Collaborative Phenotype Annotation

From phenoscape
Revision as of 19:53, 18 September 2011 by Jim Balhoff (talk | contribs) (Requirements from Phenoscape I curation workflow (that are expected to carry forward))

Requirements

A requirements and priorities document is in development and being reviewed by stakeholders.

Technology options

MX

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

  • import matrix data from file source (usually NEXUS)
    • Can import character and state labels, matrix data from a NEXUS file
  • 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

Phenex

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