Noctua Standard Annotation UI Project - Overview

[vanaukenk]

Annotation Entry

• [x] Curators can autocomplete on any annotatable entity in NEO
• [x] Gene
• [x] Protein
• [x] ncRNA
• [x] Protein-containing complex (including for now)
• [x] If a curator selects a gp2term relation, the ontology term restricts to the appropriate GO aspect, e.g. ‘enables’ restricts to MF. (Can't be done?)
• [x] Curators can autocomplete on any GO term.
• If a curator selects a GO term first, the gp2term relations restrict to the appropriate subset.
• [x] Curators can autocomplete on any ECO term.
• [x] Curators can add a reference in the form of: (CHECK LEADING/TRAILING WHITE SPACE)
• PMID. Entering a new PMID validates bibliographic data at PubMed
• doi
• GO_REF
• [x] Curators can enter a value in the With/From field
• [ ] Leading or trailing whitespace in free text fields is removed upon save (STILL NEEDS WORK)
• [ ] Split into two fields: database prefix and identifier (EXISTING CODE?)
• [ ] Curators can choose any valid annotation extension relation (IN PROGRESS) - add another extension functionality?
• [ ] Curators can enter any valid annotation extension object (IN PROGRESS)
• Ideally, restrict allowed extension relations by GO term
• [ ] Curators can add one or more comments to an annotation (NOT DONE)
• [x] Curators can negate an annotation
• [ ] Curators can add a root node annotation in one step/click (NOT DONE)
• [ ] Curators can add an interacting taxon to an appropriate ontology term (NOT DONE - NEEDS DATA MODEL DECISION)
• [x] Save checks for any missing required fields:
• Gene Product
• gp2term relation
• GO term
• Evidence code
• Reference
• [X] Curators can clear and entry to start over
• [ ] Curators can copy an entry and modify any field before saving (NOT DOING for V1)
• [ ] Curators can create a new blank entry before saving (NOT DOING for V1)
• [ ] Curators have the option to save each annotation individually or save in batch (NOT DOING for V1)

Annotation Table Display - review existing production table display

• [ ] Annotations display as a standard annotation, in GPAD file format, in the table* (see below) (EXTENSIONS NOT YET DISPLAYED, NOR CONTRIBUTOR, ASSIGNED BY or DATE)
• [x] Gene products relate to GO terms with gp2term relations
• [ ] Almost every field in the table is editable (CLARIFY?)
• For editing relations, restrict relations to appropriate ontology subsets as for annotation entry
• Curator, group, and timestamps are not editable
• [ ] Curators can add extensions to an existing annotation in the table
• [ ] Curators can add additional evidence to an existing annotation in the table
• [ ] Sorting (IF NOT DOABLE - REMOVE THE ICONS)
• [ ] Check all 'additional options' three-dot menus - make sure all functionality works, if not, remove it
• [x] Delete annotation - simple, unconnected, i.e. no causal relations, annotation

Database Work

• [ ] Add metadata to existing Noctua models to discriminate between fully GPAD compliant models vs non-GPAD-compliant models
• GPAD compliant according to GPAD file rules
• • Models with nested annotation extensions are not compliant
• • Other reasons for non-compliance: WIP

Noctua Work

• [ ] Add link to new standard annotation workbench to Noctua landing page and other places where workbenches are accessed (icons on landing page, other functions menu on the workbenches)
• [ ] Retire Noctua form - when?

Other issues

• [ ] Find in page - browser specific or something under our control?

[tmushayahama]

@vanaukenk Thank you for compiling this summary! Having the specifications outlined in checkboxes provides a clear and efficient overview lookup, making it much easier to understand and track progress. This is incredibly useful and much appreciated.