EQ Editor requirements

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?)

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.

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
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
Many species, many publications, single character
- May also use a character survey
- Would use many different papers
- Would span many different species
Specimen may be a fossil record
- Need to record geological time
- Will do that later
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)

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

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