Specimen identification

Owned by Chris Hoffman
Last updated: Feb 04, 2011Version comment
4 min read

Needed by whom and when

Basic statements about who needs the functionality and by when.

UCJEPS, UC Botanical Garden, and other Natural History collections: Significant functionality needed day one.

Overview

Note: Findings from earlier discussions on this topic are recorded in various places.

Note: User stories related to the management of natural science taxonomies are documented elsewhere.

The terms identification and determination are used more or less interchangeably.  Question: Is this true?

In most cases, identifications of specimens are made to a single term in the scientific taxonomy.  However, for plant collections, living or otherwise, hybrid specimens have two or more parents.  See the hybrid user story below and see also Plant hybrid names.  However, named hybrids (hybrid combinations that are common enough that they have a name) might be entered into the controlled vocabulary.  Hybrid names need to be available for search and subsequent identification, but their modeling in relation to the taxonomic tree is complicated.

  • Question: Do UCJEPS and UC Bot Garden include named hybrids in their taxonomic controlled vocabularies?
  • Question: What are best practices for named hybrids?
  • Question: Do UCJEPS and UCBG ever require that specimen identifications be marked as provisional so that they can be reviewed and approved by an authorized user?

Note about user interface: Taxonomic identification (primary, accepted, or current) must be prominently displayed on the primary cataloging/object screen (because the specimen name is effectively the taxonomic identification). Taxonomic identification can not just be a relationship on the right panel.  The scientific name effectively becomes the object title or object name for the specimen.

Common use case: Scientists recognize that one species is really two.  Of the current specimens associated with the old term, some subset will need to be moved to the new term.  Best practice: Create new term based on existing term; perform batch update on selected set of specimens to new taxonomic term.

User stories for definition

Please feel to rewrite these or eliminate completely!  Then move to the prioritized headings below.

  • Specimen identification: While adding or editing a specimen, the user can search (or browse?) the hierarchical taxonomic tree.   Question: What is best practice for searching the tree, especially with regard to synonyms, common names, wildcard searches that bring back multiple matches from  different parts of the taxonomic tree?
  • Specimen identification: User can identify specimen with a term in the taxonomic tree (at any level in the taxonomic tree).  The association between the specimen and the taxonomic term is not a simple relationship.  Numerous attributes on the relationship are required, e.g.,
    • determination agent - the person who made the determination (may include order if determined by group)
    • data entry agent - who entered the identification
    • determination agent institution - the institution for the agent
    • determination date - date determination was made
    • determination type - qualifies determination (e.g. field id, molecular data, ID of kin)
    • accepted determination flag - flags "accepted" identification.  Note: Different domains have different terms (e.g., "valid" vs. "accepted")
    • level of confidence in the identification
    • type of identification (e.g. "fide")
    • citation for the identification (if published somewhere)
    • determination remarks - additional notes/remarks
  • Specimen identification: User can change the taxonomic identification of a specimen (and associated annotations).  History of identifications is maintained and accessible in the user interface.
  • Specimen identification: User can give the specimen multiple "current" determinations – from the collector, from another scientist studying the specimen, from a DNA sequencing lab. User can (or must) mark one record as "primary" or "accepted".
    • Question: Is there an accepted rule for this?
  • Specimen identification: Hybrids - User can enter multiple current identifications for a specimen (e.g. A X B, A or B, A and B).  The relation between the taxonomic terms can be specified as "hybrid".  Question: What other terms for relation types are needed?
  • Specimen identification: User can enter a new (provisional?) term in the taxonomic tree while performing an identification.
  • Specimen identification: User (with appropriate role) can approve provisional identifications, marking them as current and primary.
  • Specimen identification: User can give the specimen multiple "current" determinations – from the collector, from another scientist studying the specimen, from a DNA sequencing lab. User can (or must) mark one record as "primary" or "accepted". Question: Is there an accepted rule for this?
  • Specimen identification: See batch processing - Programmer with appropriate permissions can find a set of specimens and change their identification.  History of identifications will be maintained and visible in the user interface.
  • Specimen identification: See batch processing - User with appropriate permissions can find a set of specimens and change their identification.  History of identifications will be maintained and visible in the user interface.

Prioritization of user stories

As definitions and priorities are clarified, the user stories above should be moved into relative order below.

Must have for 1.x-MUSEUM (when they go live in system)

Placeholder for required functionality.  As a general rule, functionality that you need and use now should go here or where you have existing data.  However, this is up to the museum.  We will have to balance requirements against resources and timelines.

Placeholder

MUSEUM could wait six to twelve months

What could wait?  These will be re-prioritized at a later date.

Placeholder

MUSEUM would like to have this eventually

These are nice to have but not a near term requirement.

Placeholder