what the data is showing
File Format – how the data is stored, for example excel spreadsheet
Factors Studied – what were the measurements in this experiment (e.g. concentration, pH or gene expression). If you are uploading directly through SEEK, you can chose from a drop-down list
Measured Item – what was measured in this data, e.g. concentration of glucose. Measured items should be named using controlled vocabulary terms wherever possible, for example, glucose has chEBI name glucose and chEBI ID CHEBI:17234
Units – how the measurements were taken, e.g. concentration in mmol, or mass in grams.

Models

Filename/archive name – the title of the asset
Description – free text to describe what the model is showing
Model Type – what kind of mathematical equations does your model contain e.g. ODE, algebraic
Model Format – e.g. SBML, CellML. If uploading directly through SEEK, you will be able to chose from a drop-down list
Model Execution Environment and URL – how do you run a simulation on your model? This field should provide a link to a tool or resource which would allow you to run your model
Linking Models to Data – this section allows you to specify how and where data files were used to a) construct your model b) validate your model, or c) record simulation results from your model. If you are uploading directly through SEEK, you can find the relevant files by searching a drop-down list. If uploading through a JERM Harvester, you should use the data file title or SEEKID

SOPs

Title – as described above. All assets should have a title
Description – free text to describe what the SOP is used for
Experimental conditions – what was standardised and fixed in this experiment (e.g. concentration of nutrients, pH, temperature). If you are uploading directly through SEEK, you can chose from a drop-down list
Units – how the measurements were taken e.g. concentration in mmol or mass in grams.

Publications

PubmedID or DOI – the SEEK can extract publication abstracts from PubMed, when supplied with a PubmedID. When the paper abstract is retrieved, you can verify which people from a drop-down list are authors from within the consortium, so that we can link to their profile
Currently, publications are linked to people and projects. In the next version, publications will be linked to other SysMO assets to allow you to use the SEEK as a supplementary data store

Attribution – Some assets are based on others, for example, a model may use data from an experimental assay, or a SOP may be a modified version of another. The attribution section allows you to specify when this is the case