AM-CC DATABASE FIELDS GLOSSARY

Transcription

1 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: 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. Example: Herpetology, Bronx Zoo, WCS Department / Partner #: the catalogue number allocated by the museum department, institution or program to the tissue sample. Example: ABC

2 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.) 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. Example: 14, 14m Field Catalogue # : the number allocated by the collector to the sample in the field. Example: RANT 1; CONGO 123 Other ID # : Identification number allocated by another institution, collector or donor. al 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. al 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. In case of two or more individuals, list all pertinent names. Example: The American Museum of Natural History; M. Breedlove 2

3 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. al 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. Example: R *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. 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. Example: for private research use only Permission: whether an official release is needed from the institution/collector/donor for making sample loans. 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. 3

4 Example: Name and date of institution/person to notify Accession #: the ZOOs accession number (For Zoo specimens only) Format: numerical Example: Death #: the ZOOs number recording the death of the animal (For Zoo specimens ONLY) Example: P Administrative Notes: any additional information not specified in the defined fields,or an explanation of an unusual entry in a defined field. Example: illegible data sources, data corruption, reason for blank fields etc. 4

5 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. Example: Brown Lemur GenBank/EMBL#: the GenBank sequence numbers associated with the specimen s species al Example: AF Note: Link to GenBank: NCBI #: the number given by the NCBI website for a given species Format: numerical Example: Note: Link to the NCBI website: 5

6 Citation: the designation of a reference work that was used to determine the taxon name. Example: Mittermeier, etal ; The Lemurs of Madagascar 1994 Taxonomic History: field used to record any note-worthy historical changes of a species taxon classification. Example: Cnemidophorus tigris x Cnemidophorus marmoratus; specimen belongs to group A 6

7 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: Season of Collection: season during which the sample was collected. 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. Example: Mediterranean, Hudson Bay, Atlantic Ocean, Hudson River Country: the country in which the sample was collected. Example: Belgium, USA, France, Bolivia. Geo. Division 1: the primary administrative division of the country in which the sample was collected. 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. 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. Example: Yellowstone National Park, Farafra Oasis, New York 7

8 UTM: Universal Transverse Mercator value Example: NO Latitude and Longitude: the latitude and longitude of the actual collecting locality. Example: (N) (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

9 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. 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. Example: ETOH, flash-freeze etc Storage method: how the sample was stored for shipping or transport after initial field preparation. Example: -80 C, ambient temperature, etc Field notes: general field notes 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. 9

10 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. Example: Vat A, Vat D Section: the vat division each rack is stored in. There are 6 sections per vat in the MVE 1830HE. 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. 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. Example: 1-13 Position: the placement of each cryogenic vial within a box. There can be up to 100 vials per box. Example: Initial: the original weight or volume of the aliquot in grams or milliliters. 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. Example: 1.2, 5.0 Note: Tissues are denoted in units of grams, while body fluid samples are denoted in milliliters. NOTE: The fields above in italic are for the use of the AM-CC ONLY 10

11 Results Tab Aliquot Type: The tissue type in storage. Example: blood, heart, skin, hair etc. Assay: the specific analysis performed on an aliquot. Example: DNA extraction, spectrophotometric analysis, PCR Results: information generated from an assay. 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. Example: thawed, centrifuged, heated. Medium Tab Storage medium: the fluid the sample was placed in for preservation. Example: ETOH, TE Buffer NOTE: The fields above in italic are for the use of the AM-CC ONLY 11

12 PHYSICAL CHARACTERISTICS Sex: applies to the sex of the sample Format: drop-down box Example: male, female, hermaphrodite, unknown Age: applies to the relative or chronological age of the sample Example: juvenile; 50 y.o. Height: applies to size measurement of the sample (metric) Example: 1.50m, 50 cm, 2mm Weight: applies to size measurement of the sample (metric) Example: 1.50kg, 50 g, 1mg Length: applies to size measurement (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. 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 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 Example: live animal, deceased, decayed, full skeleton, 12

13 Physical Characteristic Notes: any other measurements or notes taken that are specific to the specimen s physical condition. Example: red belly, brown back, tail length. Sire ID: ID number of the male parent of the specimen (For Zoo specimens only) al Example: A Dam ID: ID number of the female parent of the specimen (For Zoo specimen only) al Example: B Sire Institution: Institution of origin of the male parent of the specimen (For zoo specimens only) Example: Bronx Zoo Dam Institution: Institution of origin of the male parent of the specimen (For zoo specimens only) Example: San Diego Zoo NOTES This is an open section for free text and any other additional information accompanying the data sources. 13

14 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., drop down box Example: Loan Notes: free text section for any additional information pertaining to specimen or aliquot handling. 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 information or changes into the program. 14