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Instructions and Guidelines for use of Controlled Vocabularies in IOOS-compliant data services
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Vocabularies

IOOS Instructions and Guidelines for use of Controlled Vocabularies in IOOS-compliant data services

Outline

Introduction

Controlled vocabularies clarify the meaning of common concepts and enable more interoperable data systems through more precise definitions and machine readable online references. This document describes the policies and relevant controlled vocabularies that have been adopted or developed by the IOOS community, including context and specific instructions for use and implementation in data services. They primarily target SOS service requests, but are of general applicability in other services and IOOS DMAC areas as well. The content is intended primarily to serve consumers and providers, including software developers and data managers.

All controlled vocabularies and vocabulary mappings developed or adopted by IOOS (except for Darwin Core biological terms) are currently hosted on the Marine Metadata Interoperability (MMI) Ontology Registry and Repository. These IOOS-endorsed vocabularies encompass all vocabularies required to support SOS and other data services: platform types, observed properties (also known as parameters, variables or phenomena), organizations, societal sectors, data decriptor definitions, etc.

Referencing Vocabulary Terms

Terms on MMI-hosted vocabularies are accessible as URL references pointing to human-readable HTML pages; URL's are also available for machine-friendly formats like JSON and RDF. In IOOS SOS and other data services, vocabulary terms must be referenced using complete, valid MMI term URL's, or if the service syntax requires it, the URL separated into two parts: vocabulary base URL and term name. For example:

MMI vocabulary terms are case sensitive and must be referenced accordingly.

Specific term referencing patterns vary depending on service response encoding standards. IOOS SOS Milestone 1.0 response provide complete illustrations of all SOS vocabulary term referencing patterns.

REST access to machine-friendly formats for MMI terms is straightforward, and is obtained by simply adding a format extension to the term reference URL; for example, see the JSON and RDF responses available for the acidity example above.

Vocabulary Selection and Use

The first step to using controlled vocabularies is finding an appropriate one. Criteria for selecting the best controlled vocabulary should be based on: Content; Is it community-maintained? Is it well-managed? Is it interoperable? IOOS-endorsed vocabularies described in this document generally meet these criteria; all terms found on these vocabularies are supported.

Vocabulary users are required to search terms from IOOS-endorsed registered vocabularies on MMI or other well-established, community maintained vocabulary systems before proposing new terms.

The Climate and Forecast (CF) Standard Names Parameter Vocabulary plays a central role in IOOS vocabulary policies. It is intended to be the first-priority source for observed property names and definitions to be referenced in IOOS SOS service requests. In the case of CF compliant netCDF files or OPeNDAP equivalent, the CF standard names parameter vocabulary is the only appropriate vocabulary to use for the standard_name variable attribute. This preference exists to support interoperability with the wider community using CF. However, the scope of CF standard names is limited, and as such this vocabulary will often be insufficient.

The steps below provide an outline of the general term identification and selection process to be followed by data providers:

  1. Search Primary Vocabularies When available and in wide use, IOOS will strive to adopt and support existing community vocabularies. Such "primary", IOOS-endorsed vocabularies should be searched first for selecting terms. Currently the use of primary community vocabularies is largely limited to Observed Properties.
  2. Search Secondary Vocabularies. When a relevant term is not found among primary vocabularies, IOOS-maintained "secondary" vocabularies should be searched. Such vocabularies are hosted on MMI and are described in the sections below, by vocabulary topic.
  3. Propose and Adopt New Terms. When primary and secondary vocabularies don't contain a relevant term, a new term can be adopted by borrowing from other, non-IOOS vocabularies, or developing it following common naming conventions such as CF Standard Names naming conventions. The data provider does not need approval before implementing new terms. However, the provider must confer with the IOOS Program Office about new terms, in order to maintain the highest level of interoperability. The IOOS Program will facilitate the process to include new terms in the appropriate IOOS registered vocabulary or seek approval of term with the CF standard community or another accepted vocabulary standards group. The IOOS Program will notify the data provider when the term has been registered.

This section describes the categories and specific instances of controlled vocabularies IOOS currently supports. Brief instructions for usage are provided, including links to more detailed resources. Additional, related concepts are also used in IOOS services, some of which have also been implemented as MMI vocabularies but have not been fully endorsed and described by IOOS.

Observed Properties

IOOS supports the inclusion and standard referencing of a large set of observed properties (also referred to as phenomena, parameters, or variables). Any property encompassed by the following vocabularies is supported:

  1. Primary Vocabularies
  1. Secondary Vocabularies
  • IOOS Parameter Vocabulary v.2.0. An MMI-hosted vocabulary created via an IOOS community polling of terms in use by the 11 RA's in 2009-2010, and a follow-up process of QA/QC, refinement and consolidation of duplicates. It encompasses additional physical, chemical and biological terms not found among CF Standard Names. For convenience and completeness, this vocabulary incorporates CF terms that are widely used in IOOS. An MMI-based ontological mapping has been created between IOOS Parameter and CF terms, such that a reference to a term in one vocabulary is automatically linked to an appropriate term on the other vocabulary if such a match exists.
  • IOOS Biologicah Data Terminology. A vocabulary that lists biological data fields with names, descriptions, and format notes. It was based on ratified Darwin Core, Dublin Core and proposed IOOS vocabularies. XML guide was based on Darwin core XML guidance. CF Conventions had been applied to biological data definition at the field level.
  1. Vocabularies registered on MMI
  • US IOOS and OBIS-USA Marine Biogeography Terms v2.1 The following table contains the Darwin Core and MBG Extension terms that are used by OBIS-USA and US IOOS. The collection of terms published here constitutes the version of the standards referred to as MBG 2.1. Darwin Core terms are from the TDWG-Ratified Darwin Core reference at http://rs.tdwg.org/dwc/terms/index.htm MBG terms ("Marine BioGeography") are those terms added through the Darwin Core extension protocol to meet specific requirements identified by OBIS-USA and US IOOS.
  • IOOS Core Variables to Climate Forecast Standard Name Map Mapping of IOOS core variables to climate forecast (CF) standard names (v27)
  • IOOS Parameter to Climate Forecast Standard Name Map Mapping of IOOS parameter vocabulary (v2) to climate Forecaset (CF) standard names (v27)
  • IOOS Partner Organizations The list of organizations that are part of the US IOOS Enterprise by supporting observing platforms, collecting data, providing data to the public, managing data, operating models and supporting outreach to the public.
  • IOOS vocabulary for definition of SOS SWE element types Vocabulary of terms reflecting specific IOOS conventions for use in standard SOS SWE elements. For instance, what to expect in a given SWE dataRecord based on the elements definition. The links in the reference attribute give examples where the term is used in the IOOS SOS Milestone 1.0 templates (note that line numbers may be approximate).
  • Metadata Conventions for IOOS Passive Acoustic Recordings (v1.0) This metadata supports the mission of the Integrated Ocean Observing System (IOOS) for acquisition, archiving, and dissemination of ocean passive acoustic data. This host metadata list describes passive acoustic datasets from various platforms and sensors.
  • A metadata convention for animal acoustic telemetry data The purpose of the metadata convention for animal acoustic telemetry data document is to describe the conventions for the attribute fields necessary to describe tag and receiver and detections.
  • IOOS Biological Terms This is a vocabulary of biological/ecological terms intended to be used by the IOOS observing community. The list will expand with the need for additional terms.
  • A metadata convention for processed acoustic data from active acoustic systems (v1.0) The purpose of this document is to describe a metadata convention that details the attribute fields necessary to describe processed water column acoustic volume backscatter data (Sv (dB re 1 m2) , Simmonds and Maclennan (2005)) obtained from active acoustic systems. Processed Sv data are generated by applying procedures to the instrument acquired acoustic data that address data quality and calibration and, in many cases, resampled to a lesser resolution than the acquired data. Unless stated otherwise in the metadata, appropriate calibration offsets and time varied gain (TVG) corrections will have been applied. Metadata attribute fields are provided that will allow description of processing procedures specific to the data set. Adhering to this metadata convention will facilitate discovery and exchange of processed acoustic data while ensuring its archivability and longevity.
  • IOOS Vocabulary and Category Definitions
  • IOOS Platform Vocabulary The IOOS Platform Vocabulary is a list of platform types and their definitions, references and links to example images. Lists of possible platform types were extracted from the 2011 IOOS Asset Inventory and IOOS Regional Build-Out Plans and SECOORA Asset Inventory. A platform in this context is a structure or vehicle designed to hold one or more sensors such that the intended oceanographic or atmospheric variable(s) can be monitored or measured in a manner designed for the ocean observing system or scientific hypotheses. Herein, we attempt to describe the nature of the different types and provide a hierarchy through SKOS mappings (see map_platform) to assist data managers to find the type need to insert into IOOS SOS templates.
  • IOOS Platform to MMI Platform Ontology Map
  • IOOS Platform to IOOS Platform Hierarchy Within the IOOS Platform Vocabulary, some types of platforms can be considered more general while others have more specific characteristics such as motility and associated environments. The categories are mapped using simple broaderThan (>) and narrowerThan (<) relationships. SPARQL searches list the hierarchy, thus helping data managers pick platformType for SOS and allow IOOS Asset Inventory to search SOS based on different categories.
  • Harmonic Constituent Definitions List of definition for harmonic constituents for NOAA's Center for Operational Oceanographic Products and Services (CO-OPS).
  • IOOS Parameter Vocabulary v2.0 This is a vocabulary of the parameters used in IOOS. It has been developed, in coordination with SECOORA, the COARDS Climate-Forecast Standard Names, and input from the 11 Regional Associations in IOOS and the NOAA IOOS Program Office.
  • Datum Definitions List of definition for datums for NOAA's Center for Operational Oceanographic Products and Services (CO-OPS).
  • Water Level Definitions List of definitions for water level for NOAA's Center for Operational Oceanographic Products and Services (CO-OPS)related to qc flags (http://mmisw.org/ont/mmi/resourcetype/qualityflag).
  • Ocean Acidification Definitions This is a list of ocean acidification terms for use by the ocean observing community.
  • CO-OPS QC Flag Definitions A list of NOAA's Center for Operational Oceanographic Products and Services (CO-OPS) quality control flags.
  • IOOS Core Variable Vocabulary IOOS Core Variables in Table 3-3, in U.S. Integrated Ocean Observing System: A Blueprint for Full Capability Ver 1.0 (Nov 2010). http://www.ioos.gov/library/us_ioos_blueprint_ver1.pdf. Accessed July 31, 2012.
  • IOOS Parameter to IOOS Parameter Map Mapping of IOOS Parameter Vocabulary to terms within the IOOS Parameter Vocabulary.
  • IOOS Societal Benefit Area Definitions IOOS Societal Benefit Areas in Table 3-3, in U.S. Integrated Ocean Observing System: A Blueprint for Full Capability Ver 1.0 (Nov 2010). http://www.ioos.gov/library/us_ioos_blueprint_ver1.pdf. Accessed July 31, 2012.
  • IOOS Category Vocabulary Additional Categories (not listed in IOOS Core Variables Table 3-3).
  • IOOS Core Variable Map Mapping of IOOS Parameter Vocabulary to IOOS Core Variables.
  • IOOS Societal Benefit Areas Map Mapping of IOOS Societal Benefit Areas to IOOS Core Variables.
  • IOOS Organization Societal Sector IOOS Organization Societal Sector. This vocabulary does not distinguish non-US organizations as such, and should be applicable within their national contexts; for example, a Canadian provincial agency can be described as "gov_state".
  • IOOS Vocabulary v1.0 IOOS Vocabulary Version 1 from the "Guide for IOOS Data Providers Version 1.0, June 2, 2006". This vocabulary is currently under consideration as an official standard for the IOOS Data Management and Communications (DMAC) Steering Team.

Haines et al (2012) (1) have provided a detailed discussion of IOOS vocabulary strategy and use regarding observed properties, focusing mainly on physical and chemical properties (CF Standard Names and IOOS Parameter Vocabulary, above).

Usage in SOS request parameters and XML responses. See the IOOS SOS Milestone 1.0 response templates for complete implementation details and direct reference.

SOS Operation Request parameters Response: XML block (XPath)
GetCapabilities - /sos:Capabilities/ows:OperationsMetadata/ows:Operation/ows:Parameter/ows:AllowedValues/ows:Value
GetCapabilities - /sos:Capabilities/sos:Contents/sos:ObservationOfferingList/sos:ObservationOffering/sos:observedProperty
GetObservation TimeSeries feature-type, multi-sensor response
GetObservation observedProperty /om:observedProperty
GetObservation observedProperty /om:result/swe:DataStream/swe:DataChoice/swe:item/swe:DataRecord/swe:field/swe:Quantity
DescribeSensor - /sml:SensorML/sml:member/sml:System/sml:components/sml:ComponentList/sml:component/sml:System/sml:outputs/sml:OutputList/sml:output/swe:Quantity[@definition]
  • None, Not applicable_

* Preceded by /om:!ObservationCollection/om:member/om:Observation_

Selecting a vocabulary term

TODO: This section seems redundant with above. Combine the two.

The term identification and selection procedure described above should be used. a search for terms should start with Primary Vocabularies for observed properties, particularly the CF Standard Names parameter vocabulary. Where equivalent or nearly equivalent terms exist, CF terms are preferred over DwC terms. If an appropriate observed property term is not found among primary vocabularies, the secondary IOOS vocabularies listed above should be searched.

If the desired parameter is not found on primary or secondary vocabularies, IOOS should be notified and engaged to discuss adding the term to the IOOS Parameter Vocabulary, following a publicized and accepted process that's reasonably fast and a reasonably small burden on participants. In parallel, IOOS will maintain an engagement with the CF community to discuss adding parameters that are not currently present.

Composite Properties

The CF standard names vocabulary only defines scalar properties. Previously, IOOS defined three composite ("vector") properties made up of two or more scalar properties: winds, waves and currents. These composite properties are supported via the IOOS Parameter Vocabulary and should be referenced like any other term there (eg: http://mmisw.org/ont/ioos/parameter/wave). Additional descriptions of IOOS guidance regarding composite properties are available from the IOOS SOS Milestone 1.0 WSDD

Station Platform Types

The IOOS Platform Vocabulary references and defines platform types used to describe each station asset. This vocabulary was developed by IOOS (with guidance from MMI) in 2012-2013 through a concerted effort drawing from current needs and previous IOOS and MMI experiences. This effort, the vocabulary itself, and instructions for usage are described elsewhere. The vocabulary of approximately 35 terms provides a consistent terminology to describe a wide array of platform types on which sensors are attached and data sets collected. These terms must be used as classifier entries in SOS DescribeSensor SensorML responses.

Organization Descriptors and Roles

IOOS has implemented as MMI vocabularies two kinds of organization or institutional descriptors: Organization Identifier and Organization Societal Sector.

The MMI-hosted IOOS Partner Organization vocabulary provides list of organizations that serve in one or more IOOS partnership roles. The organization roles currently defined by IOOS are: sponsor, operator, publisher, and parentNetwork.

All organizations, including IOOS, IOOS Regional Associations (RAs) and Federal Agencies, should be referenced using terms corresponding to standard RA and agency acronyms (eg, GLOS, SECOORA, USACE) as listed in the IOOS Partner Organization vocabulary.

Asset platform sponsorship is defined as financial or other kinds of support. Platforms that are partially or fully supported by IOOS must be attributed with a sponsor classifier entry of "IOOS" on the SOS DescribeSensor response; more than one sponsor organizations may be listed, as appropriate.

Usage in SOS request parameters and XML responses. See the [IOOS SOS Milestone 1.0 response templates] (http://code.google.com/p/ioostech/source/browse/#svn/trunk/templates/Milestone1.0) for complete implementation details and direct reference.

SOS Operation Response: XML block (XPath) Comment
GetCapabilities /sos:Capabilities/ows:OperationsMetadata/ows:Operation/ows:Parameter/ows:AllowedValues/ows:Value Required Keywords
GetObservation - No Organization reference
DescribeSensor /sml:classification/sml:ClassifierList?/sml:classifier[@name="ParentNetwork?"]/sml:Term[@definition="http://mmisw.org/ont/ioos/definition/parentNetwork"]/sml:value *Required ParentNetwork? Also use <sml:codeSpace xlink:href="http://mmisw.org/ont/ioos/organization"/>
DescribeSensor /sml:classification/sml:ClassifierList?/sml:classifier[@name="publisher"]/sml:Term[@definition="http://mmisw.org/ont/ioos/definition/publisher"]/sml:value Required Publisher. Also use <sml:codeSpace xlink:href="http://mmisw.org/ont/ioos/organization"/>
DescribeSensor /sml:contact[@xlink:role="http://mmisw.org/ont/ioos/definition/publisher"]/sml:ResponsibleParty?/sml:organizationName Required. Publisher (under contact information)
  • None, Not applicable

* Preceded by /sml:SensorML/sml:member/sml:System

IOOS Organization Societal Sectors

The IOOS Organizational Societal Sector vocabulary distinguishes between different segments of government (eg, federal, state, municipal), and academic, tribal, industry and other divisions. It is currently used primarily to specify the operator sector, corresponding to the organization that manages and operates the monitoring station. The operator's societal sector is attributed as an operatorSector classifier in the SOS DescribeSensor response. The sector vocabulary does not distinguish international, non-US organizations as such, and should be applicable within their national contexts; for example, a Canadian provincial agency should be described with the term "gov_state". The identification of international providers is handled by specifying a required country name in the SensorML Operator role contact information. US-based organizations must be assigned "USA" as the country name.

General and SWE Definitions

The IOOS Vocabulary and Category Definitions is an MMI vocabulary used for clarifying the meaning of roles, classifiers and other general terms used throughout the SOS web services, particularly the DescribeSensor SensorML response. It defines commonly used categories to facilitate interpretation, and may be of general value beyond the SOS services. The IOOS SOS SWE Element Definitions Vocabulary is a narrower MMI vocabulary of definitions that reflect specific IOOS conventions for use in standard SOS SWE elements. References available on the MMI vocabulary page give examples of where to use these terms in IOOS SWE SOS templates.

Keywords

Recommendations for Keywords usage have yet to be developed. In the meantime, for local to regional provider the relevant IOOS RA should be used as a keyword, using the spelling from the IOOS Organization vocabulary. Additional recommended keywords include geographical regions and parameters (observed properties) served.

Higher-level categories and vocabulary mappings

The background, IOOS use, and mappings of high-level categories and vocabulary mappings vocabularies for observed properties is partially described in (1). Terms from these vocabularies may be useful as service Keywords and for other data-discovery uses. These MMI-based resources include:

Units of Measure

Units of Measure do not make up a vocabulary per se, but rather a mix of vocabulary terms and a syntax for combinations. At this time, IOOS encourages but does not require the use of UCUM or UDUNITS; UDUNITS is the de-facto standard in the CF convention. Versions of these units systems should be kept in mind (eg, UDUNITS-1 vs UDUNITS-2). ERDDAP/NOAA CoastWatch has a very useful page that includes comparisons of UDUNITS and UCUM, converters among the units systems, and a discussion of UDUNITS-1 and UDUNITS-2]. Another relevant effort is [QUDT](http://www.qudt.org/ QUDT), previously sponsored by NASA and now managed by a group that includes OGC O&M developer Simon Cox.

Vocabulary Search Testing

Testing capability of SPARQL queries to assist catalog searches

Most catalog services provide some search mechanisms of the metadata fields. However, these tend to be limited to exact matches or specific fields but not able to find data that is somewhat related or same data that is labeled differently. Searching for like or similar terms is an important step towards improving the search capability within data catalogs like THREDDS or geoportal catalog services. In this section, IOOS is testing automated search capabilities and discovery of terms based on relationships established in mapping vocabulary. This is an attempt to create a tunnel or mechanism by which more intelligent searches can be made. But what is returned is only as good as the SPARQL query and the mappings in the vocabulary.

SPARQL Endpoint

Numerous examples exist in PERL, Python, and HTML Forms that illustrate how to issue SPARQL queries to vocabulary search services. SPARQL Endpoints can return the data in different formats (HTML, JSON, CSV, RDF, N3), but accessing all these formats is not always obvious. Of the Python code, SparqlWrapper seems to be the most robust (note: a github fork is also available). The MMI Endpoint returns XML, CSV, JSON, and HTML. As a proof-of-concept, python script examples were created to show how to submit a SPARQL query with a JSON return, being the easiest format of response to work with python.

SPARQL - IOOS Examples

SPARQL - Python Examples

CSW - Python Examples

Visualizing Vocabularies, Mappings, and Search Results

Developing recipes for geoportal programmers to issue SPARQL queries to MMI ORR is one key to demonstrating how MMI ORR can enhance catalog search. Another key to this development is to visualize what the search results are. Visualizing the terms and their mappings will be the next step in making registered vocabs on MMI ORR more useful.

Examples

References

(1) Haines, S., V. Subramanian, E. Mayorga, D. Snowden, R. Ragsdale, C. Rueda and M. Howard. 2012. IOOS vocabulary and ontology strategy for observed properties. Proc. MTS/IEEE Oceans'12 (Hampton Roads, VA), doi:10.1109/OCEANS.2012.6405083. Final, submitted paper is available here as pdf.

(2) Graybeal, J., A. W. Isenor, and C. Rueda. 2012. Semantic mediation of vocabularies for ocean observing systems. Computers & Geosciences 40: 120-131, doi:10.1016/j.cageo.2011.08.002 pdf available here

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