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