Lesson: OBIS standards and formatting

1. Data in OBIS

To publish data in OBIS, datasets that combine species occurrence data with environmental data and sampling details are assembled into three different data files:

  • OCCURRENCES: contains the information about the taxonomy and identification, the occurrence record, and location and time (if no event file).
  • EVENTS: contains the information about the sampling event, coordinate position, time and depth, and can have an hierarchy of events (cruises, stations, samples or subsamples, etc.). Note: Sampling effort and methods are stored in "Measurement or Facts".
  • MEASUREMENTS OR FACTS: contains the information about biotic measurements/facts (abundance, biomass, body size, fatty acid profile, etc.) and abiotic measurements/facts (water temperature, salinity, sampling device, etc.) and sampling facts (e.g. instruments, sample size, sampling effort etc) related to your occurrence record or sampling event.

Datasets are published through IPT (the Integrated Publishing Toolkit). This tools allows you to add metadata (description of the dataset) and map the column names of each file with DarwinCore terms (see Module 3). Once published, OBIS can harvest the dataset and integrate it into the OBIS central database.

Depending on the types of data you can organize your dataset in three different ways:

Case 1: One OCCURRENCE file (Occurrence Core). Entering only the details of the occurrences. This is appropriate when your dataset does not contain any biological or environmental variables or sampling facts. This is often the case for museum collections, grey literature, old research papers, etc.

Case 2: Two sets of files:

  1. OCCURRENCE (Occurrence Core), the same as in the previous case.
  2. MEASUREMENTS (Measurement or Fact extension), including the measurements or facts made on each specimen or sample (e.g. size, abundance, wet weight, life stage, etc).

Case 3: Three sets of files:

  1. EVENT (Event Core), the sampling event details (position, time, depth of each site, station, sample etc).
  2. OCCURRENCE (Occurrence extension), the same as in the previous case.
  3. MEASUREMENTS (Measurement or Fact extension), including environmental data, the measurements made on each specimen (e.g. size, wet weight), sampling facts.