Annotation guidelines

This page contains the most current version of ENVO's general annotation guidelines. If you would like further information or clarification, please contact us.

Annotating environments with EnvO classes
An annotation of an entity's environment with EnvO classes will feature at least one class from each of the biome, environmental feature, and environmental material hierarchies of the ontology. While no formal relations between the entity of interest and EnvO classes are currently defined, general annotation guidelines are presented below.

Notes on microbial samples
Annotating microbial environments present a special case of ENVO annotation. Unless very fine-grained information about the surroundings of the microbe (or, more likely, the microbial community) is available, most ENVO annotations will actually target a small portion of the environmental material that was sampled. For example, one would annotate the environment of the gram of sediment sampled, which was then processed for metagenomic analysis. Additional notes are presented in indented sub-sections of each section below.

Biome classes
EnvO's biome class and its subclasses are intended to identify the ecosystem in which an entity of interest is embedded (i.e. the entity is a component of that system). In order for an ecosystem to qualify as a biome, ecological communities (or representatives thereof) resident in an ecosystem must have evolved adaptations to that ecosystem. Thus, biomes possess an evolutionarily consequential degree of temporal and spatial stability. Currently, instances of EnvO's biome class (or its subclasses) are not dependent on spatial or temporal scale.

Notes on "biomes" in the microbial realm
Due to the potentially rapid rate of microbial adaptation (relative to macro-organisms), it may be argued that microbial "biomes" with conserved community adaptations may exist at small spatial scales. This is at odds with the predominant usage of the term "biome" by most ecologists. Nonetheless, we will host well-defined and empirically supported small-scale biome classes if they are requested, noting the discrepancy with most existing and accepted classifications. 

In addition to any small-scale biome classes, we encourage annotators to use broad-scale biome terms. Consider, for example, a mucus sample from an intestine (intestine environment [ENVO:2100002]) destined for microbiome characterisation. While there are microbial communities which show adaptations to this environment (hence, rendering it a potential "biome"), it is vital to record if these communities were embedded in, e.g., an urban biome [ENVO:01000249], a mangrove biome [ENVO:01000181], or a neritic epipelagic zone biome [ENVO:01000042]. Such information will grant useful and actionable perspectives on what ecological forces the microbial entities in this sample are exposed to, allowing valuable data discovery and mobilisation.

Environmental feature classes
EnvO's environmental feature class and its subclasses are intended to identify environmental entities which have a strong, causal influence upon an entity of interest at the time of observation or sampling. For example, consider the observation of a camel watering at an oasis. While the camel is a component of a desert biome [ENVO:01000179], it is strongly influenced by a desert oasis [ENVO:00000156] during the observation. Multiple subclasses of environmental feature may be relevant to a given observation or sample.

Notes on environmental features relevant at the micro-scale
The material entities that are strongly influencing a microbial community are likely to be both micro- and macroscale entities. For example, a cold seep and a nearby particle of marine snow can both be said to have strong causal influence on a microbe or microbial community. We will be happy to add any classes that are needed, on request. 

Environmental material classes
EnvO's environmental material class and its subclasses are intended to identify the medium or media present in an environment displaced by or in contact with a given entity. A pelagic fish swimming in the middle of the Atlantic Ocean would thus have ocean water [ENVO:00002151] as its environmental material. Similarly, an individual from the species Helicobacter pylori found in the human gastric mucosa could be annotated with mucus [ENVO:02000040] as its environmental material. Many entities will displace more than one environmental material and, ideally, all of these should be identified.

Notes on environmental materials at the micro-scale
Envrionmental materials are likely to be applicable across most scales, including the micro-scale. Should users annotating microbial lifeforms require any further classes, please request them.


Comments