Checklist for testing development updates

• Create new gene
• Delete gene
• Add and delete synonym, protein synonym
• Add and delete gene product, description
• Add and delete public and private curator note
• Add researchers

• Create Curated Model with curator tools and change gene coordinates using Apollo
• Create a second curated gene model from the same Gene Prediction (as for fused genes)
• Merge gene
• Split gene
• Reconcile two Gene Predictions to the same curated gene model; make sure that both gene predictions show up on the Gene Page
• Check off 'incomplete support,' 'pseudogene,' etc. for a Curated Model
• Check off supporting evidence for a Curated Model
• Test dictybaseID mapper (on Feature Curation page)

• Search all fields: Gene names/synonyms, GenBank accession numbers, Gene products, GO terms, Colleagues, Authors, dictyBaseIDs
• Make sure links to search results work
• Search with wildcards, search case-insensitive
• Make sure resulting Gene Pages are displayed properly
• Search 'Landmark or Region' by gene name and dictyBaseID; case-insensitive and wildcard

• Zoom in and out, navigate left and right
• Dump decorated FASTA files, Watson and Crick
• Check that tracks are displayed properly
• Use Gbrowse search: gene names, dictybase IDs, ESTs, wild cards

• Add annotations:
  
  • Use with/from field; with one and more than one object
  • Share annotations with other genes
• Check Gene Page: terms inserted, links work (check links to GO terms in dictyBase, AmiGO links and external links)
• Delete annotations
• Test cases for with/from field:

      At2g17950|CBS:TMHMM|DDB:DDB0001836|EC:1.1.1.1|ENSEMBL:ENSP00000265949|
      ENZYME:1.1.1.1|FB:FBgn0000055|GR:P93436|GDB:306600|GeneDB_Gmorsitans:Gmm-0142|
      GeneDB_Lmajor:LM5.32|GeneDB_Pfalciparum:PFD0755c|GeneDB_Spombe:SPAC890.04C|GeneDB_Tbrucei:Tb927.1.5250|
      InterPro:IPR000001|KEGG_PATHWAY:ot00020|LIGAND:cpd:C00577|LocusID:3195|MGI:80863|MaizeGDB:881225|
      MetaCyc:ASPARAGINE-SYN|NCBI_gi:30580598| PDB:pdbId=1A4U|RGD:2340|SGD:S000006169|TAIR:gene:2062713|
      TC:9.A.4.1.1|TIGR_CMR:VCA0557|TIGR_EGAD:74462|TIGR_GenProp:GenProp0120|TIGR_Pfa1:PFB0010w|
      TIGR_Tba1:25N14.10|UniProt:P51587|WB:lin-12|ZFIN:ZDB-GENE-990415-103
  

• Search phenotype ontology; insert annotation with check boxes
• Insert phenotype annotation by phenotype number
• Insert multiple annotations to the same phenotype term using different references
• Share phenotype annotation
• Delete phenotype annotation

• Insert new summary:
  
  • Add links to genes, GO terms, and references
  • Check Gene Page: terms inserted, links work
  • Share paragraphs with other genes
• Insert summary for gene without summary and with an existing summary; check for warning message
• Edit summary
• Sample summary for insertion:

      <summary>
      The Slob (Slowpoke-binding protein) family of protein kinases (<go id="4672"/>) was
      originally identified in <i>Drosophila melanogaster</i> as a binding partner with
      Slowpoke, a potassium channel complex (<reference pmid="10230800">Zhou <i>et al.</i>
      1999</reference>).
      <br/>
      Two putative Slob family sequences exist in the <i>Dictyostelium</i> proteome
      (<reference reference_no="11307">Goldberg <i>et al.</i> 2006</reference>).
      <locus name="slob1"/> contains an FYVE domain, which is involved in
      <go id="8270"/>, and a WH2 domain, which has been shown to interact with actin.
      <locus name="slob2"/>, similar to Slob1, contains a proline-rich region near the
      C-terminus in addition to a kinase-like domain.
      </summary>
      
  

• Verify that the correct sequence gets pasted (when starting BLAST from a Sequence Info Page)
• Verify that the correct BLAST program gets selected
• Verify that the BLAST works, including output (layout, score, E value, etc.)
• Try all programs, verify that correct errors get generated when trying to run a protein program with a DNA database or a DNA program with a protein database
• Try "BLASTP at NCBI" from the Gene Page and from the Sequence Info Page
• Download BLAST databases, check that the files look okay

• Select topics, make sure they are correctly added
• Link and unlink genes
• Share annotations with other genes
• Link a PubMed reference

• Create new colleague (internally and externally)
• Update colleague
• Delete colleague
• Be sure to use the colleague record for a dictyBase team member; the person being updated is notified via e-mail, even on testdb!

• Keep same name; rename
• Delete gene product

• NCBI protein, DNA, GeneDB, UniProt (Example: dstA)
• Links to microarray and in situ hybridization (Example: carA)
• Links to Baylor insertional mutants (Example: sadA)
• Links to STKE (Example: carA)
• Links to Ensembl from Gbrowse

• Add, delete, modify strains
• Add multiple synonyms; search on synonyms
• Link strains to genes
• Unlink strains from genes