SCAR-MarBIN Data Schema (OBISschema v1.1)
Below is a table with the data schema adopted by OBIS (July 2005), and which is now in use at SCAR-MarBIN. The OBIS schema is an extension of DarwinCore 2. Following this standard allows seamless data exchange between databases through the Internet. You can have more information on the implementation of the OBIS schema here. You can download a template table here to start encoding your data immediately, and according to OBIS standards.
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. |
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 | OBIS does not encourage the use of this field - it is a legacy field. Indicates who gave the record to the data provider. Can indicate a literature citation, an electronic dataset, etc. Is used to provide credit. |
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 |
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 http://gcmd.gsfc.nasa.gov/Data/portals/gcmd/location_search/top.html |
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. |
Observed Individual Count | Optional | 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. |