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EQ Editor requirements draft 1

This draft of the EQ Editor requirements is now out of date. See the current version.

EQ Editor requirements

The EQ Editor will be used by curators to annotate phenotypic descriptions of Ostariophysi using EQ syntax and ontologies.

The curator will use the EQ Editor to code phenotypic data from an existing publication into the EQ format. This data consists of descriptions of character state values for corresponding species (or, more precisely, specimens). A published character state description may contain: the species or higher taxonomic specification, a textual description of the character state value, reference to a voucher specimen for this description, an image showing the character.

Data Model

The following are essential data elements to be captured by the EQ Editor for each character state description (format is in parentheses). EQ coding will be performed at the level of character states, but there may be a facility for dynamically viewing entries in a character matrix format. See “EQ for character matrices” for a discussion - at the June 5 PI meeting we decided to work with only character states.

Workflow

Sources of data

The publication being coded may contain data in one of a few different formats. The given data format may suggest its own style of workflow. These publication types include 3 main forms:

  1. Description of many characters for many species and higher taxonomic levels; no character-by-taxon matrix published.
  2. A data matrix with multiple species and multiple characters. There is a character state value for each cell in this matrix.
  3. A single species description of values for many characters.
  4. Description of a single character for many species (perhaps less common than the other formats?). If focusing on a single character the data may come from multiple publications.

It seems like scenarios 2 and 3 can be treated as special cases of scenario 1. For each character, an interface is required for choosing the Entity and Quality from their respective ontologies, and entering free text such as the original character descriptions, as well as other relevant data.

Detailed steps

The standard workflow would be a curator dealing with a single publication during a session of working with the EQ Editor. Steps might be:

  1. Create a new EQ Editor document.
  2. Enter document-wide data:
    1. publication information (author, title, journal)
    2. list of specimens - input specimen info, choosing museum institutions from a pick list, and choose taxon from taxonomic ontology for each one
  3. Begin making character state annotations:
    1. Select a specimen or multiple specimens to which this character state applies (there should be facilities for efficiently choosing sets of specimens/taxa)
    2. Create a new EQ statement
    3. Choose Entity from anatomy ontology
    4. Choose Quality from PATO (usually a Value term)
    5. If the Quality is an Attribute term (such as “length”), enter a measurement and its units
    6. If the Quality is relational, enter a second Entity from the anatomy ontology
    7. If dealing with a single specimen, enter optional image data (URL). Images may not be applied to multiple specimens at once.
  4. At any point, the curator can save the current work to a document (or database).

Working with EQ statements

Questions

Technology

Some technology choices may figure into the application requirements, particularly if integration with another application or system is a desired feature. The major distinction to begin with is between a web-based application and a standalone (desktop) application: