EQ Editor

EQ Editor requirements

Minimum data entry capabilities to begin EQ curation

• species name (free text until taxonomic ontology is available?)
• EQ statement for character (i.e. Q should be an attribute rather than value)
  • E from fish anatomy (ontology ID)
  • Q from PATO (ontology ID)
  • E2 from fish anatomy (if Q is descendant of "relational quality of continuant" or "relational quality of occurrent") (ontology ID)
• Q for value, either:
  • Q from PATO, descendant of Q in character (ontology ID)
  • measurement (number followed by unit name)
• original character description (free text)
• original state descriptions (free text)
• publication/citation (DOI? older publications don't have DOI, do they?)
• image or URL for image (image data or URL)
• voucher specimen ID (format?)

Interface technological possibilities for EQ editor

This list will need to driven by further discussion of the EQ editing requirements - for now it's just an illustration of some possibilities.

• Mesquite plug-in + extensions to NEXUS format
  • this would allow a curator to work locally and begin working with data before any database is created
  • data would be stored in extended NEXUS format files
  • would provide community value, since Mesquite is general and widely used

• Custom web application
  • could have a more customized interface
  • interface will not depend on integrating into Mesquite; this might allow faster development
  • would a central database need to be set up to store the data?

• Specialized additions to Phenote
  • already has lots of development behind it
  • does not work well with a matrix mindset (Phenote works with a list of value descriptions)
  • development for this purpose might not mesh well with more central uses of the application

EQ Editor requirements (February discussion)

These requirements are a first stab taken at the PI meeting at NESCent on Feb 26-27, 2007.

Morphologist Workflow

1. One reference publication, many species, several characters
   • Have reference publication about taxonomic group, with figures, for skeletal characters
   • May proceed section by section; need to specify section, or figure, or generally part of a reference
   • Need to denote species, choose anatomical entity, choose quality, such as anterior margin, specify value
   • May have questions, or need to input free text comments, e.g., about uncertainties
2. Single species, single publication, multiple characters
   • Might also have a paper describing a single species
   • Curator would use a specimen to confirm accuracy of annotation
3. Many species, many publications, single character
   • May also use a character survey
   • Would use many different papers
   • Would span many different species
4. Specimen may be a fossil record
   • Need to record geological time
   • Will do that later
5. Specimen-based annotation is not part of the project

• Need to reference "traditional" character: should be able to verbatim quote original character description, also give publication reference; there are often differing, even conflicting, definitions for the same character
• Need to be able to see what is already present about a particular character; may also need to look at "similar" characters (as defined by, e.g., characters using sibling terms and sibling qualities)
• Need to see the values that have been assigned already for a character

• There may be conflicting character states reported in different publications; the data curator will decide whether these conflicts need to be kept or can be reconciled.
• Verification of characters descriptions and state values by Data Curator or even Morphologist, e.g., using actual specimen(s), and attributing the verification

• Want all annotations to be associated with voucher specimens (may only be a photograph though)

UI requirements

For example, the Fink & Fink paper

• start by setting the reference we will be working with
• define a set of species we are going to work on
• select skeletal region as a focus, e.g. the gill arch region, or tail fin
• look at what has already been annotated for this region, as a character-by-taxon matrix
  • expect several hundred taxa, and between 50 and 200 characters, depending on how feature-rich the region is
  • a source paper may not give the character at the species level, so the taxon may be a higher-level taxon
• if characters are already present, just add the reference
• otherwise define new character
  • choose existing entity term, initially this will be an anatomy term; term may not exist yet in which case we need to work with a provisional term
  • choose attribute term from PATO; term may not exist yet in which case we need to work with a provisional term
  • denote original character description, with reference (which will probably be the paper we are working with)
• edit/view character: will see the images that have been used for the different states (values) that have been assigned
• assign/edit character states using a table with only the set of species chosen earlier, and one or more characters that correspond to the original character definition
  • denote original character state description, with reference (which will probably be the paper we are working with)

• Taxonomic naming challenges: need to map original names to current classification; should never have two distinct rows for what is currently considered (as defined by the taxonomic ontology) the same species

Database requirements

• Need to have references to digital information, such as specimen record and image