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Background documents

by bowers last modified Oct 02, 2009 12:58 PM

Some reference materials for the upcoming community meeting, Oct. 7-9, 2009



[1] Extensible Observation Ontology (OBOE)

OBOE is a generic conceptual model for representing observations and measurements, with a primary focus on supporting the description of ecological data sets. OBOE is implemented in OWL-DL and can be used together with the Ecological Metadata Language (EML) for describing and annotating data sets. The following papers describe OBOE in more detail: 


[2] OpenGIS Observations and Measurements Encoding Standard (O&M)

The OGC O&M is a general conceptual (UML-based) model and XML encoding for representing observations and measurements. The current draft of the O&M OpenGIS specification is available here.  The O&M standard defines the observation model used within the other OGC Sensor Web Enablement standards.


[3] CUAHSI Observations Data Model (ODM)

ODM is a relational data model (schema) for storing and retrieving hydrological observations. The aim of the system is to optimize data retrieval for integrated analysis of information collection by multiple investigators. ODM is designed to store hydrologic observations and sufficient metadata about data values for interpreting and using raw measurements. Additional information about the ODM specification is available at the CUAHSI Hydrologic Information System website. The CUAHSI ODM controlled vocabularies are available here. The following papers also describe ODM in more detail. 


[4] ALTER-Net Socio-Ecological Research & Observation Ontology (SERONTO)

SERONTO is an OWL ontology that is based on an earlier version implemented within the ALTER-Net Monitoring and Research Information System (MORIS). The goal of SERONTO is to provide a common model for structuring ecological and socio-ecological observations, to provide a common representation of observation across domains, and to define a common set of domain concepts.  SERONTO is described in more detail here.


[5] Phenotypic Quality Ontology (PATO) 

Unlike the above approaches that focus explicitly on modeling observations, PATO specializes in being an ontology of phenotypic qualities. Phenotypic qualities are types of "measurement traits" or "characteristics" (related to organisms or parts of organisms). The primary use of PATO is for annotation and is part of the OBO Foundry. Detailed information about PATO can be found here.  


[6] Chado Schema

Chado is a relational database schema underlying the Generic Model Organism Database project and is used to represent a variety of types of data used in molecular biology including sequences, sequence comparisons, phenotypes, genotypes, ontologies, and phylogeny. Chado also provides a mechanism for representing feature annotations of sequences in which features are drawn from controlled vocabularies. Chado is divided into a number of modules, each supporting different types of data (example modules include 'organism', 'phenotype', 'phylogeny', 'sequence', 'controlled vocabulary', and 'stock'--information about specimens). More information about Chado and modules can be found here. The following paper also provides additional information about Chado.


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