# Presentation: 060916

## NCI-Nature Pathway Interaction Database(http://pid.nci.nih.gov)

- NCI-Nature Pathway Interaction Database(http://pid.nci.nih.gov)

- Carl Schaefer
- _[schaefec@mail.nih.gov](mailto:schaefec@mail.nih.gov)_
- National Cancer Institute
- Center for Biomedical informatics and Information Technology
- November 12, 2008

## Reference

- Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay & Kenneth H. Buetow. _[PID: The Pathway Interaction Database](http://nar.oxfordjournals.org/cgi/content/full/gkn653?ijkey=mLTywfXZf0X4Hph&keytype=ref)_. *Nucleic Acids Research* | doi:10.1093/nar/gkn653; published online October 2, 2008

## Slide 3

## Pathway Interaction Database (http://pid.nci.nih.gov)

- Network relations – producer/consumer, cause/effect
- Some goals:
- overcome arbitrariness of pathway boundaries
- be specific when possible (UniProt ids, PTMs)
- but allow for generalization (families, macroprocesses, abstract state, unspecified location, network encapsulation, ...)
- be credible (literature citations at interaction level)
- But...
- Not a collection of graphics
- Not an encyclopedia
- Not a proposal for a new controlled vocabulary
- At present, no reaction concentrations, rates

## Model (simplified)

- interaction

- molecule

- molecule

- molecule

- role

- role

- role

- molecule types:
-     protein
-     complex
-     rna
-     small molecule

- role types:
-     input (consumed)
-     output (produced)
-     positive regulator
-     negative regulator

- interaction types:
-     protein/small molecule
-     protein/protein
-     translocation
-     transcription
-     macroprocess

- molecule use :
-     post-translational mod
-     abstract activity state
-     location

## Contents (October, 2008)

|  | NCI-Nature | BioCarta | Reactome | KEGG* |
| --- | --- | --- | --- | --- |
| Pathways | 79 | 254 | 64 | 208 |
| Subpathways | 44 | 0 | 759 | 0 |
| Interactions | 4474 | 3003 | 3535 | 5083 |
| Total proteins | 2619 | 4218         | 2843 | 11109 |
| Proteins used simply | 1623 | 1078 | 1259 | 3493 |
| Proteins used in complex | 1342 | 917 | 1767 | 120 |
| PTM | 1238 | 0 | 401 | 0 |
| Protein with PTM | 423 | 0 | 150 | 0 |
| Protein subunits | 198 | 68 | 727 | 0 |
| Precursor proteins | 83 | 57 | 540 | 0 |
| Complexes | 1981 | 880 | 1942 | 42 |
| Small molecules | 135 | 205 | 629 | 2162 |

- *KEGG data only for comparison; data has not been loaded into the PID database

## Interactions Curated from the Literature

*expert review / curation*

*initial curation*

*fully reviewed data*

*web queries*

## Import & Export

- BioPAX

- BioPAX

- XML

- BioPaths
- (data capture)

- other analytical tools

- KGML

- caGRID

- Pathway.pm

- load files

- GraphViz

## Operations

- Retrieve sets of interactions
- by predefined pathway
- by involved molecules
- by adjacency
- Assemble interaction sets into connected networks
- Color molecules of interest in predefined or novel pathways
- e.g., co-visualize mutation and amplification
- Traverse/interpret networks
- e.g., propagate active/inactive state

## caBIO Model for PID Data (full model) – still in draft

## caBIO Model for PID Data (pathway & interaction)

## caBIO Model for PID Data (participant and physical entity)

## caBIO Model for PID Data (integration with caBIO objects)

## caBIO Model for PID Data (integration with caBIO objects)

## Understanding High-Throughput Molecular Data

*Network*

*Genome*

*Expression Cluster*

## Batch Query

## Batch Query on Predefined Pathways

## TCGA Data on p53 Pathway (mutations in red, amplifications in blue)

## Acknowledgments

- Nature Publishing Group
- curators: Kira Anthony, Shiva Krupa, Mhairi Skinner
- Matt Day
- NCI/CBIIT
- Jeff Buchoff, SRA
- caBIO: Juli Klemm, Konrad Rokicki, Lalitha Viswanath, Jim Sun
- help with BioPAX
- Ethan Cerami and Emek Demir, MSKCC
- Gary Bader, U. Toronto
- Guanming Wu, CSHL