Collection Objects

A place for information about specimens and related collection items.

As a researcher, as an ecologist, as a collection manager, you want to gather, access, learn from, manage, (and later, share) data describing the Collection Objects (CO) that you steward. Inside TaxonWorks the CollectionObject model offers you a rich set of concepts and the ability to add custom Data Attributes as needed to store and share more data.

New collection object Task: This task suits digitization data capture workflows designed to support use of stub or skeletal records. Minimal data captured here, including text blocks, can be parsed later.

The New collection object task best suits minimal or skeletal data record creation

New Collecting Event Task: In addition to the data about the what (that is, the physical specimen itself), information about the where, how, who, and when, etcetera fit in the TaxonWorks data model in the New Collecting Event (CE) Task.

Use the New collecting event task to capture events

Comprehensive specimen digitization Task (CSD): Combined into one screen, much of the data you have related to a specimen can be entered inside this one window. Inside this task, you have access to buffered data from stub records and verbatim data that can be parsed for you. You'll find you can add people, locality information, biological association data, and add custom fields you need. The following screenshot highlights the different sections of this task in TaxonWorks.

Exploring the Comprehensive Digitization Task in TaxonWorks

Customize the layout and reorder fields

In the top right of the above screenshot, note the options to change the layout of the Comprehensive specimen digitization task. Using these options, you can hide some content if not wanted or needed and move fields into a more optimum order for your data capture strategy.

Layout settings

  • Click on Layout settings in the top right of the Comprehensive specimen digitization task.
  • In the pop-up (see next), select the sections you want to display. Any un-checked sections do not appear on your screen.
Inside this Pop-up, a checked box means that section of the CSD will display

Collection object section inside Comprehensive specimen digitization Task

In the top section of the CSD screenshot, you see sections for Catalog number, Repository, Preparation, Buffered, and Depictions.

Catalog number: TW provides several ways for you to add Catalog numbers to ensure you can find or subset your CO items as needed. Note the Namespace concept in TW which keeps Catalog numbers unique inside a TW Project.

  • Select an existing Namespace for this CO or add a New one if needed
    • You can Search to find the one you want.
    • Recent offers you items you've selected not too long ago.
    • Pinboard gives you the option to attach a given Namespace to the foreseeable items you plan to add at the moment.
  • Add your Catalog number identifier.
  • Check the increment box if you want to create records with numbers that increase accordingly.

Repository: Search for the place where the specimen resides.

  • Use Quick to search using a few letters to find the place.
  • With Recent option you can make us of the last entries made if you might be entering data for items being cared for at the same insitutions.
  • The Pinboard option lets you pick an option (for quick easy access) to be there always unless you remove it from the pinboard.

Preparation: Select the storage method type from options shown. Note you can add to this list if need be as follows.

  • Navigate to the Data tab
  • Search for Preparation types and click on the result
  • In the Preparation types window, click New
    • Type in the name of the method
    • Type the definition of what this term means.
    • Click Create Preparation type

Buffered: Information here can be typed in OR might come from a different task in TaxonWorks that involves capturing an image of labels (and specimens) and getting label text from either typing or from OCR. Data in these fields is not expected to change or be edited.

Depictions: Drag and drop any relevant media (images or figures) into this box.

Determinations section inside Comprehensive specimen digitization Task

Operational Taxonomic Unit (OTU):

  • Select the taxon concept applied (the Determination) to the specimen.
    • Quick for searching names
    • Recent to choose from names you've used for the last few records
    • Pinboard to keep a name handy you'll be selecting a lot
  • Search to select the name of the person who identified the specimen.
  • Enter the date (as much as you know) the Determination was done.
    • Year needs to be 4 digits
    • Enter 2 digits for the Month (e.g June would be 06)
    • Enter day as one or two digits. One-digit days will be standardized to have a leading zero to display in the YYYY-MM-DD format.
      • Please Do Not use zeroes as placeholders for information you do not have for year, month, or day.
  • Click Add

Collecting Event inside Comprehensive specimen digitization Task

Here you find the information about the who, when, and where for the specimen collected. Note this is a separate task in TW. (See New Collecting Event (CE) Task ). The CE fields offered here make it easier to enter all relevant information in one window, in one task. Note the CE has 3 columns, Verbatim, Parse, and then label printing and locality preview.

Verbatim Collecting Event column

  • Label: Enter data here from the label.
    • You may wish to try Parse fields for the software to help you move the label text into the correct atomized fields.
  • Locality: Enter verbatim information from the label or other source describing where on the planet this specimen was collected.
  • Latitude: if provided on label or in another related souce, enter the latitude as it is shown in the image or relevant document.
  • Longitude: if provided on label or in another related souce, enter the longitude as it is shown in the image or relevant document.
  • Geolocation uncertainty in meters: a number expected to already to be meters
  • Elevation: if provided on label or in another related souce, enter the elevation as it is shown in the image or relevant document.
  • Habitat: if provided on label or in another related souce, enter the habitat as it is shown in the image or relevant document.
  • Date: if provided on label or in another related souce, enter the date as it is shown in the image or relevant document.
  • Datum: if provided on label or in another related souce, enter the datum as it is shown in the image or relevant document.
  • Collectors: if provided on label or in another related souce, enter the collectors as they appear in the image or relevant document. This would have the collector information as it appears on your document.
  • Method: if provided on label or in another related souce, enter the method as it is shown in the image or relevant document.
  • Trip identifier: if provided on label or in another related souce, enter this identifier as it is shown in the image or relevant document.

Parse section of CE This section helps to atomize all the information about when and where and who into separate bits of information. Some features offered here include tools to help you georeference, to indicate units of measurement, and to auto-parse data from the Verbatim information.

  • Geographic area: Search to find the desired higher-level geography (e. g. State, or Country). Again (as above) you have options to use Quick, Recent, or Pinboard to speed finding the place. Additionally, you can use Map and then click on the desired place in the resulting map presented.

    • Note that you may find multiple options offered to you. Example, for Alabama, we are offered 4 choices (from various gazetteers). Some are used by many specimens. Choose the one that seems correct (or as outlined by your Project needs documentation).

  • Start date: Enter the start date (YYYY MM DD)

  • End date: Enter the end date (YYYY MM DD) for the CE

  • Elevation: note a range and uncertainty can be added here. Please declare the units.

  • Start time: If relevant and provided, enter the time the event started.

  • End time: If relevant and provided, enter the time the event ended.

  • Collectors section: Search to find the collector(s). Click the desired Collector from the drop-down list. If you have more than one, Search to find the next collector and again, Click the desired name from the drop-down list. If the name you are searching for is not there, type the name (family name, given name) and Click add new. Repeat until you have all the collectors added for that Collecting Event.

  • Trip code section: The trip code comes from the combination of a Namespace and an Identifier. Together, they server as your unique identifier you assigned to this Collecting Event.

  • Namespace : Search to find the desired Namespace (if desired). You may need to add a Namespace. To do that see New namespace task.

  • Identifier: Enter the alphanumeric value that was selected for this Collecting Event.

  • Group: This is a geological term. From Wikipedia, "a lithostratigraphic unit consisting of a series of related formations that have been classified together to form a group." Enter the Group name.

  • Formation: The full name of the lithostratigraphic formation from which the dwc:MaterialEntity was collected sensu Darwin Core dwc:formation

  • Member: The full name of the lithostratigraphic member from which the dwc:MaterialEntity was collected sensu Darwin Core:dwc:member

  • Lithology: From Wikipedia, "the lithology of a rock unit is a description of its physical characteristics visible at outcrop, in hand or core samples, or with low magnification microscopy." Enter the rock description here.

  • Minumum MA: The value representing an estimation for the minimum age of the material in million year units. MA is "megaannus".

  • Maximum MA: The value representing an estimation for the maximum age of the material in million year units.

  • Custom attributes section: Each project in TaxonWorks can add new (customized) fields to their Collecting Events or their Collection Objects. Examples might be:
    -WaterBody: The name of the water body in which the dcterms:Location occurs. This term concept (its definition and expectations) comes from the Darwin Core standard, see dwc:waterBody -georeferenceSources: A list (concatenated and separated) of maps, gazetteers, or other resources used to georeference the dcterms:Location, described specifically enough to allow anyone in the future to use the same resources. This term concept (its definition and expectations) comes from the Darwin Core standard, see dwc:georeferenceSources -lowestBiostratigraphicZone: The full name of the lowest possible geological biostratigraphic zone of the stratigraphic horizon from which the dwc:MaterialEntity was collected. This term concept (its definition and expectations) comes from the Darwin Core standard, see dwc:lowestBiostratigraphicZone.

    To add new fields to either your CollectingEvent or CollectionObject data model, you will need to access

    • the Manage Controlled Vocabulary Terms task and
    • (For Project Administrators), the Project Preferences to associate the newly added terms with the correct TW Object (e. g. the CollectionObject or CollectingEvent) so these terms will appear in the relevant tasks.

Biological Associations inside Comprehensive specimen digitization Task

in progress

Type material inside Comprehensive specimen digitization Task

in progress