The OBIS Schema Version 1.1

Last updated on Wed, 2014-11-19 10:27. Originally submitted by evberghe on 2010-12-13 16:35.

Definition of the data standard OBIS uses; an extension of DarwinCore 2; 08 July 2005

Name Required Type Description
Date Last Modified Optional for OBIS (Required for GBIF/Darwin Core servers) DateTime The date and time the record was last modified. Format: ISO 8601 compliant stamp in UTC (GMT) when the record was last modified. Example: "November 5, 1994, 8:15:30 am, US Eastern Standard Time" would be represented as "1994-11-05T13:15:30Z" (see W3C Note on Date and Time Formats - http://www.w3.org/TR/NOTE-datetime). While this field is required by the Darwin Core, OBIS can accommodate datasets without it.
Institution Code Required Text A "standard" code identifier that identifies the institution to which the collection belongs, if there is one. Use the code that is "standard" in your discipline, if there is one (no global registry exists for assigning institutional codes). If not, use a short version of the name of the institution. (e.g. "NMNH" for Smithsonian National Museum of Natural History or "Duke" for Duke University).
Collection Code Required Text A unique alphanumeric value which identifies the collection within the institution (e.g. "FishBase").
Catalog Number Required Text / Numeric A unique alphanumeric value which identifies an individual record within the collection, i.e. the key. It is recommended that this value provides a key by which the actual specimen/observation can be identified. If the specimen/observation has several items such as various types of preparation, this value should identify the individual component of the specimen.
Record URL Optional Text Gives the web address of the page where more information on this particular record (not on the whole dataset) can be found.
Scientific Name Required Text The full name of lowest level taxon the Cataloged Item can be identified as a member of; includes genus, specific epithet, and subspecific epithet (zool.) or infraspecific rank abbreviation, and infraspecific epithet (bot.) Use name of suprageneric taxon (e.g., family name) if Cataloged Item cannot be identified to genus, species, or infraspecific taxon. Check spelling of names against World Register of Marine Species; see notes with the schema for further details on taxonomy.
Basis of record Highly Recommended Text An abbreviation indicating whether the record represents an observation (O) (this can include a visual observation, a survey catch, a commercial landing record, etc), a collected living organism, such as a tree in a botanical garden (L), a specimen in a collection/museum (S), a collected germplasm/seed (G), a photo (P), or derived from literature, where original basis unknown (D).
Source Optional Text Indicates who gave the record to the data provider. Can indicate a literature citation, an electronic dataset, etc. Is used to provide credit and to leave an 'audit trail'. Especially in datasets of mixed origin, this field is important and its use highly recommended.
Citation Highly Recommended Text Indicates how this record should be attributed if used. (e.g. "Jones, T. 2005. Electronic atlas of eel distributions version 3. www.eels.com"). It can contain several layers of credit - e.g. of the original data provider and an intermediate data portal. If all records within a dataset should be credited the same way, the citation field in the dataset metadata can be used instead. It should be <4000 characters long.
Kingdom Highly Recommended Text The kingdom to which the organism belongs. Check classification against World Register of Marine Species; see notes with the schema for further details on taxonomy.
Phylum Optional Text The phylum (or division) to which the organism belongs
Class Optional Text The class name of the organism
Order Optional Text The order name of the organism
Family Optional Text The family name of the organism
Genus Highly Recommended-when known Text The genus name of the organism. While this field is highly recommended when the identification to genus is known, it should not be filled in if the identification cannot be made down to genus with confidence
Subgenus Optional Text The subgenus name of the organism
Species Highly Recommended-when known Text The specific epithet of the organism
Subspecies Optional Text The sub-specific epithet of the organism
Scientific Name Author Optional Text The author of a scientific name. Author string as applied to the accepted name. Can be more than one author (concatenated string). Should be formatted according to the conventions of the applicable taxonomic discipline. Parentheses should be applied as appropriate for the relevant rules of Nomenclature (ICZN/ICBN) for the name. For example, if the name of an animal has undergone a genus revision, the authority and year should be placed in parentheses. Example: (Hastings, 1986)
Identified By Optional Text The name(s) of the person(s) who applied the Scientific Name to the Cataloged Item.
Year Identified Optional Numeric The year portion of the date when the Collection Item was identified; as four digits [-9999..9999], e.g., 1906, 2002.
Month Identified Optional Numeric The month portion of the date when the Collection Item was identified; as two digits [01..12].
Day Identified Optional Numeric The day portion of the date when the Collection Item was identified; as two digits [01..31].
Type Status Optional Text Indicates the kind of nomenclatural type that a specimen represents, for example holotype, syntype, paratype, lectotype, paralectotype, neotype, schizotype, allotype, hapantotype. OBIS users should select from this list when applicable, but can enter other type categories as needed. In rare cases, a single specimen may be the type of more than one name.
Collector Number Optional Text An identifying "number" (really a string) applied to specimens (in some disciplines) at the time of collection. Establishes a link between different parts/preparations of a single specimen and between field notes and the specimen.
Field Number Optional Text A "number" (really a string) created at collection time to identify all material that resulted from a collecting event, e.g. station or sample numbers
Collector Optional Text The name(s) of the collector(s), people or organisation(s) responsible for collecting the specimen, taking the observation, fishing the catch or doing whatever is the underlying basis of the record.
Year Collected Highly Recommended Numeric The year (expressed as an integer) the sample/observation/record event occurred. The full year should be expressed (e.g. 1972 must be expressed as "1972" not "72"). Must always be a four digit integer. Where the event covers a range of values for year, indicates the mid-point of that range.
Start Year Collected Optional Numeric For samples/observations/record events that were taken over time this gives the start year of the collecting event. The full year should be expressed (e.g. 1972 must be expressed as "1972" not "72"). Must always be a four digit integer
End Year Collected Optional Numeric For samples/observations/record events that were taken over time this gives the end year of the collecting event. The full year should be expressed (e.g. 1972 must be expressed as "1972" not "72"). Must always be a four digit integer
Month Collected Highly Recommended Numeric The month of year the sample/observation/record event occurred in the field. Where the event covers a range of values for month, indicates the mid-point of that range. Leave blank if even spans multiple years.
Start Month Collected Optional Numeric For samples/observations/record events that were taken over time this gives the start month of the collecting event. Possible values range from 01...12 inclusive
End Month Collected Optional Numeric For samples/observations/record events that were taken over time this gives the end month of the collecting event. Possible values range from 01...12 inclusive
Day Collected Highly Recommended Numeric The day of the month the sample/observation/record event occurred in the field. Possible value ranges from 01..31 inclusive. Where the event covers a range of values for day, indicates the mid-point of that range. Leave blank if event spans multiple months.
Start Day Collected Optional Numeric For samples/observations/record events that were taken over time this gives the start day of the collecting event. Possible value ranges from 01..31 inclusive
End Day Collected Optional Numeric For samples/observations/record events that were taken over time this gives the end day of the collecting event. Possible value ranges from 01..31 inclusive
Julian Day Optional Numeric The ordinal day of the year for the sample/observation/record event; i.e., the number of days since January 1 of the same year. (January 1 is Julian Day 1.). Should be an integer from one to 365, i.e. of the form (([0-3][0-9][0-9)|([0-9][0-9)|([1-9])). Where the event covers a range of values for Julian day, indicates the mid-point of that range. Leave blank if event spans multiple years.
Start Julian Day Optional Numeric For samples/observations/record events that were taken over time this gives the start ordinal day of the year for the collecting event; i.e., the number of days since January 1 of the same year. (January 1 is Julian Day 1.). Should be an integer from one to 365, i.e. of the form (([0-3][0-9][0-9)|([0-9][0-9)|([1-9])).
End Julian Day Optional Numeric For samples/observations/record events that were taken over time this gives the end ordinal day of the year for the collecting event; i.e., the number of days since January 1 of the same year. (January 1 is Julian Day 1.). Should be an integer from one to 365, i.e. of the form (([0-3][0-9][0-9)|([0-9][0-9)|([1-9])).
Time of Day Highly Recommended Numeric The time of day a specimen was collected expressed as decimal hours from midnight (e.g. 12.0 = mid day, 13.5 = 1:30pm)
Start Time of Day Optional Numeric For samples/observations/record events that were taken over time this gives the start time of day of the collecting event expressed as decimal hours from midnight local time (e.g. 12.0 = mid day, 13.5 = 1:30pm)
End Time of Day Optional Numeric For samples/observations/record events that were taken over time this gives the end time of day of the collecting event expressed as decimal hours from midnight local time (e.g. 12.0 = mid day, 13.5 = 1:30pm)
Time Zone Highly Recommended Text Indicates the time zone for the Time of Day measurement, given as +hh:mm or -hh:mm from Coordinate Universal Time (also called Greenwich Mean Time). For example, a local time for Tokyo would have "+09:00" in the Time Zone field.
Continent Ocean Optional Text The continent or ocean from which a specimen was collected or in which the sample/observation/record event occurred. OBIS recommends that ocean names follow the NASA Global Change Master Directory list of Bodies of Water
Country Optional Text The country or major political unit from which the specimen was collected or in which the sample/observation/record event occurred. ISO 3166-1 values should be used. Full country names are currently in use. A future recommendation is to use ISO3166-1 two letter codes or the full name when searching
State Province Optional Text The state, province or region (i.e. next political region smaller than Country) from which the specimen was collected or in which the sample/observation/record event occurred. There is some suggestion to use the values described in ISO 3166-2, however these values are in a continual state of flux and it appears unlikely that an appropriate mechanism (by ISO) will be in place to manage these changes. Hence it is recommended that where possible, the full, unabbreviated name should be used for storing information. The server should optionally handle abbreviations as an access point. Note: this is a recurring theme (country and state) abbreviations. Check the existence of an attribute type to deal with abbreviations from the bib-1 profile
County Optional Text The county (or shire, or next political region smaller than State / Province) from which the specimen was collected
Locality Optional Text The locality description (place name plus optionally a displacement from the place name) from which the specimen was collected or in which the sample/observation/record event occurred. Where a displacement from a location is provided, it should be in un-projected units of measurement (e.g. "7 miles north of Hawaii"). It is strongly recommended that Locality be used, to allow cross-checking of the latitude and longitude fields
Longitude Required Numeric The longitude of the location from which the specimen was collected or in which the sample/observation/record event occurred. This value should be expressed in decimal degrees (East & North = +; West & South = -). GPS-derived data should be referenced to the WGS/84 datum.
Start Longitude Optional Numeric For samples/observations/record events better represented as line features rather than point features (e.g. extended trawls or transects) this indicates the starting longitude location from which the specimen was collected. Express in decimal degrees (East & North = +; West & South = -). GPS-derived data must use the WGS 84 geodetic reference system (http://www.wgs84.com/).
End Longitude Optional Numeric For samples/observations/record events better represented as line features rather than point features (e.g. extended trawls or transects) this indicates the ending longitude location from which the specimen was collected. Express in decimal degrees (East & North = +; West & South = -). GPS-derived data must use the WGS 84 geodetic reference system (http://www.wgs84.com/).
Latitude Required Numeric The latitude of the location from which the specimen was collected. This value should be expressed in decimal degrees (East & North = +; West & South = -). GPS-derived data must use the WGS 84 geodetic reference system (http://www.wgs84.com/).
Start Latitude Optional Numeric For samples/observations/record events better represented as line features rather than point features (e.g. extended trawls or transects) this indicates the starting latitude location from which the specimen was collected or in which the sample/observation/record event occurred. This value should be expressed in decimal degrees (East & North = +; West & South = -). GPS-derived data must use the WGS 84 geodetic reference system (http://www.wgs84.com/).
End Latitude Optional Numeric For samples/observations/record events better represented as line features rather than point features (e.g. extended trawls or transects) this indicates the ending latitude location from which the specimen was collected or in which the sample/observation/record event occurred. This value should be expressed in decimal degrees (East & North = +; West & South = -). GPS-derived data must use the WGS 84 geodetic reference system (http://www.wgs84.com/).
Coordinate Precision Highly Recommended Numeric An estimate of how tightly the locality was specified in the Latitude and Longitude fields; expressed as a distance, in meters, that corresponds to a radius around the latitude-longitude coordinates. Use NULL where precision is unknown, cannot be estimated, or is not applicable.
Start/End Coordinate Precision Optional Numeric An estimate of how tightly the locality was specified in the Start/End Latitude and Longitude fields; expressed as a distance, in meters, that corresponds to a radius around the latitude-longitude coordinates. Use NULL where precision is unknown, cannot be estimated, or is not applicable.
Bounding Box Optional BOUNDING BOX This access point provides a mechanism for performing searches using a bounding box. A Bounding Box element is not typically present in the database, but rather is derived from the Latitude and Longitude columns by the data provider.
Minimum Elevation Optional Numeric OBIS does not encourage the use of this field - it is a legacy field. The minimum distance in meters above (positive) or below sea level of the collection/record locality.
Maximum Elevation Optional Numeric OBIS does not encourage the use of this field - it is a legacy field. The maximum distance in meters above (positive) or below sea level of the collection/record locality.
Minimum Depth Highly Recommended Numeric The minimum distance in meters below the surface of the water at which the collection/record was made; all material collected was at least this deep. Positive below the surface, negative above (e.g. collecting above sea level in tidal areas).
Maximum Depth Highly Recommended Numeric The maximum distance in meters below the surface of the water at which the collection/record was made; all material collected was at most this deep. Positive below the surface, negative above (e.g. collecting above sea level in tidal areas).
Depth Range Optional-not preferred Text For data sets that have the depth range expressed in one field (e.g. "150-200 m") it can be entered here as free text. Separate, numeric Minimum and Maximum Depth fields are the preferred format; the Depth Range option is included for legacy data sets.
Temperature Optional Numeric The temperature recorded with the collection/record event. Is assumed to be taken at the collection depth. Expressed in degrees Celsius.
Sex Optional Text The sex of a specimen or collected/observed individual(s). The domain should be a controlled set of terms (codes) based on community consensus. Proposed values: M=Male; F=Female; H=Hermaphrodite; I=Indeterminate (examined but could not be determined; U=Unkown (not examined); T=Transitional (between sexes; useful for sequential hermaphrodites); B = Both Male and Female
Life Stage Optional Text Indicates the life stage present. Will require developing a controlled vocabulary. Can include multiple stages for a lot with multiple individuals.
Preparation Type Optional Text The type of preparation (skin. slide, etc). Probably best to add this as a record element rather than access point. Should be a list of preparations for a single collection record.
Individual Count Optional Numeric The number of individuals present in the lot or container. Not an estimate of abundance or density at the collecting locality.
SampleSize Highly Recommended Text Samplesize: the size of the sample from which the collection/observation was drawn. It can be a volume (e.g. for a phytoplankton sample), a linear distance (e.g. for a visual transect or net haul), a surface area (e.g. for a benthic core), etc. This field must also include the units, e.g. ?200 m? for a transect, or ?0.25 m^2? for a benthic grab (use ^ to denote a superscript). Note that when multiple collections/observations are reported from the same physical sample, a code identifying the sample can be placed in the Field_Number field to allow all collections/observations from a single sample to be connected.
Observed Individual Count Highly Recommended Numeric The number of individuals (abundance) found in a collection/record event.
Observed Weight Optional Numeric The total biomass found in a collection/record event. Expressed as kg.
Previous Catalog Number Optional Text The previous (fully qualified) catalog number of the Cataloged Item (or collection/record) event if the item earlier identified by another Catalog Number, either in the current catalog or another Institution / catalog. A fully qualified Catalog Number is preceded by Institution Code and Collection Code, with a space separating the each subelement. Referencing a previous Catalog Number does not imply that a record for the referenced item is or is not present in the corresponding catalog, or even that the referenced catalog still exists. This access point is intended to provide a way to retrieve this record by previously used identifier, which may used in the literature. In future versions of this schema this attribute should be set-valued.
Relationship Type Optional Text A named or coded valued that identifies the kind relationship between this Collection Item (or record event) and the referenced Collection Item. Named values include: "parasite of", "epiphyte on", "progeny of", etc. In future versions of this schema this attribute should be set-valued.
Related Catalog Item Optional Text The fully qualified identifier of a related Catalog Item (a reference to another specimen); Institution Code, Collection Code, and Catalog Number of the related Cataloged Item, where a space separates the three subelements.
Notes Optional Text Free text notes attached to the specimen record
 
OBIS EXPERIMENTAL FIELDS: The following are not part of the current OBIS Schema, but are under consideration for future versions. They represent format recommendations/good data practices.
GML Feature Optional Text Geographic Markup Language(GML) description of the feature for representing complex shapes such as lines and polygons, per Open GIS Consortium (OGC) standards - http://www.opengis.net/gml/01-029/GML2.html.
OBIS is a project of:
IOC-UNESCO
IODE Sponsored by:
Martin International and Les Grands Explorateurs
With in-kind support from:
Marine Geospatial Ecology Lab, Duke University
Universidad Simón Bolívar Flanders Marine Institute

OBIS strives to document the ocean's diversity, distribution and abundance of life. Created by the Census of Marine Life, OBIS is now part of the Intergovernmental Oceanographic Commission (IOC) of UNESCO, under its International Oceanographic Data and Information Exchange (IODE) programme.