Database Standards

• Biodiversity Information Standards (TDWG) (formerly the Taxonomic Database Working Group) – develops standards and protocols for sharing biodiversity data.
• Darwin Core
• Schemas and Protocols
• Access to Biological Collections Data (ABCD) – schema/protocol.
• Biological Collection Access Services (BIOCASE) – schema/protocol.
• Distributed Generic Information Retrieval (DiGIR) – schema/protocol.

Data Aggregators

• GBIF – Global Biodiversity Information Facility. Serves data from collections from around the world across all organisms and includes iNaturalist “Research Grade” data.
  
• Symbiota – Data are served via Portals. Each portal specializes in a certain geographic region (e.g. Southeast USA) or a particular organismal group (e.g. Bryophyte portal).
• iDigBio – Serves data from collections from around the world across all organisms
• JSTOR Global Plants – Serves data from select herbaria, especially type specimens and other historical specimens.

Database Programs

• MS-Excel (Windows, Mac) – a spreadsheet program that is very basic and easy to use. It is useful for simple data handling. It is an excellent import/export tool.
• MS-Access (Windows, Mac) – a fairly easy to learn program in which you may develop robust databases.
• MS-SQL Server (Windows) – corporate-level database server, may become expensive to use.
• MySQL (Windows, Mac, Linux) – open source, free database program.
• PostgreSQL (Windows, Mac, Linux) – open source, free database program.
• OpenOffice (Windows, Mac, Linux) – open-source software for word processing, spreadsheets and database development.

Database Applications for Herbarium Collections

• Brahms: Botanical Research and Management System – widely used, especially in Europe, Africa and Latin America for cataloguing herbaria.
• EMu – electronic museum management system, providing solutions for: museums, art galleries, historical societies, herbaria and botanic gardens. Used by many major institutions (New York Botanical Garden, Field Museum, Yale University). Quite expensive!
• Specify: “The Specify Software Project supports biological collections with data management software, data conversion services, helpdesk support and training.” Development supported by NSF and used by hundreds of museums.

Specialized Applications

• Tolkin – The Tree of Life Knowledge and Information Network. “support collaborative projects by providing shared access to a variety of data on voucher specimens, taxonomy, bibliography, morphology, DNA samples and sequences.”
• Lucid – interactive key software… “a flexible and powerful knowledge management tool that helps users make an identification or diagnosis.”

Programming (Scripting) Languages and Frameworks

• HTML, HyperText Markup Language, – the core programming language of the web.
• Java
• JavaScript
• PHP – “general-purpose scripting language that is especially suited for Web development and can be embedded into HTML”.
• PERL – high-level programming language widely deployed for use on web sites for connecting to and searching databases.
• Ruby – “open source programming language with a focus on simplicity and productivity.”
• Ruby on Rails – open-source web framework.
• XML – markup language for documents containing structured information.