Ecology Module - serratus-bio/open-virome GitHub Wiki

Ecology

This module displays Geolocation and WWF Biome data derived from BiSsamples

A three-step pipeline was implemented to progressively resolve a geographic location from a subset of contextually-related metadata attributes, when present. The steps are as follows: gather attribute names which are likely to contain geographic information, classify their corresponding attribute values into categorical sources of geographic information, and then resolve the values into valid geographical coordinates depending on their inferred category

Attribute values could reference geographical locations mainly in two ways; either a location name is entered (e.g. country and city names, institutions, landmarks, etc.) or an explicit set of coordinates is provided (e.g. 43.6532°N, 79.3832°W), for which different resolution (i.e. the process of turning a string of text into latitude and longitude coordinates) strategies have to be devised.

A significant number of BioSamples end up having more than one geographical location associated with them due to them having attributes alluding to different kinds of location information (e.g. institution names, sample collection site, etc.).