Phenotype annotation requirements

Requirements from Phenoscape I curation workflow (that are expected to carry forward):

• import matrix data from file source (usually NEXUS)
• hold a reference to a publication as the source for the matrix
• view and edit matrix
• free text entry for characters and character states for a matrix
• free text entry for OTUs
• annotate OTUs with taxonomy ontology ID
• add specimens for each OTU, select museum code from ontology
• ontology term autocomplete for term input
• term info panel for terms selected in autocomplete
• ontology tree browsing panel or linkout to term in BioPortal tree view
• output to Excel report - consistency review; author page
• output to KB - currently requires NeXML

Requirements expected to newly arise (or arise at a more demanding level) in Phenoscape II

• Integrate with ORB:

• request temporary term
• check temporary terms for official ID
• use previously requested temporary terms in data

• Improved UI usability:

• UI (data entry) and data model (OWL output) support for pre-configured frequently occurring types of characters (such as presence/absence (neomorphic), qualitative, count, relative phenotype)
• as few clicks as possible for reaching features for composing annotations
• avoid right-clicks where possible
• ability to attach images to character states or entities
• interface that unifies access to pdfs, svn, matrix editor, orb, etc.

• Support collaborative phenotype annotation

• real-time teaching of the curation tool, practices, and results to project curators
• simultaneous editing of different parts of single data matrix
• ability to edit a data matrix without regard to current activities of other editors
• ability to tie into real-time collaborative editing frameworks (such as Google’s upcoming one, codenamed BRIX)
• ability to share pdfs

• Support annotation of homology

• evidence codes
• attribution

• Facilitate wider use and adoption

• easy tool deployment to users, including software updates
• easy deposition of annotation output to a shared repository
• easy digitization of the published matrices
• minimize or ideally obviate the need for maintaining 3rd party software dependencies (such as Mesquite, or SVN tools)
• support for deposition into TreeBASE

Action items

- Have stakeholders review above requirements (phone call 19 Sep 2011 will present to Paul, David, Nizar, other MOD curators?)

- Jim will prepare technology comparison of Phenex and MX relative to these requirements (will take ~ 1 afternoon)

- schedule next phone call (Jim, Wasila, Paula, Hilmar)

Stakeholders

• Curators of evolutionary characters in Phenoscape II:

• Wasila, (Paul Sereno + Nizar starting in 4 weeks), (David Blackburn - starting in 1 yr), Paula

• Other prospective users of the annotation tool:

• Students and interns: Ben Frable (intern at NESCent - starting in 2 weeks), Alyssa Block (USD - working now), possibly someone from Vertebrate ToL (Naylor’s group)