1. Annotator Interface
GUS 3.0 Workshop
June 18-21, 2002

2. Outline Current annotation efforts Motivation for new annotation tool
Requirements for new annotation tool
Thoughts on design and implementation
Future plans

3. Current Annotation Efforts

4. Overview of Current Efforts
Automated annotation has been applied to the DoTS transcripts
Predicted gene ownership (clustering of assemblies)
BlastX against NR
Automated assignment of descriptions based on similarity
BlastX against ProDom and RPS-Blast against CDD
Predicted GO Functions
Framefinder
Predicted Protein Sequences
Blat alignments
EPCR, Index Words, etc…
Manual annotation efforts have focused on
validating the automated annotation and
adding additional information at the central dogma level
Manual annotation of the gene index utilizes an annotation tool, the GUS Annotator Interface, which directly updates the GUSdev database.

5. “Unassembled” clusters (generate consensus sequences)
DoTS RNA transcripts
Incoming
Sequences (EST/mRNA)
GenBank, dbEST sequences
Make Quality (remove vector, polyA, NNNs)
The assembly of sequences generates
a consensus sequence or DoTS transcript
“Quality” sequences
Block with RepeatMasker
Blocked sequences
Blastn to cluster sequences
“Unassembled” clusters
Assemble sequences with CAP4
CAP4 assemblies
(generate consensus sequences)
BLASTn DoTs
consensus sequences
(98% identity, 150bps)
Gene Cluster
(RNA s in the Gene)
Dots Consensus
sequences

6. Current Efforts: Gene Annotation (1)
RNA
RNAInstance
RNAFeature
Assembly
Generate
DoTS
transcripts
RNA_1
RNA_5
RNA_2
RNA_3
RNA_4
Instance_1
Instance_5
Instance_2
Instance_3
Instance_4
Feature_1
Feature_5
Feature_2
Feature_3
Feature_4
Assembly_1
Assembly_5
Assembly_2
Assembly_3
Assembly_4
Gene_A … … … …
Task 1: Validation of Gene Membership

7. Current Efforts: Gene Annotation (2)
RNA
RNAInstance
RNAFeature
Assembly
Generate
DoTS
transcripts
RNA_1
Instance_1
Instance_5
Instance_2
Instance_3
Instance_4
Feature_1
Feature_5
Feature_2
Feature_3
Feature_4
Assembly_1
Assembly_5
Assembly_2
Assembly_3
Assembly_4
Gene_A
RNA_2
RNA_3
Gene_B
RNA_4 … … …
RNA_5
- Removing RNAs from the cluster results in the creation of a new Gene
An entry is made in the MergeSplit table for tracking purposes
Similar process followed when an RNA is added to a Gene

8. Current Efforts: Gene Annotation (3)
Task 2: Assign Reference RNA
will be annotated further
RNA table
Task 3: Assign Approved Gene Name/Symbol
Gene Table
Evidence: Comment (specifies database link)
Task 4: Assign Gene Description
Evidence: Comment
Task 4: Associate known Gene synonyms
GeneSynonym table

9. Current Efforts: RNA Annotation
Annotation of “Reference Sequence”
Task 1: Assign/Confirm Description of assembly
RNA table
Task 2: Confirm/Add/Delete GO Functions
ProteinGOFunction (in GUSdev, GO tables have been re-designed in GUS3.0)
Evidence: Comments or Similarity (ProDom, CDD-Pfam, CDD-Smart, or NR)

10. Current Annotator Interface Architecture
Erebus
Zeus
Annotator Interface
JDBC (Query Only)
GUSdev
JavaServlet
writes
executes
“XML” file
Perl
Object
Layer
DBI(Insert/Update/Delete)
reads
AnnotatorInterface
Submitter
GA-Plugin

11. Current Annotator Interface

12. Current Gene Annotation
Validate Cluster and Assign Reference RNA/Assembly

13. Current Gene Annotation (cont.)
Assign Gene Name/Symbol
Assign Gene Description
Assign Gene Synonym(s)
Evidence

14. Current RNA (and Protein) Annotation
RNA Description
Evidence
GO Functions

15. Allgenes Display of Gene Annotation

16. Allgenes Display of RNA Annotation
RNA Description
(Confirmed or manually added GO Functions)

17. Status of Current Annotation (as of June 20, 2002)
1289 manually reviewed genes
1003 with gene name
697 with gene synonyms
1046 with description
6146 manually reviewed RNAs/DoTS assemblies
949 ‘proteins’ with reviewed GO function

18. Motivation for new tool
Want to annotate using genomic sequence
Create “curated” gene models specifying structure
Increase structure of annotation in GUS
Annotation of proteins
Redefinition of annotation tasks
Current interface not designed for this purpose

19. Some Other Annotation Tools
Artemis
Developed and used at Sanger
Reads and writes flat files
Supports rich set of annotations
Save as EMBL format
Apollo
Combined effort including members from Sanger and Berkeley
Flat files (CORBA access to ENSEMBL)
2 versions, currently being merged
Sanger: annotation viewer
Berkeley: focus on editing
No Existing Tool To Meet All of Our Needs

20. Requirements At a High Level

21. Requirements: Graphical View
Provide alignment of features on genomic sequence
could potentially display any feature type currently stored in GUS3.0
features can be selected and used to generate “curated” features
similar to display and functionality in Apollo
Toggle (or configure) the display of each feature type
Zoom to sequence level and will include links to functionality relevant to the feature highlighted
Also support creation of features “from scratch”
based on literature, etc.
Detail editors provide ability to change endpoints, etc.

22. Gene Annotation Create curated gene model specify gene boundaries
specify location of exons (and thus introns)
5' exon boundary (putative transcription start site)
3' exon boundary (include poly adenylation signal)
automatic creation of Gene entry
merge with existing gene instances through GeneInstance table
tables/views affected:
GeneFeature
ExonFeature
GeneInstance
Gene
MergeSplit
evidence: features used to create model, PubMed ID
should be as easy as clicking on existing features and saying make curated (then can modify endpoints, etc. if needed)

23. Gene Annotation (2)
Assign (HUGO or MGI approved) abbrievated gene name/symbol
Gene Table
Evidence: ExternalDatabaseLink
Assign full gene name (MGI or HUGO full gene name)
Assign abbrievated gene name/symbol synonyms (non-approved gene symbols)
GeneSynonym Table
Assign full gene name aliases
GeneAlias Table

24. Gene Annotation (3) Assign gene category (e.g. non-coding)
Gene Table
Evidence:
ExternalDatabaseLink/Literature Reference
Similarity (eg. to known non-coding RNA)
Confirm/assign gene chromosomal location
GeneChromosomalLocation
RH mapping data
Alignments/Features
OMIM Link assignment (verification if computationally determined)
ExternalDatabaseLink

25. RNA Annotation (1) Create “curated RNAs”
Define RNA transcript forms of gene (create RNAs)
Using exons defined by curated gene
5' and 3' UTRs
Automatic creation of RNA entry
Merge existing RNA instances
Tables affected:
RNAFeature
UTRFeature
RNAInstance
RNA
Evidence: Features used to create
Assign RNA categories to created RNAs (e.g. alternative form)
RNARNACategory Table

26. RNA Annotation Assign (or confirm computed) RNA description
RNA table
Evidence: Gene from which it is derived
Anatomy expression assignment(s)
RNAAnatomy
RNAAnatomyLOE
Evidence:
ExternalDatabaseLink/Literature references
Assembly anatomy percent from DoTS
RAD experiments
Assign GO terms to curated RNA (non-coding RNAs, e.g. small RNA involved in splicing)
GOTermAssociation
GOTermAssociationEvid
Evidence: ExternalDatabaseLInk, Literature References
Computational analysis performed on curated RNA sequences
Annotation workflow
Framefinder translation, GO terms, Similarities, etc.

27. Requirements: Protein Annotation
Confirm/assign GO Function
GOTermAssociation, GOTermAssociationEvid
Evidence: ExternalDatabaseLink and/or Literature References
Confirm/assign GO Biological Process
Confirm/assign GO Cellular Component
Assign protein name
Protein Table
Evidence: ExternalDatabaseLink, Literature Ref, Similarities
Assign protein name synonyms

28. Evidence will be associated with all annotation
Protein Annotation (2)
Assign protein category (post-translational modifications)
ProteinProteinCategory
Evidence: ExternalDatabaseLink, Literature References
Protein-protein interactions assigned
Interaction
InteractionInteractionLOE
Evidence: PubMed ID, etc.
Protein pathway assignments
PathwayInteraction (for newly created interactions)
Still under consideration: What is best way to link with existing pathway
for example, Pathway is represented in DoTS, and we want to say that this curated Protein is really the same as a protein in a pathway.
Assign post translational modification category
Assign interactions involving this protein
Assign pathway protein is known to be involved in
Assign protein family
Ability to modify and/or delete curated protein
Evidence will be associated with all annotation

29. Potential New Architecture
Java Application
more control over graphical interface
faster then web-based
Java Object Layer
simplifies handling of complex updates

30. Next Steps/ Open Issues
Completion of Java Object Layer
Decision regarding BioJava wrappers
What exactly will this give us to aid in interface development (eg. FeatureRenderer, etc…)
Discussion on layout of interface
Joan’s input after experimentation with other tools
Depending on the above :
Client Side portion which communicates with remote GUS Server
Interface Implementation