Glossary

ABCD Data Schema (Access to Biological Collection Data): XML data schema used for publishing specimen collections and observational databases to primary biodiversity networks such as BioCASe and GBIF. The current version of ABCD is 2.06.

Apache HTTP Server (“Apache”): Widely used open-source web server software. Apache is available for most operating systems and recommended for running BioCASe.

BioCASe Installation: An installation of the BioCASe Provider Software that offers one or several BioCASe Web Services.

BioCASe Web Service: A web service offered by a BioCASe installation. A BioCASe web service provides access to the database to be published and can be queried using the BioCASe Protocol. It is uniquely identified by its URL, which is a combination of the BioCASe installation’s URL and the name of the data source, for example http://www.myinstitution.org/biocase/pywrapper.cgi?dsa=Herbar. See DatasourceSetup for more information on how to set up a BioCASe Web Service.

BioCASe (Biological Collection Access Service) Network: A network of primary biodiversity data providers. Currently, BioCASe offers three different data portals: One on the German flora (http://search.biocase.de/botany), one for the biodiversity of Europe (http://search.biocase.org/europe) and one for global occurrence data (http://search.biocase.org/edit).

BioCASE Project (Biological Collection Access Service for Europe): EU-funded project (2002-05) that developed standards and software for publishing primary biodiversity data (specimen collections and observational databases). Within the first years, the results comprised the BioCASe Protocol, the ABCD data schema and the BioCASe Provider Software.

BioCASe Protocol: The protocol for querying a BioCASe web service. The protocol defines three types of requests: Capabilities for introspecting the configuration of a BioCASe web service, Scan for getting the distinctive values for a concept provided by the web service, and Search for retrieving the full set of information published for certain records.

BioCASe Technology (Biological Collection Access Service): The suite of standards and software developed by the BioCASE Project and its successors. Currently, the main components are the BioCASe Protocol, the ABCD data schema, BioCASe Provider Software, the SYNTHESYS Cache Generation System and the BioCASe Data Portal Software.

Cache: A component (in the BioCASe context, usually a database or several database tables) that temporarily stores data from another source. In most cases, this is done in order to increase performance for information retrieval.

Configuration tool (also Config Tool): Set of dialogs used for configuring a BioCASe installation or BioCASe web services.

Database View: A virtual table in a database that offers another view on the data stored in the database. A view can combine data from several tables and transform, that is, translate, concatenate or pivot them. Updates of the underlying tables are always reflected in views drawing data from these tables.

Datasource: In the BioCASe context, a datasource is database that is to be published as a BioCASe web service. Do not confuse that with an ODBC datasource that defines the connection parameters for connecting to a database through ODBC.

Denormalisation: In a relational database, the information for real world objects are split into several tables, which is called normalisation. Denormalisation is the process of intentionally reversing this step for the sake of faster information retrieval.

Firewall: Usually one device, a combination of several devices or a software shielding a local area network (LAN) from the internet. A firewall filters all network traffic between the LAN and the Internet, blocking unwanted protocols (i.e. applications) and ports. In a BioCASe context, servers should be placed in a way that no firewall is located between the web server running the Provider Software and the database server. In case there is a firewall in between, the port used by the database management system (e.g. 3306 for MySQL) must be opened.

Global Biodiversity Information Facility (GBIF): International organisation for promoting free and universal access to worldwide primary biodiversity information. One of the main services offered is the GBIF Data Portal (http://data.gbif.org).

Harvester: Application that retrieves all records published by a (BioCASe) web service and stores them in a local database. Harvesters are run by projects and initiatives that consume or aggregate primary biodiversity information, for example by GBIF for running the GBIF data portal.

Identifier: In a database table, an identifier is a field that names a record in that table. Identifiers are usually unique, that means the identifier is different for each record.

Internet Information Services (IIS): Web service platform integrated into Microsoft’s server operating systems (Server 2000, 2003 and 2008); can be used for running the BioCASe Provider Software.

Local Query Tool: Component of the BioCASe Provider Software that can be used to access a BioCASe web service. The Query Tool offers a customizable, very simple and no-frills search interface for querying one (!) BioCASe web service.

Mapping Editor: Page of the configuration tool for mapping concepts of the published data schema to the source tables/columns in the database.

Metadata: Data about data. In the BioCASe context, this is a set of information describing the database published as a whole - title, description, curator’s name, ownership, date of last modification, terms of use etc.

Open Database Connectivity (ODBC): Standard Interface for accessing relational database management systems. The connection parameters for connecting to a database through ODBC are defined in an ODBC Datasource.

OS: Operating System (Windows, MacOS, Ubuntu, Debian, Ret Hat, Solaris etc.).

Python: Platform independent programming language used for the BioCASe Provider Software.

PyWrapper: Synonym for the BioCASe Provider Software (BPS), created from "Python Wrapper". Sort of "wraps" around the database to be published, exposing the data as a BioCASe compliant web service.

Query Form: Component of the Provider Software for sending requests to a BioCASe web service and displaying the result documents; usually used for debugging a web service.

Schema Mapping: The part of the configuration that tells the Provider Software how to create documents in a specific published data schema from the source database. A BioCASe web service can support several schemas (e.g. for ABCD and DarwinCore) by having several schema mappings.

SQL (Structured Query Language): Language for managing data in relational database management systems, e.g. for information retrieval.

Subversion: Software versioning and revision control system used for the BioCASe Provider Software. When installing BioCASe, the software can be downloaded directly from the Subversion repository (See Installation#Downloading from the Subversion Repository).

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