Animal diseases

ABCD (Access to Biological Collection Data)

The Access to Biological Collections Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data). The ABCD Schema attempts to be comprehensive and highly structured, supporting data from a wide variety of databases. It is compatible with several existing data standards. Parallel structures exist so that either (or both) atomised data and free-text can be accommodated.

The ABCD Schema was ratified as a standard by the Biodiversity Information Standards Taxonomic Databases Working Group (TDWG) in 2005. It was developed as a community-driven effort, with contributions from CODATA, BioCASE and GBIF among other organizations.

ABCD Zoology

ABCD Zoology is an application profile of ABCD tailored for use in zoological contexts. It was the first official application profile to use the RDF-based version 3.0 of ABCD.

Darwin Core

A body of standards, including a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries.

Sponsored by Biodiversity Information Standards (TWDG), the current standard was last modified in October 2009.

EML (Ecological Metadata Language)

Ecological Metadata Language (EML) is a metadata specification particularly developed for the ecology discipline. It is based on prior work done by the Ecological Society of America and associated efforts (Michener et al., 1997, Ecological Applications).

GBIF Metadata Profile

Established by a global network of countries and organizations, GBIF is a web portal promoting and facilitating the mobilization, access, discovery and use of biodiversity data. The portal uses a profile of EML; a How-to Guide and Reference Guide for using the profile are available.

OME-TIFF (Open Microscopy Environment TIFF)

A specification of how to embed OME-XML metadata within a TIFF or BigTIFF image file.

OME-XML (Open Microscopy Environment XML)

OME-XML is a vendor-neutral file format for biological image data, with an emphasis on metadata supporting light microscopy. It can be used as a data file format in its own right, or as a way of encoding metadata within a TIFF or BigTIFF file (for which purpose there is the OME-TIFF specification).

The standard is maintained by the Open Microscopy Environment Consortium, and was last updated in June 2012.

Wildlife Disease Data Standard

Our goal with the wildlife disease data standard is to describe interactions between hosts and parasites with sufficient detail and structure as to be useful, but not burdensome on the end user. In this case a parasite can be anything from a micro-parasite like a virus to a macro-parasite like a tick. We use this broad term because systems are complicated and a researcher may want to monitor interactions at multiple levels. The standard has two components disease data and project metadata. The disease data component describes the contents and structure of data related to the detection (or not) of a parasite in/on a given host and is focused on data exchange. The project metadata component describes the contents and structure of data related to the creation of the disease data component and is focused on data discovery. The disease data component allows us to create a collection of datasets that can be re-used, aggregated, and shared, while the project metadata component provides context for the data, makes it easier to find the dataset, and gives clear information about attribution and use