Browse the glossary to learn more about terms and definitions used within Synapse.
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Annotations can be based on an existing ontology or controlled vocabulary, or can be created as needed and modified later as your metadata evolves.
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Anonymous
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access
This is a type of data access setting—data set at this tier is available for anyone on the web, without Conditions for Use.
The other data access tiers are: private access, controlled access, and open access.
Learn more about data access here.
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API
Abbreviation for Application Programming Interface, this is a type of software application that allows for the integration or connection between otherwise unconnected services. Synapse uses API clients to allow for the programmatic use of certain tasks, such as uploading and downloading data.
Find more information, including installation instructions, on Sage’s API clients here.
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Certified User
This is one of four user account types in Synapse, which determines what actions a user can perform. Certified users have full access to Synapse functionality.
The other user account types are: anonymous users, registered users, and validated users.
Find more information on user account types here.
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Challenges
An open-science, collaborative competition framework for evaluating and comparing computational algorithms.
Read more about Challenges here.
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Command line
Controlled Access Tier -
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Data dictionary -
Data science -
Data model -
Digital object identifier -
Docker -
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Entity -
Experimental mode -
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FAIR -
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Governance -
J
JSON -
JSON schema -
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Key-value pairs -
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Markdown -
Metadata -
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Ontology - Explanation
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Controlled access
This is a type of data access setting—data set at this tier is available to registered, certified, or validated users that fulfil specific requirements for data access.
The other data access tiers are: private access, open access, and anonymous access.
Learn more about data access here.
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Data dictionary
This is essentially a repository for metadata used throughout the Synapse site.
Need more here…
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Data science
Data science is an interdisciplinary field that uses scientific methods, processes, algorithms, and systems to extract knowledge and insights from structured and unstructured data, and apply knowledge and actionable insights from data across a broad range of application domains.
Source: Wikipedia. Is there a better / more Sage-focused explanation?
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Data model
An abstract model that organizes elements of data and standardizes how they relate to one another and to the properties of real-world entities. A data model explicitly determines the structure of data.
Source: Wikipedia. Is there a better / more Sage-focused explanation?
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Digital object identifier (DOI)
A distinct alphanumeric string assigned to uniquely label and identify a digital object. A DOI is defined by a digital location like a URL and a description of the object, which includes attribution and a creation or publication date.
Read more about DIOs here.
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Docker
A tool for creating, running, and managing lightweight virtual machines to bundle code and other dependancies. You can add a Docker container to a project and share it with your teammates. Learn more about Docker here.
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Entity
Any distinct object in Synapse, including a file, folder, project… what else?
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Experimental mode
A mode in Synapse where new features and feature updates that are still in development until they are ready to be pushed live. Anyone can test out this mode using the Experiment Mode link at the bottom right of Synapse.
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FAIR
Abbreviation for Findable, Accessible, Interoperable, and Reusable. This is the standard set of principles that we follow at Sage. FAIR data are discoverable to users through precise metadata, understandable in terms of how the data can be used, machine-readable to enable computational analysis, and ultimately, fit for reuse.
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Governance
A set of protocols, conditions, and responsibilities that Sage has established to enable the ability of our organization to ensure quality, compliance, and usability of data uploaded to our platforms.
Synapse governance is an essential component of the Synapse platform; it is a system of policies, procedures, and tools for managing and protecting data in Synapse. Our policies define the community norms, user rights, and user responsibilities. Our procedures determine how to and who can contribute, access, and use content.
Read more about Synapse governance here.
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JSON
Abbreviation for JavaScript Object Notation. JSON is a data-interchange format or language based on two structures: an object and associated values, or an array.
This may need tweaking… I tried to make it “approachable” but I may have missed key points or got something wrong.
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JSON schema
A specific JSON-based format that defines the structure of JSON data for validation, documentation, and interaction control. It provides a contract for the JSON data required by a given application, and how that data can be modified.
Source: Wikipedia. Please check for accuracy
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Key-value pairs
Key-value pairs are used in annotations, where the key defines a particular aspect of your data (for example, species, assay, file format) and the value defines a variable that belongs to that category (mouse, RNAseq, .bam).
Is this enough explanation? Are key-value pairs used outside of annotations?
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Markdown
Markdown is a simple language used for creating formatted text (such as italics, bold, hyperlinks, paragraph breaks, etc.). It is simple in that it is readable to computers while also being appealing and understandable to people.
Markdown is used in certain parts of Synapse, including wikis and discussion forums.
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Metadata
Metadata is additional, standardized information included alongside the data to give it context—data about the data, if you will. Metadata is what allows data in Synapse to be searchable, discoverable, accessible, re-usable, and understandable to others, including those who were not involved in the data generation process.
Metadata can be descriptive (i.e., the name of the file), administrative (i.e., provenance information), or research-based (i.e., information about the sampling and handling of data).
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Ontology
Open Access Tier -
P
Permissions -
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