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Transport Schema from Maii'tsoh to Darwin Core V2 (NMBCC DwC2 V1.2)


Below is a document describing a draft data exchange standard for interoperability among datasets in the Maii'tsoh database and the NMBCC Central Server. This particular document is based on revisions of the Darwin Core by MaNIS (by John Wieczorek and Barbara Stein on 15 Mar 2003 known as DwC2 V1.13 and subsequent revisions dated 17 June 2003 known as DwC2 V1.14, also known as DwC2 V1.21) of the Darwin Core, version 2 (DwC2). It is recommended that readers become familiar with the concepts and history of metadata standards for natural history collections, and with the Darwin Core in particular. The Taxonomic Database Working Group (TDWG) is also a good source of information on standards, information models, and data dictionaries for biological collections.

The INRAM data exchange standards V1.1 (as revised 23 July, 2004) differ from DwC2 V1.14 by the addition of ColloquialName, MaiitsohRecID field and Export Date. V1.1 reviewed 24 May, 2005 without revision.The NMBCC data exchange standard V1.2 differs by the addition of the IsSensitive field. Revised 20 November, 2007. Notes changed to reflect change in field content 14 May, 2009.


Concept Documentation Notes
DateLastModified ISO 8601 date and time in UTC(GMT) when the record was last modified. Example: "November 5, 1994, 8:15:30 am, US Eastern Standard Time" would be "1994-11-05T13:15:30Z" (see http:// www.w3.org/TR/ NOTE-datetime). Filemaker Pro does not support ISO 8601 date and time in UTC(GMT) and Maii'tsoh prior to V1.23 does not support a Time Last Modified stamp.

Translation assumes data entered in Mountain time zone.

For translation of records without a modification time, the Maii'tsoh Modification Date in YYYY-MM-DD is concatenated with "T07:00:00Z to arbitrarily represent noon Mountain Standard Time.

Maii'tsoh supports many more fields than can be parsed into this schema and a change in any one of these fields can trigger an update of DateLastModified. A change in the DateLastModified value may, therefore, not indicate that a change has occurred iin data provided in this schema.
BasisOfRecord A description indicating whether the record represents an observation, tissue sample, living organism, voucher specimen, germplasm/seed, genetic information, etc. An abbreviation indicating whether the record represents an observation (O), living organism (L), specimen (S), germplasm/seed (G), etc. All of our data to date are specimens (S). Data uploaded to NMBCC in 2009 or later will use "PreservedSpecimen" instead of "S" in anticipation of future Darwin Core standard vocabulary for this field.
InstitutionCode A code that identifies the institution to which the cataloged item belongs. No global registry exists for institutional codes; use the code that is "standard" in your discipline. This attribute must contain no spaces. These values are shown next to name of the collection they represent on the NMBCC Query page. It is actually the code for the collection when this differs from the code used for the overall Institution. So, for example, the code for the Museum of Southwestern Biology Arthropod Division is MSBA and not MSB or UNM (University of New Mexico)
CollectionCode A unique alphanumeric value that identifies the collection within the institution in which the item is cataloged. This attribute must contain no spaces. Values are Arth, Bird, Fish, Herb, Herp, Mamm.
CatalogNumberText An alphanumeric value which identifies an individual cataloged item within the collection. It is recommended that this value provides a key by which the individual cataloged item can be identified. All our data have numeric catalog numbers, but this is the main field we use for accession numbers (herbaria) and catalog numbers (all others). Though Catalog Numbers should be unique within a collection, there are several instances where we know they are not, so this field is never used as key field.
CatalogNumber Numeric The CatalogNumber as a numeric value, if applicable. Allows searching on numeric ranges of CatalogNumbers. Though NMBCC has support for this field, Catalog Number data is typically provided to us only in the CatalogNumberText field.
Collector The name(s) of the collector(s) of the original data for the cataloged item. We have rules for collector name entry that reduce alternative versions of the same collector name. Use "Unknown collector" and "Illegible collector name."
CollectorNumber An identifying string applied to the cataloged item at the time of collection. Serves as a link between field notes and the cataloged items. We maintain separate fields in Maii'tsoh for numeric and alphanumeric collection number and numeric collection number suffixes. For plant collections, "sn" (sans number) is used if no collection number was given. All of these are put into a single field for upload to NMBCC.
FieldNumber An identifying string applied to a set of material that resulted from a single collecting event. Not used by any of our current datasets although we do have the field for it.
YearCollected The four digit year in the Common Era calendar in which the cataloged item was collected. Populated from our fields for "Collection Date" or "Year." Year is used only for incomplete collection dates.
MonthCollected The two digit month of year in the Common Era calendar during which the cataloged item was collected from the field. Populated from our fields for "Collection Date" or "Month." Month is populated in Maii'tsoh only for specimens with incomplete collection dates, but MonthCollected is calculated for all records before export.
DayCollected The two digit day of the month in the Common Era calendar during which the cataloged item was collected from the field. Populated from our fields for "Collection Date" or "Day." Day is populated in Maii'tsoh only for specimens with incomplete collection dates, but DayCollected is calculated for all records before export.
TimeCollected The time of day the cataloged item was collected, expressed as decimal hours from midnight, local time (e.g., 12.0 = noon, 13.5 = 1:30pm). Not in use by any of our current collections. We do not have support for this field in Maiitsoh, though we do have support for it in NMBCC.
VerbatimCollecting Date The verbatim original representation of the date information for the collecting event. Not strictly Verbatim, since we do not record this in our data model. For complete dates, populated from our field for "Collection Date." For incomplete dates (typically a month and year), populated as "January, 2003." For date ranges (our field "Collection Date End" populated), formatted as "12/25/2001 to 1/5/2001." For other date values (our field "season orOtherTextDate" populated with or without values in month or year), populated as "Fall 2001", or "Late January 2001."
FieldNotes A reference to, or flag marking the existence of, notes taken in the field for the cataloged item. Not in use by any of our current collections. We have support for this field in Maiitsoh and in NMBCC.
JulianDay The ordinal day of the year (i.e., the number of days since December 31 of the previous year; January 1 is Julian Day 1) on which the cataloged item was collected. May be derived from the YearCollected, MonthCollected, and DayCollected by the provider. Only populated for records with complete dates.
HigherGeography The combination of all geographic elements less specific than locality. "Like" query operations on this element will search for a substring in any of the higher geography attributes. Includes ContinentOcean, Country, StateProvince, and County. We use commas between terms, as in: North America, USA, New Mexico, Valencia.
ContinentOcean The full, unabbreviated name of the continent or ocean from which the cataloged item was collected. Populated in Maii'tsoh from a reference locality table lookup based on the country entered in the specimens table.
IslandGroup The full, unabbreviated name of the island group from which the cataloged item was collected. Not in use by any of our current collections. We do not have support for this field in Maiitsoh, though we do have support for it in NMBCC.
Island The full, unabbreviated name of the island from which the cataloged item was collected. Not in use by any of our current collections. We do not have support for this field in Maiitsoh, though we do have support for it in NMBCC.
Country The full, unabbreviated name of the country or major political unit from which the cataloged item was collected. We use "USA" for the United States of America.
StateProvince The full, unabbreviated name of the state, province, or region (i.e., the next smaller political region than Country) from which the cataloged item was collected. All data in the NMBCC come from New Mexico (or should).
County The full, unabbreviated name of the county, shire, or municipality (i.e., the next smaller political region than StateProvince) from which the cataloged item was collected. Typically filtered for valid New Mexico county names, "County Unk." or blank. Collections along county lines or where the county is known imprecisely are allowed to be entered as a pair or more of valid county names separated by slashes in alphabetic order (i.e., Bernalillo/Valencia and not Valencia-Bernalillo).
Locality The description of the locality from which the cataloged item was collected, sans geographic information provided in other geographic fields. Some of our collections currently provide coordinate and PLSS information only in locality and not in separate fields.
DecimalLatitude The latitude of the location from which the cataloged item was collected, expressed in decimal degrees. Numeric field populated only as a calculation of a valid georeference.
DecimalLongitude The longitude of the location from which the cataloged item was collected, expressed in decimal degrees. Numeric field populated only as a calculation of a valid georeference.
HorizontalDatum The horizontal geodetic datum to which the DecimalLatitude and DecimalLongitude refer. Usually WGS84 for a valid georeference. The exception is when the label information gives another datum and the label coordinates were the basis of the georeference.
OriginalCoordinate System The name of the system in which the original geographic coordinates were recorded (e.g., "decimal degrees", "degrees minutes seconds", "UTM", etc.). When georeference is from LongLat data, the values are consistent with newer DwC standards, which is to say, allowable values are only Decimal degrees, Degrees decimal minutes, or Degree minute seconds. May also be "UTM" or "PLSS" and if PLSS gives the resolution of the data as georeferenced (TR, TRS, TRS quarter section, or TRS quarter quarter section).
VerbatimLatitude A text representation of the Latitude data in its original format in the source database. Not strictly "verbatim" since this is not recorded in Maii'tsoh. Populated with recreated text representation of latitude with appropriate separators from data entered in the latitude degree, minute, second and direction fields plus any other lat data entered on label.
VerbatimLongitude A text representation of the Longitude data in its original format in the source database. Not strictly "verbatim" since this is not recorded in Maii'tsoh. Populated with recreated text representation of langitude with appropriate separators from data entered in the latitude degree, minute, second and direction fields plus any other long data entered on label.
GeorefMethod A reference to the methods used for determining the coordinates and uncertainties. Methods currently used are the INRAM V1.3 and the Maiitsoh V3.0 protocols. Maiit'soh protocol used only for some LongLat conversions. If version of INRAM protocol isn't given, it is V1.3. INRAM protocol will state whether it is from Automated Coordinate conversion or Manual Georeferencing. In some legacy instances may be populated with "Coordinates from label" in which case it is not a true georeference method and no uncertainty will be present.
CoordinateUncertainty InMeters The upper limit of the distance (in meters) from the given latitude and longitude describing a circle within which the whole of the described locality must lie. Use NULL where the uncertainty is unknown, cannot be estimated, or is not applicable. Should be populated for all georeferences (= all records with decimal long lat data). In some rare cases may be calculated with -888 or -999 signifying that coordinates were generated through a georeferencing process, but an accurate uncertainty estimate was not or could not be generated. Zero is not an allowed value.
LatLongComments Comments about the LatLong determination. Gives information about the locality typing used in a manual georeference or the calculation used in a coordinate conversion. Some legacy data in which no true georeference was created will be populated with "Coordinates from label."
BoundingBox 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 DecimalLatitude and DecimalLongitude columns by the data provider. Not implemented in Maii'tsoh or in the NMBCC.
MinimumElevation InMeters The minimum distance in meters above (positive) or below sea level of the collecting locality. Calculated from our fields for Elevation and Elevation Units.
MaximumElevation InMeters The maximum distance in meters above (positive) or below sea level of the collecting locality. Repeats the value in elevation, unless a value is present in our field for Upper Elevation.
VerbatimElevation A text representation of the Elevation in its original format in the source database. Calculated from our fields for Elevation and Elevation Units showing the original units. If our field Elevation Range is populated, calculated as Elevation Range and Elevation Units.
MinimumDepth InMeters The minimum distance in meters below the surface of the water at which the collection 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). We do not have support for this fields in Maiitsoh. However, Depth may be represented as negative values in the MinimumElevationInMeters field.
MaximumDepth InMeters The maximum distance in meters below the surface of the water at which the collection 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). We do not have support for this fields in Maiitsoh. However, Depth may be represented as negative values in the MinimumElevationInMeters field.
VerbatimDepth A text representation of the Depth in its original format in the source database. We do not have support for this field in Maiitsoh.
ScientificName The full name of lowest level taxon to which the cataloged item can be identified (e.g., genus name, specific epithet, subspecific epithet, etc.)

Authority is included for plant and invertebrate records.

Specimens identified to Genus are recorded as Genus sp. (e.g. Bufo sp.). Specimens identified to a higher rank than genus are recorded as the Lowest Rank Recorded unk. (e.g. Pinales unk., Fabaceae unk.)

HigherTaxon The combination of names of taxonomic ranks less specific than Genus. "Like" query operations on this element will search for a substring in any of the higher taxon attributes. Variously supported for different taxonomic groups. Flowering plants and gymnosperms only have kingdom, phylum, and family.
Kingdom The phylogenetic kingdom to which the cataloged item belongs.  
Phylum The phylogenetic phylum (or division) to which the cataloged item belongs.  
Class The phylogenetic class to which the cataloged item belongs.  
Order The phylogenetic order to which the cataloged item belongs.  
Family The phylogenetic family to which the cataloged item belongs.  
Genus The phylogenetic genus to which the cataloged item belongs.  
Species The phylogenetic specific epithet of the cataloged item.  
Subspecies The phylogenetic subspecific epithet of the cataloged item.  
ScientificNameAuthor The author of the ScientificName. Can be more than one author in a concatenated string. Should be formatted according to the conventions of the applicable taxonomic discipline.  
IdentificationModifier Additional information documenting the taxonomic determination of the cataloged item (e.g., "cf.", "aff.", "subspecies in question", etc.).  
ColloquialName The common or vernacular name for this taxon. The common name. This field is not in Darwin Core2 V1.21, but we have included it anyway.
IdentifiedBy The name(s) of the person(s) who applied the currently accepted ScientificName to the cataloged item. In Maiitsoh, we have the fields Determined By and LastAnnotator. For plants, Determined By is often left blank and LastAnnotator is only filled in if the specimen was annotated. For animals, LastAnnotator is used as a last determiner field (generally populated) and Determined By is interpreted as the Initial Determiner when a different last Determiner exists. In all cases, IdentifiedBy is interpreted as the last determiner or annotater.
YearIdentified The four digit year in the Common Era calendar in which the cataloged item was identified as having the ScientificName. See IdentifiedBy. For all datasets, only the year of the Identification is recorded in Maiitsoh.
MonthIdentified The two digit month in the Common Era calendar during which the cataloged item was identified. We do not have support for this fields in Maiitsoh.
DayIdentified The two digit day of the month in the Common Era calendar during which the cataloged item was identified. We do not have support for this fields in Maiitsoh.
TypeStatus A list of one or more nomenclatural types that the cataloged item represents (e.g., "holotype of Ctenomys sociabilis. Pearson O. P., and M. I. Christie. 1985. Historia Natural, 5(37):388."). Values are Holotype, Lectotype, Isotype, Syntype, Paratype, Neotype, or Epitype.
"TYPE" is used if it is thought that it is a type, but the type of type is not known.
Sex The sex of a cataloged item (e.g., male, female, hermaphrodite, gynandromorph, not recorded, indeterminate, transitional - between sexes, for sequential hermaphrodites).  
Preparations A concatenated list of preparations and preservation methods (skin, skull, skeleton, whole animal (ETOH), slide, etc.) for the cataloged item. We include tissue preparations in here.
Tissues A concatenated list of tissues and preservation methods (whole (frozen), liver (EDTA), etc.) for the cataloged item. The NK number for a related tissue sample.
IndividualCount The number of individuals present in the lot or container referred to by the catalog number. Not an estimate of abundance or density at the collecting locality.  
AgeClass The age class, reproductive stage, life stage of the biological individual (e.g., juvenile, adult, eft, nymph, etc.).  
GenBankNum GenBank Accession number. We do not have support for this field in Maiitsoh.
OtherCatalogNumbers A list of previous or alternative fully qualified catalog numbers of the cataloged item whether in the current collection or in any other. We do not have support for this field in Maiitsoh. NK numbers are put in the field "Tissues".
RelatedCataloged Items The fully qualified identifier (Institution Code + " " + Collection Code + " " + Catalog Number) of the related Cataloged Item, preceded by the nature of the relationship (e.g., (sibling of) MVZ Mamm 1234). We do not have support for this field in Maiitsoh.
Remarks Free text notes attached to the cataloged item record. Concatenated from Maiitoh fields "Abiotic_Ecological,"BioticAssociation","Morphological," and "LabelRemarks."  
MaiitsohRecID A unique numeric identifier for each record in the Maii'tsoh database system. This is not in Darwin Core field, but relates the specimen back to its reference number in the Maii'tsoh collection management system. These RecIDs are unique across all collections that use this system.
Export Date The date that a record was taken out of the Maii'tsoh database. This is not in Darwin Core field.
IsSensitive A marker for records that the curator or collection manager has determined are sensitive. This is not in Darwin Core field. Use a "1" to mark as sensitive, otherwise leave blank.

Oringinal document by Chris Frazier, 20 October 2003
Rev. 14 May, 2009