Specify 6.8.01 Release Notes (Schema 2.9)

Specify 6.8.01 Release Notes

Specify Collections Consortium, 15 September 2021

[Specify Administrators: This release updates the Specify database schema version from v2.7 to v2.9
(v2.8 skipped). Once the database is updated, all Specify 6 workstations will need to be updated to
this release. Sites using Specify 6 and 7 concurrently will need to update both applications for schema

The improvements and extensions in this Specify 6 release are the culmination of several
months of close collaboration by SCC staff and members. Highlights include: 1) new Specify
Interactions and identifiers, 2) expanded support for item-level processing in specimen
transactions, and 3) introduction of the Specify Network with services for retrieving and
comparing remote data related to the specimens and species in your Collection. These
capabilities are summarized below along with lists of smaller enhancements, bug fixes, and
database schema update details.

1. Support for New Interactions and Identifiers

Disposals are transactions that document the reasonfor the removal of a specimen from a
collection other than gifts or exchanges. A Disposal record may be required by collection policy
when a specimen is consumed by destructive analysis, can no longer be found, was lost in
transport, not returned from a loan, or discarded due to poor condition. The new Disposal data
table supports institutions with disposal policies that require tracking of intentional and
unintended specimen removals.

Deaccessions are transactions that document relinquishingthe legal ownership of a specimen.
Deaccession transactions are similar to Disposals in that they deal with specimens that are no
longer in the collection. Disposals document the curatorial details for the removal of a
specimen, whereas Deaccession records represent a change in legal ownership. Deaccessions
can also document changes in ownership for specimens transmitted as Gifts or Exchanges. In
this release, a Deaccession requires a corresponding Gift, Exchange Out or Disposal transaction
record. Deaccessioned Collection Objects and Preparations remain in the database but they can
be filtered out with queries to exclude them from counts and exports.

Preparation Identifiers are needed to track the movementof the physical parts of Collection
Objects, Preparations. Typically, bar code labels are affixed to Preparations to uniquely identify
them. In Specify’s data model, Collection Objects logically participate in transactions such as
Loans, while one or more Preparations belonging to those CO’s represent the actual, physical,
loaned objects. IDs that identify Preparations can now be used in Transactions as well. The
BarCode field in Preparation is designed for use with a barcode reader to efficiently record
items in outgoing and returned Loans. We added further flexibility to choose which field in
Preparation will be used for internal identifiers when creating a Loan, Gift, Exchange Out or
Disposal. A user preference can be configured to specify the table and field to use for identifying

Specify 6.8.01 Release Notes, Page 2

Preparation records when one of those Interactions is created. It is important to emphasize that
these identifiers are aids for internal transaction processing only and are not intended for
publishing or external use. For globally-unique, permanent identifiers, Specify automatically
assigns UUIDs to separate GUID fields in its core data tables, including Collection Object and

Additionally, Record Sets composed of Preparation records can now be dragged and dropped
onto the Loan, Gift, Exchange Out, and Disposal sidebar actions to create and complete new
interaction records. Previously only Record Sets of Collection Objects could do this. Specify’s
Information Request function has also been extended; it can now be used to initiate Loan, Gift,
Exchange Out, or Disposal transactions.

2. Expanded Item-Level Processing

In Specify, the “Collection Object” concept logically equates to ‘lots’ for lot-based disciplines
and specimens for specimen-based catalogs. A Preparation is the physical manifestation of
Collection Object that is preserved with a particular Preparation Type, e.g, an herbarium sheet,
a pinned insect, cleared and stained fish, a mammal skull. An increasing number of SCC
collections have requested support for tracking the individual physical artifacts that can
comprise a single Preparation. Specify models the individual pieces of a Preparation as “Items”.
Examples include: the individual seeds in a seed vial, subsamples carved from a single frozen
tissue specimen, or multiple herbarium sheets that comprise a single unwieldy specimen. Item
IDs and counts come into focus when managing museum transactions. For example, the total
number of sheets (items) of herbarium specimens loaned to another institution is an important
data item on a loan form or packing list for shipping, and for verifying the completeness of a
returned loan.

In this update, Specify enables item-level processing in several Specify Interactions and data
table forms to make item counts and totals more accessible. Specify 6 had already offered
item-level processing for Loans with data fields for: total, resolved, and unresolved items. In this
update, we added Item count and total fields to: Accession, Deaccession, Disposal, Exchange
Out, and Gift processing. Item fields are virtual and not in the database schema, but are visible
in the Query Builder and can be included on data forms and in printed reports (see list below).
The new fields are placed on the default data forms in this release. Collections with customized
data forms can contact SCC Support for assistance in retrofitting their forms to include them.

Specify 6.8.01 Release Notes, Page 3

3. Introducing the Specify Network

The biological collections community is developing a vision for a global, biodiversity information
architecture that will enable powerful new methods for digital interactions among organizations
that manage specimen data. A world-wide specimen data architecture based on digital object
concepts, permanent identifiers, and APIs will transform biological collections computing by
supporting network-enabled research and curatorial workflows. Museums will benefit greatly
from network services that provide immediate access to downstream information derived from
objects in their collections.

The Specify Network, introduced here, takes a step toward that future. Technologically, it
includes: a network services Broker, an ID Resolver, and the Specify Cache. We developed these
forward-looking technologies in collaboration with the Biotaphy Project
(https://biotaphy.github.io/, NSF #1930005). Togetherthe components enable network
integrations based on Specify 6’s Collection Object GUIDs and Taxon names. The Specify
Network can be invoked while viewing a Collection Object record by using the large button in
the upper right corner of the form. Clicking the button will send the specimen record GUID to
the Specify Network for executing queries on remote services (currently including: GBIF, iDigBio,
Lifemapper, MorphoSource, and WoRMS). The Network will then create a summary web page
of any available information returned with the query results. Unlike weblinks where the path to
information related to your collection objects requires a static URL, the Specify Network
performs discovery and linking functions “on-the-fly” through dynamic, network interactions.

The Specify Cache contains copies of Specify 6 database records exported in the Darwin Core
standard. Specify 6 will export a subset of your collection’s occurrence data to the Specify Cache
that runs on a private SCC server. A new Preferences menu option enables a Collection to opt-in
to using the Specify Cache. The Cache has no web interface; its data are viewable in Specify only
through APIs with the Collection Object GUIDs from your collection. Currently, the main
function of the Specify Cache is to enable comparisons of Collection Object data fields in your
Specify 6 database with records held by aggregators and name authorities. In a future release
the Specify Cache, Broker, and Resolver will enable statistical analysis to quantitatively describe
your collection in new, research-relevant ways. Although the Specify Network will not
immediately reconcile multiple versions of specimen records and related distributed update
issues, it will provide a technical path to take on data integration challenges such as moving
occurrence records between collection management systems.

The Specify Network is a core element of the SCC’s technology vision. Specify institutions will
benefit directly from its information and computational service integrations. Growing and
extending it will help SCC institutions envision and engineer network-enabled workflows, and
will reinforce the role of museums as primary sources of vouchered species information in a
future global, biodiversity data architecture.

Specify 6.8.01 Release Notes, Page 4

Capability Enhancements

https://github.com/specify/specify6/issues/ (postpendnumber to URL to see GitHub issue)

398 (& 805) Add compatibility for .xlsx (Microsoft Excel) format files. (Note: The Specify 6
WorkBench has an admin configurable limit of 7,000 rows per import file/Data Set to
reduce the possibility of running out of Java memory with large WorkBench uploads.)

680 The Shipment subform is no longer active by default when opening a new interaction

737 GeoLocate’s map server is now the default, not NASA Whirlwind.

746 Exports that include Lat2/Long2 will no longer add ‘null’ to those fields in exported

756 Preparation Record Sets will now open in the Collection Object forms, but other Record
Sets not associated with a ‘Main’ form will offer a notification.

764 When attachment files can not be located a prompt will display: “There were no files to

810 The maximum number of matches allowed for a Tree rank in query results has increased
to 6,000.

802 Improved support for displaying and printing for 2D/DataMatrix barcodes.

821 An xml library update fixed a problem with handling Specify resource files.

822 A second redundant button for importing a schema has been deleted in the Schema &
Localization Tools window. Also if a file contains more than one language, Specify will
ask which language you want to import.

851 Taxa with associated common names can now be merged.

853 Preferred Taxon field field will now reflect the format created for the Taxon table in the
same way that Taxon field does.

854 Preferred Taxon field can now be laid out as a remarks field (textareabrief component)
on forms.

856 The WorkBench now detects inconsistent Taxon rank mappings in data sets.

885 The “Loans without Preps” sidebar item has been removed; uncataloged items can now
be added to new or existing Loans. Uncataloged items can also be added to new or
existing Gifts, Exchange Outs and Disposals through the main system of dialogs.

Specify 6.8.01 Release Notes, Page 5

910 Added support for embargo function with addition of these fields to the Collection
Object table:Reason for Embargo,Embargo Start Date, Embargo Release Date, Embargo
Authority (link to the Agent).

925 (& 941, 946) Exchange Out Number field now requires a value by default. The value is
enforced to unique (scoped to Discipline). The field is now accessible for configuring
Simple Search.

Bugs Fixed

765 Specify 6 database schemas can now be exported and shared with other Specify sites.

773 DNASequence can now be logged along with the parent information.

791 Bug causing alternate language descriptions to be indeed to fields in the English Schema
Configuration has been fixed. Original descriptions have been restored for English

794 Collecting Trip Attachments can now be used without a bogus error notification.

798 Editing Preparations with existing storage information will now update correctly without

803 Custom tree nodes have been upgraded to allow for variant punctuation.

804 When a blank Excel file template for new data is exported from the WorkBench, all of
the database upload mappings including taxonomy are now included. The mappings are
imported and re-used for uploading new data.

820 A “Confirm Override” dialog will now display after choosing to override another user
using a Specify data tree.

842 The Biostrat checkbox is no longer checked automatically when creating a Chronostrat
record from a form.

848 An issue with tree merges involving the AlternateStorageID was fixed.

892 Loan Returns now consistently require a ‘Received By’ Agent to be associated with a
Loan Return event.

913 Highlight New Cells in the Workbench will now highlight appropriately if there are

Locality or Geography fields in a Data Set mapping but no Collecting Event table fields

Here are the tables converted into tables:

Specify Schema Update (v2.9): Additions, Changes, Virtual Fields

Table Field Data Type Length
Agent Text3 text 65535
Agent Text4 text 65535
Agent Text5 text 65535
Borrow Status varchar(64) 64
Collecting Event Text6 text 65535
Collecting Event Text7 text 65535
Collecting Event Text8 text 65535
Collecting Event UniqueIdentifier varchar(128) 128
Collection Object EmbargoAuthorityID int(11)
Collection Object EmbargoReason text 65535
Collection Object EmbargoReleaseDate date
Collection Object EmbargoReleaseDatePrecision tinyint(4)
Collection Object EmbargoStartDate date
Collection Object EmbargoStartDatePrecision tinyint(4)
Collection Object Text4 text 65535
Collection Object Text5 text 65535
Collection Object Text6 text 65535
Collection Object Text7 text 65535
Collection Object Text8 text 65535
Collection Object UniqueIdentifier varchar(128) 128
Common Name Tx Citation FigureNumber varchar(50) 50
Common Name Tx Citation IsFigured bit(1)
Common Name Tx Citation PageNumber varchar(50) 50
Common Name Tx Citation PlateNumber varchar(50) 50
Deaccession Agent1ID int(11)
Deaccession Agent2ID int(11)
Deaccession CreatedByAgentID int(11)
Deaccession Date1 date
Deaccession Date2 date
Deaccession DeaccessionDate date
Deaccession DeaccessionID int(11)
Deaccession DeaccessionNumber varchar(50) 50
Deaccession Integer1 int(11)
… Continued …

Changed Database Schema Fields:

Table Field Previous Data Type New Data Type
Address Address3 varchar(64) varchar(400)
Address Address4 varchar(64) varchar(400)
Address Address5 varchar(64) varchar(400)
Borrow Material Description varchar(50) varchar(250)
Collecting Trip Collecting Trip Name varchar(250) varchar(400)
Collection Object Description varchar(255) text
Determination FeatureOrBasis varchar(50) varchar(250)
Reference Work Title varchar(255) varchar(400)

Added Virtual (Calculated) Fields:

Table Field Caption Definition
Interactions Accession Total Items # of Items that were ever part of the Accession, usually the original number
Interactions Total Current Items # of Items currently included in the Accession
Interactions Total Preps # of Preparations in the Accession
Interactions Total Collection Objects # of Collection Objects in the Accession
Deaccession Total Preps # of Preparations in the Deaccession
Deaccession Total Items # of Items in the Deaccession
Disposal Total Preps # of Preparations in the Disposal
Disposal Total Items # of Items in the Disposal
Exchange Out Total Preps # of Preparations in the Exchange Out
Exchange Out Total Items # of Items in the Exchange Out
Gift Total Preps # of Preparations in the Gift
Gift Total Items # of Items in the Gift
Loan Total Preps # of Preparations in the Loan
Loan Total Items # of Items in the Loan
Loan Resolved Preps # of Preparations returned or accounted for in the Loan return
Loan Resolved Items # of Items returned or accounted for in the Loan return
Loan Unresolved Preps # of Preparations not returned or unaccounted for
Loan Unresolved Items # of Items not returned or not accounted for
Collection Object Total Items # of Items that were ever part of a Collection Object, usually the original count of items
Collection Object Total Current Items # of Items currently subsumed by the CO
Preparation CountAmt # of Items in a Preparation
Preparation Current Count # of Items currently included in the Preparation