Creating Other Identifiers

[ https://arctosdb.wordpress.com/documentation/catalog/#parse_otherid is current ]

Under individual specimen records, Other Identifiers are a three-part field:

  • Prefix (text)
  • Number (integer)
  • Suffix (text)
All search features rely on a (stored) concatenation of these fields, called Display_Value.

The specimen bulkloader has only one field for (each of several) Other Identifiers. At load, the values provided in this field are parsed into individual fields according to the following rules.

  • Integers are loaded as Number
  • Strings consisting on a single alpha character followed by a number (V12345) are split into Prefix and Number (V and 12345, respectively)
  • Strings consisting of a number and a single alpha character (12345a) are split, as above, into Number and Suffix
  • Strings containing one or two "separator characters" (| - . ;) are split at those characters.
  • The results of the above are checked to ensure that Number is an integer
  • Finally, the re-concatenated value is checked against the original. If they don't match, the original becomes Prefix.
Examples:
InputPrefixNumberSuffixDisplayExplanation
v12345v12345NULLv12345One character plus number
v-12345v-12345v-12345v-12345Split at a separator character
v-12345-1v-12345-1v-12345-1Split at separator characters
1[12345]11[12345]1NULLNULL
1123451Brackets are treated as characters.
1-abc-21-abc-2NULLNULL1-abc-2Number is not numeric
v-00001v-00001NULL
NULLv-00001Above rules would lead to dropped leading zeroes in Number

(Much of this procedure is included in Arctos Definitions and Standards as a broader description of Other Identifiers.)

Entering Citations

[ https://arctosdb.wordpress.com/documentation/publications/#create_cite ]
Citations are a linkage between a cataloged item and a page in a publication. They contain little information, being essentially a connection between existing sets of information. Therefore in order to create citations, both the publication and the items must already be present in Arctos. The scientific name used by the authors must also be present. Most often this will be the same as the current identification of the specimen, but not always; that's why it's there.

Citations can be individually entered by finding the publication from the Publication/Project Search tab, clicking the Citation Button, and using the form (Citation.cfm) to enter the appropriate information. You will select the cited specimens by catalog number or an Other Identifier. And you will select the scientific name by which the item was cited.

In publications that cite numerous specimens, it is often possible and efficient to bulkload the citations, especially if they are in tabular form within an electronic copy of the document. This can be done by copying and pasting the table from the publication into a spreadsheet. It must then be formatted to exactly match the key fields in Arctos, and exported as a comma-delimited text file. The tool for uploading this file, and a detailed description of the file are found from Bulkload Citations on the Tool tab (BulkloadCitations.cfm).

Duplicate Agents

[ moved to https://arctosdb.wordpress.com/documentation/agent/#duplicate ]

There are duplicate agents in Arctos. What am I supposed to do about that?

First, make sure that there are actually two separate records for the agents. Identical agent names, between and among agents, is another issue and not covered here. Duplicate agents are two or more agent records that mean the same physical entity (THAT PARTICULAR John Smith; US Fish and Wildlife Service). It is not necessary for duplicate agents to share a name; in fact, they are often introduced because of misspellings. The "Agent Activity" link is a good place to make sure you're dealing with real duplicates.

Once you're sure you have duplicate agents, simply flag one of them as a "bad duplicate of" the other in Agent Relations. Generally, you will want to flag the record with least complete information and/or the least activity. The application to actually make the deletion must then be run manually.

Once agents are flagged, the actual agent cleanup process (Manage Data/Agents/Merge Bad Dup Agent) often involves individual analysis of agents in roles. Arctos will not merge agents used in Publications, those with Addresses, or otherwise differentiated at the Agent Name level. You may have to address errors individually.

Bulk-loading, an Overview

[ moved to https://arctosdb.wordpress.com/documentation/bulkloader/bulkloader-tutorial/#overview ]

New specimen records are created from a single "flat file, usually a text file in which all data for a single cataloged item are in a single row. This file can be created with any convenient client-side application (often Microsoft Access). The file is then loaded into a similarly structured table on the server, and a server-side application (the bulk-loader) parses each row into the relational structure of the database.

This approach makes keyboarding of data a client-side process, and thereby allows easy customization of data-entry applications. The process provides an independent layer of data checking before new information is incorporated into the database proper. Original data that are received in electronic format may require minimal manipulation; you can sometimes merely add the necessary columns to build a file in the bulk-loading format (download bulkloader templates or build your own with the Bulkloader Builder application).


What the bulk-loader does:
  • The bulk-loader expects to find pre-existing values in the database for
    taxonomy, agent names, and higher geography.
    Data of these types that are not already in the system must be added prior
    to bulk-loading by a user who is priviliged to modify those tables.
  • The content of several data fields is controlled by "code tables"
    which restrict the acceptable values for those fields.
    (The values you see in dropdowns in the editting screens come from these code tables.)
  • The bulk-loader evaluates each row in the submitted table.
    If the locality already exists in the database, then the bulk-loader
    uses the existing locality.
    If the locality does not exist, then (assuming that the row is otherwise acceptable)
    the bulk-loader creates the new locality and parses the row into the appropriate
    tables.
  • If no catalog number is provided by the submitted table, then bulkloader provides the next sequential catalog number from the indicated collection.

The template for this flat file handles the most common data but has limitations.
For example, if a specimen has five collectors, you could load the specimen and the
first three collectors with the bulk-loader, then add the other collectors by editting the online record. Or, you could request a change to the structure of the template.
(Ask Dusty nicely.)

Bulkloader Group Settings

[ deprecated ]

Why do the data entry applications think I have group issues?

First, make sure the user has a privileged account.

  • Users with role DATA_ENTRY may enter records for those collections they have access to.
  • Users with role MANAGE_COLLECTION may modify records in the bulkloader.
  • Users may be in any number of collection groups.

More information about Arctos groups may be found here.

Loading Records

[ moved to https://arctosdb.wordpress.com/documentation/bulkloader/bulkloader-tutorial/#loading ]

Records in the bulkloader are ready to go. Now what?

  1. Ensure that you have no group issues.
  2. NULLify LOADED using the Browse and Edit Bulkloader application under Tools.
  3. Wait for them to load. The load process runs hourly, but your records may be in the queue for several hours or even days. Note that LOADED is a functionally binary field with the following values:
    • NULL: The bulkloader may attempt to load this record
    • NOT NULL: The bulkloader must ignore this record
    Feel free to use it for comments. Enter DELETE in LOADED to get rid of a record.
  4. Check progress under Tools ==> Bulkload Specimens ==> Bulkloader Status
  5. Fix errors and NULLify LOADED as in 1).

Locality

How do I update geospatial data?

  • Option One: Update data for a single specimen.
    • Simply click the Locality tab in SpecimenDetail and make any necessary changes. Your updates will affect only the specimen you are editing.
  • Option Two: Pick a new collecting event.
    • When a suitable collecting event (dates, locality, higher geography, georeferenceing, and collecting method) exists, click the Pick New Coll Event tab, find an appropriate collecting event, and save.
  • Option Three: Update the locality.
    • First, click the Locality tab under SpecimenDetail, then click the Edit Locality link (or, find a locality under Localities). You are potentially changing localities for multiple specimens in multiple collections. Be sure you know what you are doing! Edit the locality as appropriate and save.
  • Option Four: Move the collecting event to a new locality.
    • From SpecimenDetail, click the Locality tab. Then click Edit Locality. Then click Collecting Events to see a list of all events under that locality. Locate the one you wish to move, and click on the "Coll Evnt Id" link. Click the Change Locality For This Collecting Event button. You are potentially changing localities for multiple specimens in multiple collections. Be sure you know what you are doing!

Loans

How do I create a loan?

  1. Create (or find) the loan under the Transactions tab.
  2. Add the loan to one or more Projects, if appropriate, under Edit Loan.
  3. Click Add Items from Edit Loan to find specimens you want to include in the loan. This is the standard Specimen Search screen.
  4. You should see an itemized list of available parts for each specimen in Specimen Results after a successful search. To add a part to the loan, simply fill in the Remark and Instructions boxes, check the Subsample box if you wish to create and loan a subsample, and click the appropriate Add button. Note that Remarks and Instructions apply to individual items; remarks and instructions for the entire loan may be entered under Edit Loan.
  5. From Edit Loan, click the Review Items button to remove or edit loan items. Note that you cannot remove items with a disposition of "on loan."
  6. Fill in Shipment information on the Edit Loan form. Add agent addresses under Agents if necessary.
  7. Print forms using the Print tool.
Arctos allows transactions to have any number of Agents in various Roles. Some of those Roles have special significance to the application.
  • entered by: Populated with the person creating the loan's Login information.
  • in-house contact: Single person in the originating institution who should be contacted with questions about the loan.
  • outside contact: Single person in the receiving institution who should be contacted with questions about the loan.
All other roles may be populated as appropriate. See the code table for more specific documentation.

Reminders

How do I get reminders?

Arctos will automatically send reminders when permits are expiring (365, 90, 30, and 0 days before permit expires_date) and loans are due (30 days before loan due_date). All contacts must have a valid email address. Simply enter a name in Contact Person under edit or create permits (access permits under Transactions). Loan reminders are sent to the Authorized By agent.

User setup

[] moved to https://arctosdb.wordpress.com/home/administration/ ]

How do I allow a user to enter data or perform other internal Curatorial tasks?

  1. New users must first create an account for themselves. Their account name must use only letters and numbers (ASCII characters A-Z, a-z, and 0-9) if they are to be operators. The name cannot begin with a number. (Public users can use any characters.) They must have an email address in their Profile.
  2. Under the Agents tab, create them as a new agent or locate them if they are an existing agent. Make sure they have a name-type of "login," and that their login name matches their Arctos username. These are case sensitive.
  3. From Management/Arctos/Arctos Users, click Invite to allow them to create an internal user account. They will have to ensure that their username is valid, pass certain password checks, etc. to become users.
  4. After the user has completed Step 3, assign them appropriate data and collection roles. Include the COLDFUSION_USER and DATA_ENTRY roles to enable data entry.

Data Entry Accession Format

[ moved to https://arctosdb.wordpress.com/documentation/accession/#dataentry ]

Why isn't my Accession Number accepted?

Collections own transactions by way of trans.collection_id. Collections own rows in the bulkloader/data entry application by way of collection_cde + institution_acronym. The default bulkloader behavior is to locate an accession based on the bulkloader data. Square brackets may be used to tell the bulkloader "ignore the collection in this row - go find an accession based on what's in the brackets."

Square brackets are required any time a record is to be attached to an accession belonging to another collection. Examples include.

  • A UAM Mammal Observation being entered into a UAM Mammal accession
  • An MVZ Bird being entered into an MVZ Mammal accession
Example Usage is follows. Collections are in italics.
  • Desired accession: UAM:Mamm 1234.123.Mamm
  • New Specimen: UAMObs:Mamm 9876
  • Default accession: UAMObs:Mamm 1234.123.Mamm (Does not and should not exist)
  • Value to enter for Accession: [UAM:Mamm]1234.123.Mamm
  • Desired accession: MVZ:Birds 14508
  • New Specimen: MVZ:Bird 183000 -Value to enter for Accession: 14508
  • New Specimen: MVZ:Mamm 250000 -Value to enter for Accession: [MVZ:Bird]14508
  • New Specimen: MVZObs:Bird 10 -Value to enter for Accession: [MVZ:Bird]14508

Encumbering Specimens

How do I encumber specimens?

  1. Find the specimens you want to encumber using SpecimenSearch.
  2. From the Manage tool, choose Encumbrances and click Go. You should now see a summary of your specimens at the bottom of the page, and the encumbrance finder at the top.
  3. Find the appropriate encumbrance by entering search criteria and clicking Find Encumbrance.
  4. Under the appropriate encumbrance, click the Add All Items To This Encumbrance button.

When the screen refreshes, the specimens are encumbered. Double-check that no extraneous specimens have been encumbered.

Deleting Records

How do I delete records from Arctos?

  1. Encumber the record(s) to be deleted. Create an appropriate encumbrance first, if necessary. Records may be flagged from individual specimens, or en masse by using the Manage widget from SpecimenResults. Once records are flagged, they may be deleted by users with the appropriate privileges.
  2. Find the encumbrance (under Tools). Click See Specimens and carefully review what you're about to delete.
  3. From Manage Encumbrances, click Delete Encumbered Specimens. You'll again be asked to review your decision, and must click the proceed button at the bottom of the page to delete the records from the database.
Note that there may be reasons to keep masked records in the database instead of deleting them.