Metadata Guidelines

Help Index > Metadata Guidelines

Minimum Metadata Guidelines for 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 you are uploading directly to SEEK and you are in more than one 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 you will receive an error message if the file title is not unique within your project.
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 – all investigations should have a title
Description – free text describing the purpose of the investigation
Project – all investigations should be associated with a project

Study

Title – all studies 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 wihtin the consortium, 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 – all studies 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 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 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 assay. 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 – 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

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 experimental parameters did you alter in order to study the effects in the organism (e.g. changing the pH from 5 to 7)
Measured Item – what was measured in this data, e.g. concentration of glucose
Units – how the measurements were taken, e.g. concentration in mmol, or mass in grams.

SOPs

Title – all SOPs 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 DOISEEK 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.
Publications are linked to people and projects.

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.


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