SEEK is a web-based cataloguing and commons platform, for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved.

Underpinning SEEK is the ISA infrastructure, a standard framework for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology.

Flexible and detailed sharing permissions are available to manage the catalogued items from early collaborations within projects, through to the publishing of final research results. At this point a DOI can be generated for individual items, or entire aggregates packaged as Research Objects

SEEK incorporates semantic technology, allowing sophisticated queries over the content. Metadata can be collected using standard Excel tools and processes, through the use of RightField.

A publically available instance of a SEEK commons is available - as the FAIRDOMHub.

Organise and store your data

SEEK has adopted an ISATAB style structure for organising experiments and data.

The ISA format (Investigations, Studies and Assays) is a community standardisation activity to allow the association of multiple 'Omics datasets, in the context of the experiments that created them, in order to make it easier to compare and combine different data sets. It also provides the possibility of exporting or importing data from other sources in ISA-TAB format and therefore allows data exchange with a wider community.

Explore and annotate data

Excel spreadsheets can be explored and annotated without the need to download.

Individual or groups of cells can be annotated with text. Time series data can be annotated and stored as a plot.
Along with the annotations, contents of the spreadsheets are also indexed and searchable - so data can be discovered by searching within their content.

Simulate SBML models

Most models that conforms to the SBML format can be simulated within SEEK.

The JWS Online model simulator presents a schematic diagram of the model, and allows parameters and reactions to be modified for the simulation.

Models can also be edited using JWS Online OneStop, and semantically annotated with Miriam annotations, and then saved back to SEEK as a new version.

Who's doing what, where?

We recognise that people, and their knowledge, are important.

You can find out what people using, and have expertise in, and how to get in contact with them.

The Yellow Pages is a directory of who is on which project, where they are located, and what they specialise in. This allows researchers to identify people with similar interests, or to find people with the relevant experience when troubleshooting new techniques.

With a quick glance it also is possible to see what items they have been involved with producing, what experiments they have been doing, and what registered publications they are an author of.

Flexible sharing controls

There is a lot of flexibility and control over who can see, download or edit your items.

Data files, models, SOPs and also ISA description of your investigations and experimental practices can be kept entirely private, shared with your whole project (or selected members of your project), or the whole set of registered users.

If you are working together with other people, you can give additional users full edit or manage rights.
When you are ready, especially if you are publishing, you can make your items entirely public, accessible to anonymous users without an account. The links to the item never change, so you can point to the data that supports your publications.

Semantic spreadsheet templates

RightField enabled sheets allow rich semantic descriptions of data. Our Just Enough Results Model can be used with Rightfield.

RightField is a tool we created for SEEK, but is also attracting interest from other disciplines. RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection.

Rightfield coversheets can be used in conjunction with any data files to ensure that the right metadata is used to describe the data. It has a special use in our samples framework, with all samples sheets coming with a coversheet with JERM ontology information embedded. Users can create their metadata cover-sheets too..

We are currently working on automatic extraction from these templates, after they have been filled out and use, to make adding data to SEEK and describing it easier, and also enhance the ability to discover data.