Karen Projects

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The following is a list of ongoing projects that I've been working on. I've put "action items" in blue, and the individual files that I'd like to pass along will be in a folder on cgm-1 ddb_curator named Karen. I haven't included completed projects, as all of the information I have should be in the database.

  • General curation: {action item} pass along Curation folder
  • Literature search:

- Literature imported Sunday night/Monday morning
- Use SQL statements in second worksheet of Literature2007 file (on cgm-1); change the two dates to the current Monday and Tuesday, respectively (MM/DD/YYYY)
- Run queries; enter new references in Literature table; assign curator based on past curation (see PPK table on cgm-1)
- Send new references and assigned curators to Petra and Pascale
- {action item} Make sure Petra and Pascale understand how queries are run

  • Strain statistics:

- Use SQL statements in last worksheet of dictyBase_Strain_Info file; change the 'WHERE id > n' to the highest id from the previous week (found in the New Strains worksheet)
- Run queries with 'Send to Excel' marked 'Yes'; copy and paste results in respective worksheets
- Send file to dicty@northwestern.edu
- {action item} Make sure Petra and Pascale have dictyBase_Strain_Info.xls files and understand how queries are run
- {action item} The dictyBase-specific worksheets are probably unnecessary. If you want to see that information, you can filter out Jakob's strains in Excel

  • Standard Operating Procedures:

- All SOPs have been moved to the Wiki site
- Feature curation is not up-to-date; should probably be revised to reflect current practices

  • GO progress reports

- Write dictyBase progress reports for GO meetings
- First section: update on dictyBase GO happenings; last section: other dictyBase highlights
- {action item} See Word documents with previous progress reports and SQL queries to determine statistics

  • NCBI genomes: current "genome champion" is Patti Sherman (sherman@ncbi.nlm.nih.gov)
  • GPI biosynthesis and other carbohydrate-related genes (Chris West):

- All glycosyltransferases from Loomis book have been annotated
- GPI biosynthesis genes (pig genes) not completely annotated; see PMID: 11102867, PMID: 12655644 for reviews
- {action item} See Excel file with dictyBaseIDs for pathway components (GPI_biosynth.xls)

  • Chromatin proteins (Carolyn Napoli (cnapoli@Ag.arizona.edu), chromdb.org):

- Working on integrating Dicty sequences into their database
- {action item} See Carolyn's chromatin_groups_domains.xls file; contains her classifications based on Pfam domains

  • ncRNAs (Pontus Larsson, although we've finished Soderbom's published work); {action item} the following genes are reviewed in PMID: 17171561 and should become ncRNA features:

- Wise and Weiner 1980: D2/Dd9 (PMID: 6159098, GenBank K00789, GenBank V00190); sequences map to several different places in genome
- Kaneda et al. 1983: D1/Dd8 (PMID: 6161130); can't find GenBank record but sequence in publication maps to 5:1458850..1459037
- dutA: no ncRNA gene/feature in Gbrowse; GenBank D16417 maps to 4:2979542..2980864
- msRNA (mitochondrial small RNA; PMID: 9491070, text not available electronically; available at Galter in print)

  • F-box proteins: curated several F-box proteins; {action item} see Fbox_proteins.xls file
  • Spliceosomal proteins: working with Petra and Jane Wu on splicing machinery; {action item} see spliceosomal_proteins.xls
  • GO annotations: I have several annotations that cannot be added due to flaws in the existing GO annotation tool or due to pending SourceForge items; {action item} see Excel file with list of annotations to be made (karens_go_annotations.xls)
  • Phenotypes:

- I have a few phenotypes that I was unable to add, they do not have an existing term in the dicty_phenotype ontology or they could not be added because of the old tool; {action item} see phenotype_annotations_to_make.txt
- There's a few pending issues in the 'Curator Issues' issue tracker
- Growth + environmental phenotypes still need to be changed; {action item} see growth_phenotypes_03092007.xls file
- Need to work out delayed vs. slow annotations ('delayed' has multiple meanings in the definition, as noted at committee meeting); {action item} see delayed_pheno.xls file

  • Other?

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