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The Ecosystem Ontology (ECSO)

ECSO is currently in development (as of 12/2018) and should not be used for semantic annotations yet. This status is expected to change in the near future. The latest edits to the ontology may be found in the ECSO8.owl file within the ECSO8-add_non-carbon_measurements branch (

ECSO expresses 'Measurement Types' to describe measurements present in raw data. It uses the OBOÉ observation and measurements design pattern (OBOE: to capture both the 'entity of interest' and 'characteristic measured'. ECSO is intended to be used with terms in other OWL ontologies, including ENVO, PATO, CHEBI, BCO and PCO. It is currently focused on carbon and associated measurements.

Introduction to this directory

This directory stores ontologies related to scientific observations.

This is meant to be a collaborative space as we develop ontologies that meet the annotation goals in phase 2 of the DataONE project. Partial support for these efforts also provided through the NSF Scientific Observations Network, "SONet" project, NSF INTEROP #0753144.

Candidate ontologies include:


11JUL2018 MPS status of d1-ECSO in GitHub was that we had three branches-- master, run4 (the one to which the URL's resolved), and ArcticECSO (Elizabeth's branch?). These all had outdated imports of ENVO and PATO that required refreshing, and had problems, both before and after getting new IMPORTs, with how these displayed in Protegé-- with many missing labels.

MPS started afresh with an almost complete import of the latest ENVO, a complete import of the latest UO, and a selective import of PATO (see the saved ONTOFOX files that were used to derive these imports). Protegé 5.2 was then used to load up the ENVO_IMPORT from local filesystem with a DIRECT IMPORT, followed by PATO and UO, and then URL-based imports of OBOÉ and SKOS-DL.

Then careful examination of an earlier "d1-ECSO-generated.owl" file was used to copy terms from the d1-ECSO-generated.owl file into the growing "IMPORT"-based ontology.

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