Standard Annotation

1
Three-Tiered Level of Annotation

• Standard Annotation
• Largely automated
• Provided by KB using Established Standard Sites
• Clear credit to where the annotation was done
• Community Input by Wiki-style
• Structured input with evidence/provenance
• Unpublished experimental confirmation
• For solved structure - monitored by PSI Center
• Registration of contributors
• Community Input by Free-style
• More speculative comments and hypotheses
• Comments on the validity of the annotations

2
What do we mean by annotation?

• MSAs Pfam UniProt show conserved sites
• Conserved sites on 3D Structure ET, Consurf,
• Classification SCOP, CATH, pfam
• Ligand nature, structure where, relevant?
• Substrate specificity EC structure of
  substrate
• Links to publications Synonym Tables of Protein
  Name Link to PubMed using TextMining Consensus
  authors
• Pathways and networks KEGG ProLinks Strings.
  Ecosite2 HPRD DIP, operon context
• SNPs databases, map to 3D structure
• Alternative spice forms
• Biophyscial features on 3D Structure GRASP
  SurfNet. Markus, PVSoar, NESTS
• Phylogenetic Tree TREEFAM ARBODRAW
• Cellular Localization Organ expression locations
• Disease Relatedness Links to OMIM
• Link to PSI Material Repository
• Oligomer state and evidence for this
• Structure quality assessment various servers

3
Validation of Annotation

• Weighting system of evidence
• Experimental, predicted from sequence, predicted
  from structure
• Published vs Unpublished
• Clear attribution of source
• Conflict of annotation

4
Functional Annotations

• Standard GO annotations
• Provide wiki to collect new functional terms
• Consider benchmarking of annotation tools
• Possibly collaborate with GO group to develop new
  terms

5
Integration and Visualization

• Major Opportunity for Development

6
Three-Tiered Level of Annotation

• Standard Annotation
• Largely automated
• Provided by KB using standard sites
• Clear credit to where the annotation was done
• Community Input by Wiki-style
• Structured input with evidence/provenance
• Unpublished experimental confirmation
• For solved structure - monitored by PSI Center
• Registration of contributors
• Community Input by Free-style
• More speculative comments and hypotheses
• Comments on the validity of the annotations

7
Adopt a Protein

• For every protein Selected, search literature
  to find investigators and email to them a
  solicitation to Adopt a Protein (inspired by
  Brenner suggestion on targeting)
• Uniprot provides example
• Sign up on web page to adopt protein
• Expectations need to be carefully managed strong
  caveats
• Automated - minimal opportunity for direct
  interactions except when solicited

8
Advertisement of Adopt a Protein

• Advertise the general concept at meeting of
  groups of biologists in specific fields.
• Nature Gateway
• Major Biology Center Web Sites (e.g. NCBI)
• Server Sites (e.g. ExPasy)
• Literature at Conferences
• News letters / trade magazines
• Link from Uniprot / GenBank /PDB to KB site for
  Adopt a Protein