Gene Ontology

Manual Literature Curation

Reference Genome (see also Reference Genome Inferential Annotations)

1. Lung Development Targets (November 2009 - February 2010)

Transcription-related re-annotation

This summarizes the annotations that may need to be revised due to changes in the GO's representation of transcription.

7 Molecular Function terms will be obsoleted. They are listed below with the number of manual elegans annotations associated:

• GO:0003704 specific RNA polymerase II transcription factor activity - 8 (all Kimberly)

 ceh-24 - ISS - changed to  GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity 
 ceh-27 - ISS - same as above
 ceh-28 - ISS - same as above
 elt-1 - IDA - same as above
 elt-3 - IMP - for WBPaper00004593, removed MF term (no longer comfortable with IMP MF terms from this type of experiment); 
   also made corresponding BP term less granular, from positive regulation to just gene-specific transcription from pol II promoter
 elt-3 - IMP - same as for elt-3 above
 hlh-3 - IMP - for WBPaper00031977, removed MF term for same reason as above, also made BP term less granular as above
 zip-2 - IMP - for WBPaper00035891, same as above for elt-3 and hlh-3

Semi-Automated Methods of Curation

Textpresso-Based Curation

• CCC - GO Cellular Component Curation using Textpresso

Specifications for CCC Curation from Textpresso Search Page

• MFC - GO Molecular Function Curation using Textpresso

Phenotype2GO pipeline (Sanger and Caltech)

• The old Sanger script that generates the gene_association file (from Igor's work in January 2009) was changed. Instead of an exclusion list and 'include list' that comprises papers (mostly large scale genome-wide studies) is provided to the script. This list is curator approved and explicitly agreed upon for the propagation of GO terms to genes based on their RNAi phenotypes.
• A new script is used, to use it invoke the script with the -includelist option, e.g.: Run parse_go_terms_new.pl -o gene_association.wb -rnai -include includelist.txt (this example only parses RNAi experiments, to generate full file, you should also give '-gene -var' options as before).
• If you invoke it with '-acefile <filename>' option, the script will also generate Gene-GO_term connections derived from phenotypes. This is currently done by the phenotype procedure of the inherit_GO_terms.pl script.
• The old script: inherit_GO_terms.pl does not consult any exclusion/inclusion files. To alter Sanger's version of parse_go_terms_new.pl, a patch file was provided.
• Current status:From Igor's e-mail, March 2009: I don't think the phenotype option of the inherit_go_terms script has been disabled. The script should be run without the '-variation' option, but the gene_association file still has those. Try this:

grep -i wbpheno gene_association.WS200.wb.ce |grep -v RNAi This is now resolved.

• Phenotype2GO Mappings File
• Phenotype2GO Mappings Sept. 09
• Phenotype2GO Paper Inclusion List

WormBase contributions to Gene Ontology content

2011

• in progress - centrosome maturation (2011)
• defecation motor program (2011)
• modifications to terms and definitions of cilium assembly and sensory cilium assembly (2011)
• ciliary transition zone (2011)
• regulation and pos/neg regulation of microtubule motor activity (2011)
• nickel ion homeostasis and cellular nickel ion homeostasis (2011)
• neurotransmitter receptor catabolic process (2011)

2010

• regulation of defecation, positive and negative children (2010)
• mitochondrial prohibitin complex (2010)
• cilium terms (2010, updates/revisions to terms added in 2005)
• octapamine/tyramine signaling involved in the response to food (and the regulation terms) (2010)
• alpha-tubulin acetylation (2010)
• phagosome maturation involved in apoptotic cell clearance (2010)
• phagosome acidification involved in apoptotic cell clearance(2010)
• phagolysosome assembly involved in apoptotic cell clearance (2010)
• phagosome-lysosome docking involved in apoptotic cell clearance (2010
• phagosome-lysosome fusion involved in apoptotic cell clearance (2010)
• neuropeptide receptor binding (2010)
• striated muscle contraction involved in embryonic body morphogenesis (2010)
• striated muscle myosin thick filament assembly (2010)
• striated muscle paramyosin thick filament assembly (2010)
• determination of left/right asymmetry in the nervous system (2010)
• regulation of locomotion (including positive and negative regulation child terms) involved in locomotory behavior (2010)
• detoxification of arsenic (2010)
• chondroitin sulfate proteoglycan binding (2010)
• chondroitin sulfate binding (2010)
• regulation (includes positive and negative regulation child terms) of nematode larval development (2010)
• regulation of (includes positive and negative regulation terms) dauer larval development (2010)

2009

• response to drug withdrawel (2009)
• phosphatidylserine exposure on apoptotic cell surface (2009)

2008

• regulation of synaptic vesicle priming (2008)
• chloride-activated potassium channel activity (2008)
• transdifferentiation (2008)
• Regulation of ovulation terms (2008)
• Process terms for gap junction proteins (2008)
• piRNA and 21U-RNA terms (2008)

2007

• dense body (sensu Nematoda) cellular component term (2007)
• GO:0000775, GO:0000779, GO:0000780
• D/V and A/P axon guidance terms (2007)
• palmitoyl-CoA 9-desaturase activity (2007)
• response to hyperoxia (2007)
• Cuticle component terms (2007)
• response to anoxia (2007)

2006

• dynein light intermediate chain binding (2006)
• Regulation terms for cell and nuclear division (2006)
• Several child terms for apoptosis (2006)

2005

• Cilium terms (2005)

2004

• Intraflagellar transport particle-component terms (2004)
• oogenesis (non-species specific term)(2004)

Modifications to the Ontology

• Revised definition for muscle homeostasis (2010)
• Added dense core vesicle synonym to dense core granule (2010)
• Updated definition and moved parentage for intraflagellar transport (2009)
• Added lethargus as synonym for sleep (2008)
• Change to the definitions of the component terms: GO:0000775, GO:0000779, GO:0000780 which refer to the centromeres or chromosome, pericentric region (2007)
• Change to parent of tail tip morphogenesis (sensu Nematoda) (2006)
• GO:0046536, dosage compensation complex definition (2006)

Annotation Practices

Cellular Component Annotations

If a protein contains a transmembrane domain, but expression experiments are not at sufficient resolution to show membrane localization, what annotation should we make?

Example: WBPaper00036024

WormBase use of Column 16

Column 16 refers to a column in the Gene Ontology's (GO) tab-delimited gene association file (gaf) that WormBase submits to the GO consortium on a regular basis.

Column 16 has been referred to as the Annotation Extension column in that it provides a placeholder for curation details that cannot be captured by a GO term alone, for example the substrate upon which an enzyme acts.

A number of different types of information could conceivably be entered into Column 16. The list below begins to document the use of Column 16 by WormBase curators with any additional information or questions that have arisen during the course of curation.

Column 16 curation at WormBase is just beginning and will likely be fleshed out more fully over the next few months.

In the Ontology Annotator, Column 16 data is being entered into the 'Xref to' field in the following format: Column 16: Xref ID

Biological Process Examples:

Translational Regulation

Example 1: sup-26 is annotated to GO:0017148, negative regulation of translation. The entry in Column 16 is the target of that regulation, tra-2.

In OA entry: Column 16: WB:WBGene00006605

Defense Response

Example 1: lys-7 is required for defense response to Cryptococcus neoformans

In OA entry: Column 16: NCBI:192011 (a taxon ID)

Molecular Function Examples:

Example 1: sup-26 is annotated to GO:0003730, mRNA 3'-UTR binding. The entry in Column 16 is the target of that binding, tra-2.

In OA entry: Column 16: WB:WBGene00006605

Plans/Projects in progress

Changes to the GO data model

• Add tags for accommodating data in WormBase that are already in the gene association file:
  • Qualifying an annotation with the qualifiers 'NOT' 'contributes_to' or 'colocalizes with'
  • Using the generic GO_REF tags for generic references eg., for a NOT annotation, need to add the proper database and accession syntax (need to add a field in curation interface in OA).
  • 'With' or 'From', for the use of additional identifiers with the use of certain evidence codes like IPI, IGI, etc.
  • Annotation Extension, for containing cross references to other ontologies,one of:
    • DB:gene_id
    • DB:sequence_id
    • CHEBI:CHEBI_id
    • Cell Type Ontology:CL_id
    • GO:GO_id
  • Gene Product Form ID, a canonical entry for specific variants of gene products.
    • When the gene product form ID (column 17 of ga) is filled with a protein identifier, the value in DB object type (column 12 of ga) must be protein. Protein identifiers can include UniProtKB accession numbers, NCBI NP identifiers or Protein Ontology (PRO) identifiers.
    • When the gene product form ID (column 17 of ga) is filled with a functional RNA identifier, the DB object type (column 12 of ga) must be either ncRNA, rRNA, tRNA, snRNA, or snoRNA.

Changes to the GO_term model and updating the ontology in WormBase

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