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Transport Schema from Maii'tsoh to Darwin Core V2 (INRAM DwC2 V1.1)
Below is a document describing a draft data exchange standard for interoperability among datasets in the Maii'tsoh database and the INRAM 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 given here (as revised 23 July, 2004) differ from DwC2 V1.14 by the addition of ColloquialName, MaiitsohRecID field and Export Date. This is the INRAM DwC2 V1.1. Reviewed 24 May, 2005 without revision.
| 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) | |
| 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. | We still need to establish these for ENMU and WNMU non-plant collections. | |
| 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 filled in from our Catalog Numbers anyway. | |
| CatalogNumber Numeric | The CatalogNumber as a numeric value, if applicable. Allows searching on numeric ranges of CatalogNumbers. | No explicit guarantee that Catalog Numbers are unique within a collection, although they should be. | |
| 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 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. | |
| 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 used only for incomplete collection dates. | |
| 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 used only for incomplete collection dates. | |
| 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 used by any of our current datasets. We do not have support for this field in Maiitsoh. | |
| 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 used by any of our current datasets. We do not have support for this field in Maiitsoh. | |
| 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, Taos. | |
| ContinentOcean | The full, unabbreviated name of the continent or ocean from which the cataloged item was collected. | ||
| IslandGroup | The full, unabbreviated name of the island group from which the cataloged item was collected. | ||
| Island | The full, unabbreviated name of the island from which the cataloged item was collected. | ||
| 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. | ||
| 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. | ||
| Locality | The description of the locality from which the cataloged item was collected, sans geographic information provided in other geographic fields. | ||
| DecimalLatitude | The latitude of the location from which the cataloged item was collected, expressed in decimal degrees. | Only populated when values were provided by the collector in LatLong. | |
| DecimalLongitude | The longitude of the location from which the cataloged item was collected, expressed in decimal degrees. | Only populated when values were provided by the collector in LatLong. | |
| HorizontalDatum | The horizontal geodetic datum to which the DecimalLatitude and DecimalLongitude refer. | Only populated when value were provided by the collector. If this field is populated and DecimalLatitude is not, indicates that original coordinates given were in UTM. | |
| OriginalCoordinate System | The name of the system in which the original geographic coordinates were recorded (e.g., "decimal degrees", "degrees minutes seconds", "UTM", etc.). | Only populated when original coordinate system was LatLong. | |
| VerbatimLatitude | A text representation of the Latitude data in its original format in the source database. | Not "verbatim" since this is not recorded in Maiitsoh. Populated with a text representation of LatLong coordinates with separators for degrees, minutes, seconds and N or S. | |
| VerbatimLongitude | A text representation of the Longitude data in its original format in the source database. | Not "verbatim" since this is not recorded in Maiitsoh. Populated with a text representation of LatLong coordinates with separators for degrees, minutes, seconds and E or W. | |
| GeorefMethod | A reference to the methods used for determining the coordinates and uncertainties. | We have not provided "acceptably georeferenced coordinates," but only the LatLong coordinates as provided by the collector. Signified by "Coordinates from label." | |
| 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. | None, since none of our coordiantes is georeferenced, but as given by the collector. | |
| LatLongComments | Comments about the LatLong determination. | We have not provided "acceptably georeferenced coordinates," but only the LatLong coordinates as provided by the collector. Signified by "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. | |
| 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 our value in elevation, unless a value is 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 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. | This field is not currently implemented in Maiitsoh as a separate populated field. Information, if we have it, is included in the ScientificName field. | |
| 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. | This field is not currently implemented in Maiitsoh as a separate populated field. Information, if we have it, is included in the ScientificName field. | |
| IdentificationModifier | Additional information documenting the taxonomic determination of the cataloged item (e.g., "cf.", "aff.", "subspecies in question", etc.). | This field is not currently implemented in Maiitsoh as a separate populated field. Information, if we have it, is included in the ScientificName field. | |
| ColloqualName | The common or vernacular name for this taxon. | This is not in Darwin Core2 V1.21, but will apparently be included in DC3. | |
| 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 Holo, Lecto, Iso, Syn, Para, Neo, or Epi. "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. | ||
| Tissues | A concatenated list of tissues and preservation methods (whole (frozen), liver (EDTA), etc.) for the cataloged item. | We do not have support for this field in Maiitsoh. | |
| 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. | |
| 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. | |
| Export Date | The date that a record was taken out of the Maii'tsoh database. | This is not in Darwin Core field. |
| Chris Frazier, 20 October 2003 | Rev. 23 July, 2004, CKF |