Using SEEK and NExtSEEK
An explanation of the major concepts and major pages of the SEEK/NExtSEEK data management platform
Concepts:
SEEK vs NExtSEEK
NExtSEEK is a modified wrapped, built on top of the SEEK infrastructure. The fundamental differences that differentiate the SEEK and NExtSEEK platforms are outlined in the NExtSEEK publication. Although there are differences, SEEK is required for NExtSEEK's functionality, as we leverage and use many features from the core SEEK. All data/metadata in NExtSEEK are compatible with SEEK. This compatibility is shown by using FAIRDOMHub, an instance of the core SEEK infrastructure, as the metadata repository we use to publish our research data. An example of published research data exists here.
SEEK and NExtSEEK are utilized together, each serving different purposes. Below is a very brief explanation of how the two platforms interact.
Core SEEK: fairdata.mit.edu - Functionality: Register for accounts (same account used for SEEK and NExtSEEK), create Projects/SampleTypes/Assays, administer account-project associations
NExtSEEK: nextseek.mit.edu - Functionality: Upload/Search/Download Samples, Protocols, and Data Files
We use SEEK as the administrative site (creating assets and administering roles), while NExtSEEK is used for all things data (uploading, downloading, searching).
ISA Structure
SEEK/NExtSEEK uses the ISA metadata tracking framework as described here. ISA = Investigation, Study, Assay. In our case: Investigation = Grant/Research Project, Study = Publication, and Assay = Experiment. This is a nested structure -> There are multiple Assays in a Study, and multiple Studies in an Investigation.
This is how the data is modeled in the public domain (on FAIRDOMHub), but in the scope of NExtSEEK, we treat the investigation and study as a singular node. During the research process, it's often unknown which data will be part of a particular publication, therefore, all data of ongoing research efforts (on NExtSEEK), lives underneath a single study. When data is published from NExtSEEK to FAIRDOMHub, it is then associated with a publication, and can then be in ISA format.
Types of Assets
SEEK/NExtSEEK has a few different flavors/types of assets: Samples, Assays, Protocols, and Data Files.
Samples:
A sample is any unit of biological, chemical, or data material that is subject to analysis or experimentation. It can range from a tangible entity, such as a patient or tissue specimen, to digital data outputs like raw or analyzed sequencing data files.
Samples are stored as tabular metadata (excel), and grouped into different Sample Types; each describing a specific type of data or metadata. Each sample type is unique and will contain a different subset of attributes. Some attributes are shared, such as UUID (unique identifier/primary key), Name (also needs to be unique), Protocol (A field that links to the protocol associated with the sample), Parent (unique identifier of Parent sample), and more. Sample Type Nomenclature: Samples without a prefix = Metadata samples. D.XXX = Data File, A.XXX = Analyzed Data File. Examples: PAT: Human Patient, TIS: Tissue, DNA: DNA Library, D.SEQ: Sequencing File, A.GEX: Gene Expression Analysis File.
Assays:
An Assay is a type of experiment/procedure done on a Sample, to generate another sample. These can be broad terms, or more specific. Assays always have two samples associated with them: the Parent sample that feeds into the assay, and the Child sample that is generated from the assay. Examples: PAT -> Tissue Collection -> TIS -> DNA Extraction -> DNA -> Short Read Sequencing -> D.SEQ -> Gene Expression Analysis -> A.GEX
In the above example, the PAT sample feeds into the Tissue Collection Assay and generates a TIS sample.
Assays are Study specific (see ISA format). To view the full list of assays that are visible to you, head here. To view the list of assays associated with a study, head to the study page for your specific project.
Protocols:
A description of the assay/experiment performed on the sample. Can be in any format (PDF, DOCX, XLSX, TXT, IMG, etc). Ideally, this is primary materials from a lab (primary protocols used in-house), but materials and methods sections usually suffice. Examples: Protocols describing Tissue Extraction, DNA Library Creation, Sequencing, and Gene Expression Analysis. Again, these can be Word documents, PDFs, text files, etc.
Data Files:
An actual data file. Not frequently used. We are not looking to house/manage terabytes of research data, nor be responsible for serving/housing that data to the public (in perpetuity). Instead, we push for data to live in their respective repositories, and until then, in their original home (generating lab). We can store data files on SEEK/NExtSEEK, and those data files can be downloaded by users who have access, but the majority of our use cases point to systems that are much better at managing data transfers (repositories, cloud computing environments, Globus, etc).
Pages on NExtSEEK:
Data Entry
There are three pages associated with Data Entry:
Assay Sheet Uploading: Where a user uploads samples
Data File/Protocol Uploading: Where a user uploads data files/protocols
Templates: Housing sample sheet templates for users to use (to prep and upload files)
More information on how to use these pages exists on the Uploading page.
Data Query
There are four pages associated with Data Query:
Advanced Search: A text search of the entire database (all samples). Allows complex searching (AND/OR/NOT). partial/exact matches, and sample type specificity.
Simple Search: Search a single Sample Type, by a single Attribute, by a single Value. Example: All D.SEQ whose Type contains 'RNA-Seq'
Data File Query: Search through what data files exist in a filterable table. Files are downloadable as well (single + batch).
Protocol Query: Search through what Protocols exist in a filterable table. Files are downloadable as well (single + batch).
More information on how to search / download samples exists on the Searching / Downloading page.
Sample Pages
Each sample has its own page on NExtSEEK located at: https://nextseek.mit.edu/seek/sampletree/uid=XXX (where XXX = the UUID of that sample).
The sample page has two sections: An interactive Sample Tree and a table of Metadata.
The interactive sample tree shows all connected Parent/Child samples. By clicking on a sample, you then load the sample page of that sample.
The table of Metadata is straightforward - it is the metadata associated with that sample.
Sample pages can take some time to load (as they are not all stored in the database, and are auto-generated on load)- depending on the number of nodes (child/parent) associated with the sample.
Attribute Editor
This page allows users to add/remove/edit attributes of Sample Types. This feature is only available on NExtSEEK, as SEEK does not allow for attribute editing. This is very useful when we are working with a new group, and they collect (and want us to include) a new field of a Sample Type that already exists.
Pages on SEEK:
Account Registration / Project Association:
Accounts are registered on the SEEK website (and then used on both the SEEK and NExtSEEK websites). You can register for an account here: https://fairdata.mit.edu/signup.
Once you have an account, you will need to be approved and added to a project (by an administrator) to access SEEK/NExtSEEK. This is what federates access to different Projects, and therefore access to the different assets of those projects. You must be a member of a project to access the assets, therefore allowing multiple projects to exist in the same database.
To administer project associations: https://docs.seek4science.org/help/user-guide/administer-project-members.html#add-and-remove-people-from-a-project.
You can also request to join a project: https://docs.seek4science.org/help/user-guide/join-a-project.html.
Creating Assets (Sample Types, Assays, Projects)
To create a new asset type, the SEEK website is used. Whether that is creating a new Sample Type, a new Assay, or creating a new Project.
Documentation surrounding creating these assets can be found directly on the SEEK Documentation, linked below:
Assay: There is no documentation on the SEEK website for this.
SEEK Documentation Link
A link to the full SEEK Documentation exists here: https://docs.seek4science.org/ (head to user guides).
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