Batch Upload Biocode Records -- Help Page

See also Batch Loading Photos: Help Information.
Required Fields on Collecting Events Sheet
Coll_EventID_collector Your own collecting event number (ie, "station number").
EnteredBy Person who is entering these records. Has to be a name already in the database, or you can add it to the database.
Country Country where the specimen was collected.
YearCollected Year -- must be four digits.
MonthCollected Possible values: 1-12
Required Fields on Specimens Sheet
Coll_EventID_collector Your own collecting event number (ie, "station number"). Has to be on Collecting Events worksheet, or already in the database.
EnteredBy Person who is entering these records. Has to be a name already in the database, or you can add it to the database.
Specimen_Num_Collector Your own specimen number.
Phylum The reason we ask for at least phylum is for processing back at the lab - often we might not get annotated taxonomy for a while, but we can move ahead and sequence without it - however we do need to know what primers to use - the phylum key gives us sufficient info for that for the time being.
HoldingInstitution The institution where this specimen will be accessioned. If it won't be accessioned, enter "No Voucher" into the field. If your institution isn't on the list, please email John or Joyce and we'll add it.

For taxonomy, you can either

1) use the LowestTaxon/LowestTaxonLevel columns, or
2) fill out columns with the usual taxonomy level headings (Family, Genus, SpecificEpithet, etc.) Taxonomy levels allowed are listed here.

The LowestTaxon/LowestTaxonLevel fields were created for people who want to enter data quickly but don't want 5 or 10 or 15 columns just for taxonomy in their Excel files.

LowestTaxon Any name at any taxonomic level. Please do not put multiple levels in this field, with the exception of 'Genus + SpecificEpithet' or 'Genus + SpecificEpithet + SubSpecificEpithet'.
LowestTaxonLevel Examples: Family, Tribe, Genus, Genus_and_Species. (Genus_and_Species can include the subspecies also.)
Ordr Yes, it's spelled Ordr! Order is a reserve word in mysql.
Genus Genus only.
SpecificEpithet SpecificEpithet only.
SubSpecificEpithet SubSpecificEpithet only.
Taxon_Certainty Indicates the level of certainty of the taxonomic name. Choose from the menu:
  • cf. -- "confer" (compare with)
  • aff. -- "affinis" (similar to)
  • ? -- not sure about the identification
  • Tissue Fields
    tissue_type_well The part of the organism put into the well. Examples: toe, blood, gut, flower.
    tissue_type_preserved The part of the organism preserved. Examples: whole animal, toe, gut, flower.
    tissue_barcode Unique, machine-readable barcode from vial, container or storage unit. For archival tissues.
    Other Specimen Fields
    MorphoSpecies_Description A unique, descriptive name to be applied consistently to all specimens of a recognized morphospecies or variant whose specific identity is uncertain.
    MorphoSpecies_Match Reference to a Specimen_Num_Collector that is considered to be of the same morphospecies, to indicate identity through such reference.
    For decimal latitudes and longitudes. Example: -17.49460 -149.86190
    The BerkeleyMapper required latitudes and longitudes to be in decimal format.
  • To change coordinate settings to decimal degrees in Google Earth, go under the Preferences option and change the setting.
  • Coordinate settings can also be changed in any GPS device.
  • VerbatimLatitude
    The latitude and longitude in Degrees/Minutes/Seconds format.

    Examples of acceptable formats:

    • 16° 27' 00 S
    • 156° 23' 29'' W
    • 04 0 0 N
    • 34 12 27.6 N
    • 36° 54.947' S
    • 071 27.417 W
    • S17.54990

    For deg/min/sec:
    Four fields, each separated by one space. No minus signs, no alpha characters. 3rd field can be a decimal number. 4th field must be E,W,N, or S.
    For deg/dec min:
    Three fields, each separated by one space. No minus signs, no alpha characters. 3rd field must be E,W,N, or S.

    Automatic conversion to decimal   This Lat/Lon will be automatically converted to decimal lat/longs when the record is submitted. Decimal is required for displaying points in the BerkeleyMapper.

    Please consider setting your GPS to record lat/longs in decimal degrees so we don't have to do any conversions.

    The Habitat and MicroHabitat fields are also on the collecting event sheet. You should only record them in your specimen sheet if they are different from the values in your collecting events.
    Associated_Taxon Also known as Host.

    Additional Information
    Order of columns Yes, you can move the columns around into whatever order you like, or delete columns you don't need (except for the required ones which are highlighted in yellow).
    Adding columns Many of the fields in the collecting event and specimen tables can be added to the spreadsheet, if they aren't there already. (There are a few exceptions -- some fields are generated during the upload process, such as DateFirstEntered, DateLastModified, and batch_id.) If you add a field and get an error, email Joyce or John -- even if the field is in the schema, it needs to be enabled for bulk uploads.

    The Moorea Biocode Database is a project of BSCIT   University of California, Berkeley     Comments & Questions