Suspect Data

I'd like to monitor what's going on with my collection. How can I do that?

Loan and Permit reminders are emailed to the listed contacts at 1 year, 6 months, 1 month, and upon the permit expiring or the loan becoming due. Any agent with an email address may act as a contact.

The following are available under the Management/Misc tab:

  • Publication Staging is a way to quickly capture very basic information about possible Citations in Arctos. Curators should periodically review and update the information in this form.
  • Management/Misc/Sync parent/child taxonomy finds specimens in a Parent Of/Child Of relationship which do not share current Identification, and provides a means to synchronize them.
  • Merge Dup Agents provides a means to reconcile agents in relationship "bad duplicate of".
  • Pending Relationships provides access to those cataloged item relationships created during Data Entry which have not been successfully formalized. Curatorial action is required for anything in this list.
The following are available under the Reports tab:
  • GenBank MIA is a script that periodically crawls GenBank looking for sequences that may be related to Arctos specimens and which do not already have an Arctos LinkOut (newly-linked may continue to appear in the table for a few days).
    • Query type specimen_voucher:collection are GenBank sequences with which the collector has submitted a properly-formatted link to GenBank, and are almost certainly accurate.
    • Other query types are various guesses, and may or may not accurately resolve to specimens.
  • Annotations are user-submitted annotations. The data quality contact (which may be set under Manage Collections) should also receive notification when annotations are filed.
  • Loan/Citation Stats summarizes loans by the borrower, loan status, number of citations against specimens which were loaned, and cited versus current Identification. Citations must be individually examined to determine from which loan they originated. Citation Counts may reflect repeated usage of individual specimens.
  • Audit SQL contains all UPDATE, DELETE, or INSERT statements, including those which were subsequently rolled back (e.g., due to constraint violations).
  • Oracle Roles is a summary of users by assigned roles. Curators should monitor this, particularly the collection roles (e.g., UAM_MAMM) to ensure that only authorized persons have access to their collections.
  • Funky Data/Suspect Data has several sub-options:
    • Publications without Authors should always find nothing.
    • Publications without Citations may find publications which do not properly cite specimens. This usage may still be reflected in a Project.
    • Projects with Loans and without Publications may require followup with the borrower. Note that Publications may now include things like class reports, dissertations, and brochures.
    • Loans without Specimens are probably legacy or incomplete loans and may not be effectively used to demonstrate collection usage.
  • Funky Data/Partless Specimens finds specimens which have zero specimen parts. Only observations should be in this list; all other cataloged items should have at least one part, even if that part has a disposition of "missing" or "used up."
  • Funky Data/Messy Taxonomy allows searching taxonomy by many criteria to identify various problems.
  • Funky Data/Catalog Number Gaps finds unused catalog numbers. There are no technical problems with nonsequential catalog numbers; this is purely an informational form.

Data Entry: Identification

[ moved to https://arctosdb.wordpress.com/documentation/create/bulkloader/#taxa ]


Data entry (including the Arctos screen and specimen bulkloaders) try to seamlessly construct identifications linked to taxonomy by way of taxa formulae based on user input. However, for taxa formula A {string}, more explicit input is required.

The input string must contain a valid taxonomy.scientific_name, followed by a space, followed by an opening curly bracket, followed by the verbatim identification, followed by a closing curly bracket.


Input Identification Taxonomy Problem
unidentifiable {granite} unidentifiable granite none
granite

All identifications must be linked to taxonomy
unidentifiable{granite}

Incorrect format; missing space.

Linking to Arctos and GenBank

Curators of Arctos collections should encourage researchers using their specimens for DNA sequences to submit GenBank accessions that cite the specimens by catalog number. At a meeting in early January 09, the Database Working Group of the Barcode of Life and GenBank agreed to use essentially our current three-part format for specimen citations. For example:
UAM:Mamm:123456
MVZ:Herp:78910
etc.
(Definition at TDWG)

If the correct term is entered by the owner of the GenBank accession under "source/specimen_voucher," then the catalog number will appear on the GenBank sequence page as a link to the specimen record.
(An example in GenBank.)

If the record is not cited this way, and the owner of the GenBank accession won't change it, then it can still be linked by including the GenBank accession number as an Other ID in the Arctos record. In these cases, the nightly-update links to Arctos from GenBank will appear in the LinkOut drop-down in GenBank accession records.

In an effort to lock down the abbreviations with which we are familiar, I have registered "UAM" and "MSB" with Biorepositories.org, and Berkeley has registered "MVZ." All three of these registrations have been confirmed. So, operations such as the Univeristy of Arkansas at Monticello will have to be more creative than we were! I also put in a few specific collections that I knew already had records in GenBank and listed the curators as contacts, so some of you have been contacted by Biorepositories as part of the confirmation process. This system may be too simplistic to survive the many potential conflicts, but humanity has come to accept internet domain names, so we can hope. In the meantime, what we're doing works. If your collection is not registered, you can either go do it at Biorepositories, or let me know of your interest, and I will start the process.

By including an Other ID Type of "BoLD barcode ID," Arctos records can be also linked to records in the Barcode of Life Database (BoLD). There are currently thirty Barcode IDs in Arctos. We are expecting reciprocal linkages from BoLD to Arctos soon.

Feel free to contact me with questions about this emerging process.

G.

Data Entry: Relationships

Data Entry provides for pre-creating one relationship:



Simply pick a relationship, and specify a related individual by entering an other ID type and a unique identifying number.



There is no checking at this point, and the related individual is not required to exist at this point.

With the exception of catalog numbers (see above), the related ID must be entered as it will appear in coll_obj_other_id_num.display_value. Lists, concatenations, and other strangeness will not resolve.

After the specimen is loaded, the relationship will be saved to Pending Relationships. If the other ID entered in data entry corresponds to exactly one individual (e.g., "field number 1" probably won't), the relationship will be automatically created. Otherwise, curatorial intervention is required.

Tabs and Mac

FireFox on Mac can display strange tabbing behavior.

From The How-To Geek:

Agent (and other) picks

Some controlled vocabularies in Arctos (Agents, Taxonomy) are too extensive for drop-down menus, so a "pick" is used. Recent browsers sometimes interfere with the behind-the-scenes code used to control these picks. The following simplification will help you understand, and therefore hopefully self-debug, how these picks work.

First, a simple form that includes the pick function:

We type a name into the input box....

...and hit TAB (or otherwise leave the field, firing the JavaScript onChange event. This action opens a popup....


Clicking the desired entry populates the name and, normally behind the scenes, the ID field, and turns the Name field green:



This is a successful pick and will save properly.

However, on subsequent visits, your browser may try to be helpful and remember what you've previously typed into the name field:



Selecting one of these suggestions will not open a popup, will not lookup the ID (which is what's actually used to update the database), and will not turn the name field green:



We must somehow force the onChange event to occur if we are to get the information we need to successfully submit the form. The simplest way to do this is to backspace a character from the end of the suggested value and hit the TAB key to force the popup...



...resulting in a green Name field, an ID value, and a successful save.



Note that the popups will self-close if only one possible value is available. The popup opening and closing may be very quick - you may not even see it. However, successful popups will turn the name field green, and are likely to be quite noticeable on most computers.

Label Purchase Guidelines

[ moved to https://arctosdb.wordpress.com/documentation/container/#purchase ]
Guidelines for barcode-containing labels:

  1. Barcodes should be clearly replicated in a human-readable format. The value read by a scanner should be readable by a human as well. Note that XYZ123, 123, ZYX 123, and ZYX0123 are all very different values.
  2. Avoid padding with leading zeroes. These may be handled differently by different applications. In order to keep the character strings all the same length, start the series at a high value. For example, instead of beginning a series at 000001, begin at 100001. Thus, the character string will always be six characters long, and the printed labels will format consistently.
  3. Avoid non-printing characters. Humans, and sometimes machines, can't always tell if that hole represents a space, tab, linefeed, of any of the dozens of other possibilities.
  4. Use big numbers if possible. XYZ1234567890 is less likely to cause unanticipated problems than XYZ1 is.
  5. Don't try to be too clever. You'll learn to hate "L090207" (or was it L927? Maybe L0902007?). Dumb numbers with a locally-meaningful prefix, such as UAM or UAMMAMM, will be much more sustainable.
  6. Check the Barcode Series Spreadsheet very early in the ordering process. Avoid anything that even remotely looks like it could be, or ever could become, a conflict. Duplicate barcodes will not be accepted.
  7. Talk to the Arctos folks before doing anything else. Really. It's free, and we're here to help. Ordering unusable barcodes is not free, and we'll make fun of you for doing that.
  8. Enter the series of barcodes into Arctos and update the Barcode Series Spreadsheet before placing an order or printing your barcodes.