Testing development updates

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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).

Contents

Searching

  • Search all fields: Gene names/synonyms, Gene Product Names, Gene Descriptions, Gene Ontology Terms/Synonyms, ESTs, Strains/Synonyms/Systematic Names/dictyBase Strain IDs, Phenotype Terms/Synonyms, Plasmid Names, Protein Domain names, Colleagues, Authors, dictyBaseIDs, GenBank Nucleotide Accession Numbers, Web pages
  • Make sure links to search results work
  • Search with wildcards, search case-insensitive
  • Make sure resulting Gene Pages are displayed properly
  • search deleted feature ID; see that the re-direct works

Genome Browser

  • 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, dictybaseIDs, ESTs, wild cards
  • Search 'Landmark or Region' by gene name and dictyBaseID; case-insensitive and wildcard (see also Genome Browser testing)

BLAST Server

  • 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

Check External Links

  • NCBI protein, DNA, UniProt (Example: dstA)
  • Microarray and in situ hybridization (Example: carA-1)
  • Baylor insertional mutants (Example: sadA)
  • STKE (Example: carA)
  • Ensembl from Gbrowse (any gene)
  • Kinase.com, InParanoid (yakA)
  • EC (ndkC-1, sdhA)
  • GeneDB

dictyCyc

  • Check a gene annotated with Pathways, (Example: purL)
  • Check link from 'Research Tools' menu

dictyMart

  • Search genes
  • Limit search by Gene Name, dictyBaseID, GO ID
  • Search ESTs

Gene Page Curation

  • 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

  • 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)
  • Create a Curated Pseudogene; change start/stop coordinates
  • Merge gene
  • Split gene
  • Make gene without Start and/or Stop codon
  • 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,' etc. for a Curated Model
  • Check off supporting evidence for a Curated Model
  • Test dictybaseID mapper (on Feature Curation page)

Gene Ontology

  • 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:108450|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-990415-265

Phenotype

  • Add phenotypes to strains with existing phenotype annotations
  • Add phenotypes to strains without existing phenotype annotations
  • Add Genetic Context (Phenotypic Manifestation Ontology Term)
  • Add Entity (Dicty Phenotype Ontology Term)
  • Add Quality (PATO Term)
  • Add Environment (Dicty Environment Ontology Term)
  • Add Assay (Dicty Assay Ontology Term)
  • Add Notes
  • Copy annotations
  • Edit annotations
  • Delete annotations
  • Add same annotation to one strain using multiple references


Summary Paragraph

  • 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>


Literature Curation

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


Colleagues

  • 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!


Strains

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

Load GenBank Records

Note that there is a known bug - the Genbank loader is not working see Issue tracker

  • Keep same name; rename
  • Delete gene product



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