# Presentation: 769521

## PossibleFuture Directions for caBIO

***caBIO Team***
***November 2008***

## caBIO Today: Content

- caBIO today is a repository and service for providing genomic annotations to biomedical data
- Mainly generic biomedical annotations
- Molecular biology
- Genomics
- Proteomics
- Biochemical pathways
- Microarray designs
- Some clinical cancer-related material
- Static data from CGAP/CTEP/CMAP
- Cancer Gene Index

## caBIO Today: Users	

- Internal
- Rembrandt (Pathways, Microarray annotations)
- caMOD (Sequence IDs, GO annotations)
- geWorkbench (Pathway diagrams)
- CMAP (Agents, protocols, pathways)
- webGENOME (Microarray annotations)
- External
- BioBrowser (entire model)
- .NET Working Group (demo purposes)
- NCRI ONIX (demo purposes)
- Others?

## caBIO Today: Usage

- Mainly used for annotation
- Used in a piecemeal fashion, one or two classes of interest
- Not generally used for discovery or research, but can be
- Also used as a “demo” system or “baseline” for certain caGrid applications and initiatives (e.g. the .NET WG)
- Early adopter for new caCORE SDK technology
- Innovation system for new technology to be moved into the SDK at a later date (e.g. FreestyleLM)

## Potential Future Directions

- Increased focus on cancer
- Potential cancer causes
- Potential cancer therapies
- Added support for research and discovery
- caMOD Use Cases
- Support for new annotations
- caArray Use Cases
- Mayo Use Cases
*Target publically available datasets,*
*internal (non-CBIIT) and external*

## Potential Cancer Causes

- Genomic alterations
- SNPs
- Haplotypes
- Chromosome abnormalities
- Post translational modifications (PTMs)
- Pathway signaling anomalies
- Epigenetics (gene methylation, prions)
- Environmental (carcinogens)
- Viral, immunology
*Some of these can be considered biomarkers supporting disease recognition and targeted treatment*

## Potential Cancer Therapies

- Biologics (gene therapies)
- Drugs / Small Molecules
- Nanoparticles with associated therapies
- Viruses (e.g. Seneca Valley Virus)

## Today’s Coverage

- Cancer causes
- SNP
- GeneDiseaseAssociation
- Pathway (& new PID model)
- Cancer therapies
- ClinicalTrialProtocol/Histopathology/Target/Agent
- GeneAgentAssociation
- Research and discovery
- Mouse genes, pathways
- Annotations
- Microarrays
- Genomic
- Ontologies (GO, Disease, Organ)

## Potential Future Coverage

- Cancer causes
- Haplotypes – Hapmap
- Chromosome abnormalities – ALFRED, DGV
- Post translational modifications – RESID
- Pathway signaling anomalies - ???
- Epigenetics - MethDB
- Environmental - CPDB
- Viral (oncoviruses), immunology - MeSH
- Cancer therapies
- Biologics - MeSH
- Drugs / Small Molecules - CHEBI
- Nanoparticles - caNanoLab
- Viruses - NCBI

## Potential Future Coverage (2)

- Research and Discovery
- Animal Models Use Cases
- Clinical Trials mapped to Pre-clinical trials
- Support for additional species
- Others?
- Support for Biomarkers
- Annotations
- Additional Microarray Annotations – Microarray Manufacturers
- Genetic Disorders - OMIM

## Potential Cancer Causes: Haplotypes

- “A haplotype is a combination of alleles at multiple loci that are transmitted together on the same chromosome”
- 	_[http://en.wikipedia.org/wiki/Haplotype](http://en.wikipedia.org/wiki/Haplotype)_
- HapMap project
- Some data already in PopulationFrequency

## Potential Cancer Therapies:Viruses

- “SVV-001 has oncolytic activity against adult tumors with neuroendocrine features but is not harmful to normal human cells”
- 	_[http://www.nature.com/mt/journal/v13/n1s/abs/mt2006622a.html](http://www.nature.com/mt/journal/v13/n1s/abs/mt2006622a.html)_
- Add Seneca Valley Virus and similar viruses as separate Taxons
- Add Proteins and ProteinSequences linked to the Taxon
- 	_[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=209363551](http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=209363551)_
- Other organisms?

## Research and Discovery:Biomarkers

- “A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. A biomarker may be used to see how well the body responds to a treatment for a disease or condition. Also called molecular marker and signature molecule.” – NCI’s Dictionary of Cancer Terms
- New feature in SDK 4.1 allows us to mark classes with interfaces
- Biomarker interface could be applied to Gene, Proteins, SNP, etc

## Data Visualization

- Pathway diagrams via URL
- Ontology visualizations (trees, graphs)
- Prototype: _[http://biowiki.dnsalias.net/ontology/diseaseOntology.html](http://biowiki.dnsalias.net/ontology/diseaseOntology.html)_

## Data Visualization (RGraph)

## Data Visualization (Hypertree)

## caBIO Vision Statement Draft

- Future versions of caBIO will always be concerned with what data to include and what to leave out
- A vision statement can help focus the scope
- Possible draft statement:
- 	caBIO is a repository of biomedical data aimed at providing researchers and developers with convenient remote access to proven annotations and findings in molecular biology, bioinformatics and oncology.

## ScopingRecommendationsfor the Next caBIO Release

## Recommended Features for caBIO Next Release

- New coverage areas
- Additional data on cancer causes and therapies
- Datasets TBD
- Added support for research and discovery
- Marker Interface
- Support for new annotations
- Microarray Annotations (Mayo / caArray)

## Recommended Features for caBIO Next Release (2)

- Continued Product Enchancements
- Templated Search in caBIO Home Page
- Clients/APIs
- .NET Ajax client
- Upgrades to Python/AJAX clients
- FreestyleLM model registration
- Upgrade to newest SDK version

## Recommended Features for caBIO Next Release (3)

- Feature Requests
- [#15637] Filter on object class from FreestyleLM query results
- [#16246] Display CVS tag on caBIO home page
- [#16737] Provide Attribute Level Data Provenance
- [#16738] Upgrade caCORE Perl API to Use caBIO 4.x
- Defect Resolutions
- [#16772] Revisit eager loading of collections in Annotation API
- [#16868] Support for pagination with Range Query API

## Recommended Features for Portlet Next Release

- Advanced Query Builder
- PID Portlet (in coordination with the PID team)
- [#16733] Add Pathway Search and Display Portlet
- Custom user templates (Templated Search)
- Feature Requests
- [#17018] Option to choose the number of results listed per page

## Recommended Features for Grid Service Next Release

- New version for caBIO 4.2
- [#16757] Implement caBIO 4.2 Grid Services
- Support for Range Queries
- [#16740] Implement Range Query caBIO Grid Services
- Support for FreestyleLM
- [#16741] Implement FreeStyle Search caBIO Grid Services
- Dependency on FreestyleLM model registration

## Discussion