Note: If you are familiar with this material, skip to section 2.

Data Sharing is a generic term covering all methodologies and technologies for passing information from one system to another, to be used by another person, tool, or calculation. Data Sharing methodologies exist on a spectrum of automation. At one end of the spectrum there is very manual sharing like shipping files to a collaborator on a hard drive. On the other end of the spectrum there is full automation where data can travel between software systems freely and automatically, without human intervention.

Programmatic Access is the ability to read and interact with data using software. If a system or database has Programmatic Access, then someone should be able to write a new piece of code which can access the data in an automated way.

Data Federation is a software model where a collection of databases become highly interoperable, to the point where they appear to be parts of a single system to the outside world. An external tool should be able to query all the databases in the federation in the same way. An external tool should also be able to retrieve connected, interoperable data from multiple sources in the federation. An end user may not even care which source the data comes from, as long as it is available somewhere in the federation.

Interoperability
- A measure of how easy it is for two or more systems to interact and share data and has three facets: semantics, syntax, and protocol.

 - Semantic Interoperability: The ability of computer systems to exchange data with unambiguous, shared meaning. For example, in different systems, 'plant height' may mean the distance from the soil surface to the tip of the inflorescence, to the top leaf, or to the top of the stem, excluding leave

 - Syntactic interoperability: The structure of data and how it is organized. For example, the taxa information might be organized “genus species sub-taxa” or “sub-taxa species genus” in different systems, even though they contain the same information.

 - Protocol Interoperability: The mechanism for how data transfers from one place to another. For example, one system only provides file downloads and another system only provides an API. These two systems could use the same semantics and syntax, but are still not interoperable.

An API is the part of a system or database which provides Programmatic Access to the data. There are many different types of API, but typically (in this context) we are referring to Web Service API’s, which use the Internet to provide Programmatic Access to the outside world.

Data annotation is the process of labeling data objects with ontology terms so that computers can understand the data.

Functional annotation is the process of attaching biological information, related to the function of the gene or section of the genome,  to sequences of genes or proteins, using ontology terms from the Molecular Function branch of the Gene Ontology.

Structural annotations are labels applied to physical regions of a genome that encode a genomic feature. Examples of such annotations are genes, mRNA, transcript, repeat sequences, etc.