AM-CC DATABASE FIELDS GLOSSARY
GENERAL TERMS
(?): any illegible or questionable data from an original data source Aliquot: divisions of the sample
Example: DNA extraction, White blood cells (WBC), plasma, whole blood
Collection: an assemblage of biological specimens maintained by an educational or research institution to be used as a research resource, typically in biological systematics, ecology, population genetics, etc.
Internal Barcode ID: the unique number allocated to all aliquots of a sample by the Frozen Tissue Collection (AM-CC) Laboratory.
Example: 100353
Sample: original object of a collecting event taken by the collector; can be composed of one individual, multiple parts of one individual, or many individuals.
Example: whole blood, heart, liver, plasma Specimen: an individual of a species
Example: Eulemur fulvus fulvus (brown lemur)
ADMINISTRATIVE DATA
AMNH registrar number: the number allocated by The American Museum of Natural History upon receipt of the sample.
Format: Example:
Department / Partner: the department of the museum, the institution or the program the AM-CC Lab has a biomaterial banking agreement with.
Format: text
Example: Herpetology, Bronx Zoo, WCS
Department / Partner #: the catalogue number allocated by the museum department, institution or program to the tissue sample.
Format: alphanumeric Example: ABC12345
ISIS #: the number designated by the International Species Information System (I.S.I.S.) to track basic biological information such as age, sex, parentage, place of birth, and circumstance of death. (ISIS is a computer-based information system for wild animal species held in captivity. The ISIS central database holds information on 1.44 million zoological animals of nearly 8,000 species held in 576 institutions in 54 countries.) Format: alphanumeric
Example: 168
Studbook #: the number used to register and keep records of the pedigrees and
performance of animals to promote the breeding and genetic improvement of animals of a kind or of a specified breed.
Format: alphanumeric Example: 14, 14m
Field Catalogue # : the number allocated by the collector to the sample in the field. Format: alphanumeric
Example: RANT 1; CONGO 123
Other ID # : Identification number allocated by another institution, collector or donor. Format: alphanumerical
Example: Duke University Primate Center ID number: 5950f eVoucher#: photo(s) of the sample
Format: alphnumeric
Example: lateral, ventral, dorsal
Gel Pic #: Image file number of electrophoresis Gel associated with the specimen. Format: alphanumerical
Example: Gel123
Collected by: the name of the individual(s) who were responsible for collecting the original sample.
Format: the full last name followed by the initial of the first name. Always include, whenever possible, the middle initial following the first name initial.
In case of two or more individuals, list all pertinent names.
Example: Webster, B R,Wright, A L; Corthals, A P; Hanner, R ; Grand, I
Note: this category refers only to the individual(s) who acquired the sample, and should not be confused with the individual(s) who donated or prepared the sample
Donor: the individual(s) or institution which donated the sample(s).
Format: The name of the institution. or the full last name of the donor(s) followed by the initial of the first name. Always include, whenever possible, the middle initial following the first name initial.
Notes: this category should not be confused with the individual(s) who collected the sample.
Expedition: the name and/or number of the expedition from which the sample was acquired.
Format: alphanumerical or text Example: UU 99
Date of Accession: the date the sample was entered by AM-CC lab personnel into the FreezerWorks database.
Format: mm/dd/yyyy Example: 07/06/1973
Voucher #: the number designated to the Voucher Specimen*; used to determine the taxonomy of the sample.
Format: alphanumeric Example: R-124578
*Notes: A Voucher Specimen is a representation of the species as determined by the institution, collector , or donor. This may or may not be the actual organism from which the sample was taken.
Disposition: the location of the voucher specimen. Format: institution name, collection name, etc.
Example: Bronx Zoo; The American Museum of Natural History, Hall of African mammals.
Data Source: the number attributed to each batch of samples entering the AM-CC facilities. The number also refers to the binder in which all documentations for those samples are kept.
Format: alphanumeric Example: CaseBinder 054
Availability: whether the tissue sample(s) are available for loan. Format: Drop-down box: Yes or No
Restrictions: defines reason(s) for lack of availability. Format: text
Example: “for private research use only”
Permission: whether an official release is needed from the institution/collector/donor for making sample loans.
Format: text
Example: Yes or No and name of person(s) whose permission is needed.
Notification: whether institution/collector/donor wants to know to whom the specimen was loaned to.
Format: alphanumeric
Example: Name and date of institution/person to notify
Accession #: the ZOOs accession number (For Zoo specimens only) Format: numerical
Example: 938049
Death #: the ZOOs number recording the death of the animal (For Zoo specimens ONLY)
Format: alphanumeric Example: P2001-61
Administrative Notes: any additional information not specified in the defined fields,or an explanation of an unusual entry in a defined field.
Format: text
Example: illegible data sources, data corruption, reason for blank fields etc.
TAXONOMY
Kingdom, Phylum, Class, Order, Suborder, Family, Sub-Family, Genus, Species, Sub-species:
All the above catagories refer to the sample’s scientific classification, reflecting the name of a taxon that conforms to the Code.
Determined by: the individual who, or institution that determined the taxonomy. Format: the full last name followed by the initial of the first name. Always include, whenever possible, the middle initial following the first name initial.
In case of two or more individuals, list all pertinent names. Example: Webster, B R; Bronx Zoo
Authority: the individual who first described the species and the year it was first determined
Format: last name, year Example: Darwin, 1850
Note: If the name is in parenthesis, make sure not to forget them!
Type: any specimen which is a representation of the type series (allotype, holotype, lectotype, etc.)
Format: drop-down box; Yes or No
Questionable ID: to denote whether the collector/institution/donor is questioning the taxon classification of the species.
Format: Drop-down box; Yes or No
Common Name: a name of an animal in a language used for general purposes as opposed to a name proposed only for zoological nomenclature.
Format: text
Example: Brown Lemur
GenBank/EMBL#: the GenBank sequence numbers associated with the specimen’s species
Format: alphanumerical Example: AF258110
Note: Link to GenBank: http://www.ncbi.nlm.nih.gov/Genbank/index.html NCBI #: the number given by the NCBI website for a given species Format: numerical
Example: 56734
Citation: the designation of a reference work that was used to determine the taxon name. Format: text
Example: Mittermeier, etal ; “The Lemurs of Madagascar” 1994
Taxonomic History: field used to record any note-worthy historical changes of a species taxon classification.
Format: text
Example: Cnemidophorus tigris x Cnemidophorus marmoratus; specimen belongs to group A
FIELD DATA
Collect Date 1: specific date of collection. If not known, best estimate of earliest possible collection date.
Format: mm/dd/yyyy Example: 09/08/1975
Collect Date 2: best estimate of the latest possible date of collection. Format: mm/dd/yyyy
Example: 10/01/1975
Time of Collection: actual and estimate time of collection Format: hh.mm (24 h clock)
Example: 15.00
Season of Collection: season during which the sample was collected. Format: text
Example: Autumn, Winter, Monsoon, Hurricane season etc. Continent: continent in which the sample was collected. Format: drop-down box
Body of water: body of water in which the sample was collected. Format: text
Example: Mediterranean, Hudson Bay, Atlantic Ocean, Hudson River Country: the country in which the sample was collected.
Format: text
Example: Belgium, USA, France, Bolivia.
Geo. Division 1: the primary administrative division of the country in which the sample was collected.
Format: text
Example: Quebec, Tuscany
Geo. Division 2: the secondary administrative division of a country such as the county, parish, district or department. A major island group is defined as the largest geographic division of island groups.
Format: text
Example: Utmali district, Aswan district, Feroe Islands
Specific locale: the common name given to the park, preserve or zoological institute or city in which the sample was collected.
Format: text
UTM: Universal Transverse Mercator value Format: alphanumeric
Example: 36 308436 NO 5690485
Latitude and Longitude: the latitude and longitude of the actual collecting locality. Format: alphanumeric
Example: 28 52 30 (N) 15 10 05 (W)
Elevation: the actual altitude (list units) of the locality in which the sample was collected.
Format: numeric
Example: 3000m, 3000ft
CPI: the Coordinate Precision Index used to indicate the reliability of the coordinates recorded of the collecting locality.
Format: numeric (1 to 9 index) Example: 1; 8.6
Notes: the codes for CPI are:
1.1 = coordinate data (using GPS technology) as entered by collector. Accurate to +/- 10m
1.2 = coordinate data (extrapolated using a 1:24000 topographic map) as entered by collector.
Accurate to +/- 100m
1.3 = coordinate data (extrapolated as using 1:100000) entered by collector. Accurate to +/- 1km
2 = coordinate data looked up in table listing coordinates for various place names on the globe,
Accurate to 3 miles of coordinates given.
3 = coordinates data computerized from relative distance data (Included center coordinates for
small islands and other small geographic features).
4 = center coordinates for larger geographic features given in the collector’s data where no
precise information is given. Does cover most of the US counties and larger islands. Accurate to +/- 30 miles of coordinate given
5 = center coordinates for larger geographic features such as larger US counties, small states
and countries, and very large islands.
Accurate to +/- 100 miles of coordinate given.
6 = larger US counties, small states and countries and very large islands. Accurate to +/- 300 miles
7 = center coordinates for very large geographic features such as “Asia” or “Europe”. Accurate to > 300 miles from coordinate given.
8.X = an interim value based on one of the above values of precision but where the data have the potential of more precision. This marks them for future reference when the coordinates for this place name may be found. The X represents the current precision level used.
9 = no locality available
Purpose of Sample Collection: the determination of the type of assay that will be done on the sample.
Format: drop-down Example: DNA analysis
Ancillary Collections: records the collection of any other preparations and documentation accompanying the sample.
Format: text
Example: parasites, slides, eggs, stomach content.
Prepared by: the name of the individual(s) who prepared the sample.
Format: the full last name followed by the initial of the first name. Always include, whenever possible, the middle initial following the first name initial.
In case of two or more individuals, the names should be separated by a semi-colon. Example: Webster, B R
Wright, A L Corthals, A P Hanner, R ; Grand, I
Notes: this category should not be confused with the collector, donor or AM-CC employees.
Field preparation method: protocol used to prepare the sample for the purpose of storage.
Format: text
Example: ETOH, flash-freeze etc
Storage method: how the sample was stored for shipping or transport after initial field preparation.
Format: text
Example: -80 C, ambient temperature, etc Field notes: general field notes
Format: text
Example: method of trap setting, excavation techniques, observed behavior
Habitat Description: a description of the physical and biotic environment at the time and place of collection.
Example: vegetation type, soil type, geomorphic features, physical/chemical measuements (temp.,rainfall,pH, etc).
ALIQUOTS
Positions Tab
Vat: the cryo-freezer an aliquot is stored in. Format: text
Example: Vat A, Vat D
Section: the vat division each rack is stored in. There are 6 sections per vat in the MVE 1830HE.
Format: alphanumeric Example: 1 through 6
Rack: metal framework with compartments for up to 13 boxes. There are nine racks per vat section. There are a total of up to 54 racks per vat in the MVE 1830HE.
Format: alphanumeric Example: 1-54
Box: a plastic,cardboard or metal container that can hold up to 100 cryogenic vials or one cryostorage bag. There are up to 13 boxes per rack.
Format: alphanumeric Example: 1-13
Position: the placement of each cryogenic vial within a box. There can be up to 100 vials per box.
Format: alphanumeric Example: 1-100
Initial: the original weight or volume of the aliquot in grams or milliliters. Format: alphanumeric
Example: 1.2, 5.0
Note: Tissues are denoted in units of grams, while body fluid samples are denoted in milliliters.
Current: the weight or volume in storage of the aliquot, in grams or milliliters, available for use.
Format: alphanumeric Example: 1.2, 5.0
Note: Tissues are denoted in units of grams, while body fluid samples are denoted in milliliters.
Results Tab
Aliquot Type: The tissue type in storage. Format: text
Example: blood, heart, skin, hair etc.
Assay: the specific analysis performed on an aliquot. Format: text
Example: DNA extraction, spectrophotometric analysis, PCR Results: information generated from an assay.
Format: alphanumeric Example:
Protocol Tab
Protocol date: the date the sample or aliquot was prepared for assay. Format: date
Example: mm/dd/yyyy
Protocol: the preparations taken in order to prepare a sample or aliquot for assay. Format: text
Example: thawed, centrifuged, heated. Medium Tab
Storage medium: the fluid the sample was placed in for preservation. Format: text
Example: ETOH, TE Buffer
PHYSICAL CHARACTERISTICS
Sex: applies to the sex of the sampleFormat: drop-down box
Example: male, female, hermaphrodite, unknown
Age: applies to the relative or chronological age of the sample Format: alphanumeric
Example: juvenile; 50 y.o.
Height: applies to size measurement of the sample Format: alphanumeric (metric)
Example: 1.50m, 50 cm, 2mm
Weight: applies to size measurement of the sample Format: alphanumeric (metric)
Example: 1.50kg, 50 g, 1mg
Length: applies to size measurement Format: alphanumeric (metric) Example: 1.50m, 50 cm, 2mm
Molt Status: applies to the molt condition of specimen at time of sampling. Format: drop-down box
Example: Molting, not molting, unknown
Reproductive Condition: reproductive cycle the specimen is in at the time of sampling. Format: text
Example: lactating, embryos, etc. Date of Death: if applicable Format: mm/dd/yyyy
Example: 08/06/1959
Cause of Death: circumstances of specimen’s death Format: text
Example: Natural, Disease, Euthanized
Birth Type: circumstances of specimen’s birth Format: Drop-down box; Wild or Captive
Preservation Type: records the physical state of the specimen at the time of sampling Format: text
Physical Characteristic Notes: any other measurements or notes taken that are specific to the specimen’s physical condition.
Format: text
Example: red belly, brown back, tail length.
Sire ID: ID number of the male parent of the specimen (For Zoo specimens only) Format: alphanumerical
Example: A008983
Dam ID: ID number of the female parent of the specimen (For Zoo specimen only) Format: alphanumerical
Example: B869789
Sire Institution: Institution of origin of the male parent of the specimen (For zoo specimens only)
Format: text
Example: Bronx Zoo
Dam Institution: Institution of origin of the male parent of the specimen (For zoo specimens only)
Format: text
Example: San Diego Zoo
NOTES
This is an open section for free text and any other additional information accompanying the data sources.
For use by the AM-CC Only
TRANSACTIONS
Aliquot #: a number assigned by the database program in to each aliquot of each sample. Format: numerical
Example: Aliquot 2, 3
Date: the date the aliquot has been handled for any reason by a AM-CC employee. Format: date
Example: mm/dd/yyyy
Activity: the specific action performed by an AM-CC employee to a sample or aliquot. Format: text, drop down box
Example: Loan
Notes: free text section for any additional information pertaining to specimen or aliquot handling.
Format: text
Example: Loaned to Phaedra Doukakis
AUDIT TRAIL
Database defined and controlled area that tracks any changes made to the FreezerWorks program. Keeps track of each date and time any AM-CC Lab employee enters
