Difference between revisions of "Collaborative Phenotype Annotation"
From phenoscape
Jim Balhoff (talk | contribs) (→MX) |
|||
| Line 6: | Line 6: | ||
=== MX === | === MX === | ||
| − | + | ====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 |
| − | * output | + | ** 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]] === | === [[Phenex]] === | ||
Revision as of 19:49, 18 September 2011
Contents
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)
- 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
Pros:
- outputs files ready for KB; workflow in place
- integrates OBO-Edit code for ontology visualization and query
- "simple", targeted interface
- easy to point to customized versions of ontologies
Cons:
- less flexible interface
- requires use of version control system for collaboration
- tightly coupled to OBO format
- updates must be manually downloaded and installed
