Overhaul Curation Updates

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Contents

General Big Curation Issues

  • Reconcile all dictyBase curation tools (no difference between literature and gene model and other curation tools for login)
  • Eliminate Wiki from active curation (updating gene name)

General Gene Info

  • Add gene info directly on web page with login
  • Gene names, synonyms, gene products, summaries, gene model annotations, etc.
  • name description: add automatic formatting/constraints
  • private and public notes: enter also directly on page (maybe pop up window), private notes will be hidden from public view.
  • Curation status: push buttons to update: Comprehensive, Basic, or Gene Model. We need to talk about special community curation notes!
  • Community curation: Summary, description with login (see also below)
  • Colleague link: Editable by us and logged in super user from colleague entry

Bulk/Copy annotations

  • Bulk/copy annotations for multiple genes. Maybe command line or integrated in above web-based tool to 'copy' annotations. Descriptions may be completely copied, summaries also.
  • gene products may be the same except the gene name. Maybe also copy and edit these.
  • Bulk annotate also phenotypes, strains, plasmids.

GenBank Entry Import

  • Current GenBank loader: Querying is still working, loading into dictyBase is broken. Curators still need to control which GenBank records to import into database, want to discriminate against Patents. Sidd said maybe can be integrated into Jaybrowse/webapollo.

Colleagues

  • Make entries for collaborators/supervisors etc. more 'fool proof', e.g by showing existing colleagues as people type. However, they need to be able to add new colleagues to the database.
  • We need an easy way to see if there are more than one profile for a single user.
  • Send alert to curators for when colleagues update/add new profiles.

Strains

  • Strain search (same with plasmids). On search result page the buttons link overwrites current view. Should open in new window or be able to open in tab.

Strain annotation

  • Annotate strains directly on strain page (discussed with Sidd); pop up for private note.
  • Other non-public fields in current strain annotations (obtained_as, keywords, SC phenotypes) will be moved (to inventory) or deleted.
  • When adding parental strain, automatically add genotype of parent, so that additional stuff can be added
  • When adding plasmid autofill from plasmid database

Phenotypes

  • Ontologies: Mark secondary terms as such and show PRIMARY TERM
  • Environment terms: new terms do not show up anymore, NEEDS FIX (old annotations still show, e.g. sadA-)

Community Annotation

  • User login, direct interaction: maybe make those genes curatable for a user (restricted fields) where the user and gene are linked. Let users link themselves to genes.
  • Look at Pombase community annotaion tool

Stock center projects

  • Bulk upload of strain/plasmid annotations
  • Show plasmid keywords on the user side / List of unique strain/plasmid keywords
  • Show plasmid synonyms
  • Provide a pop-up of the keywords as a help to search plasmids
  • Show in plasmid list when plasmids have Maps and/or Sequence
  • Allow plasmids to be linked to genes by curator interface
  • Add the orders done through e-mail
  • Making strains/plasmids publicly visible/invisible through curator interface ('hide' button)
  • Stats for time of receipts -> shipped/growing from issuetracker
  • Make plasmid description searchable
  • New field for 'parental vector' for plasmids
  • Plasmid searches do not accept wildcard character (Dave Knecht)
  • Have extra 'Contact DSC' link on all DSC pages (dictystocks@northwestern.edu)

MyDSC

  • Create User login (regardless of grant)
  • Create order history? Status upate?
  • Provide way of curator manipulate orders right in the database, not in separate Issue tracker

User requests/Issue trackers

  • Automatically add to some "Issue Tracker" when people email dictyBase@ and Dictystocks@.
  • Make it possible that curators can forward an email they get personally to the collection

Usability/Display Issues

  • Searches
    • Exp: search for all PMID associations (Genes, GO, Strains, Phenotypes). Petra thinks INTERMINE will allow searches like this.
    • BUT: Interestingly, the Stock Center Strain search finds strains by PMID, however, the Plasmid search does not and it's not indicated anywhere.
    • Sidd said he wants to 'unify search, specific SC searches might have to go away, Intermine?! Needs dictyBase discussion!

Protein Domains

  • In table view, make domains clickable to display all genes which have that particular domain.

GO

  • Separate manual and electronic (IEA) annotations on gene page
  • Display annotation extensions (former column 16); look at Pombase

Literature curation/Gene associations

  • Delete all PubMed associations to deleted genes, e.g. actin has hundres of 'uncurated' papers attached.
  • Create extra curator click to check when a paper is curated. Maybe also when a paper is inspected but 'uncuratable' would be nice)
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