dictyBase SOPs: Checklist for testing development updates
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Checklist for testing development updates

Last updated April 26, 2006

When the developers make major updates to the database, curators need to check the curation process to ensure that the curation tools are still working properly. Test each of the following items in all browsers (Internet Explorer, Mozilla Firefox, Safari).

Gene Page Curation [TOP]
  • 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

Feature Curation [TOP]
  • 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)

Searching [TOP]
  • 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

Genome Browser [TOP]
  • 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

Gene Ontology [TOP]
  • 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:
        MetaCyc:ASPARAGINE-SYN|NCBI_gi:30580598| PDB:pdbId=1A4U|RGD:2340|SGD:S000006169|TAIR:gene:2062713|

Phenotype [TOP]
  • 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

Summary Paragraph [TOP]
  • 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:
        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>
        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.

BLAST server [TOP]
  • 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

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

Colleagues [TOP]
  • 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!

Load GenBank records [TOP]
  • Keep same name; rename
  • Delete gene product

Check External links [TOP]
  • 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

Stock Center Strains [TOP]
  • Add, delete, modify strains
  • Add multiple synonyms; search on synonyms
  • Link strains to genes
  • Unlink strains from genes

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