# Presentation: 372095

## Project NameCancer Gene Index

***Presenter – ***
***Kevin Groch, ICR Chair***
***Kathleen****** ******McCormick,Cotar***
***Date 8/11/08***

**April 30, 2008**

## Overview

**Project Objective: ****There are seven primary objectives:**
**Identify and annotate relationships between 80% ****genes and disease**** for the 310 HF genes based on the April 1st, 2007 refresh (previous project).**
**Identify and annotate relationships between ****genes and compounds**** for the 310 HF genes based on the April 1st, 2007 refresh (previous project).**
**Update and refresh the MEDLINE abstract corpus to October 1, 2008.**
**Identify new cancer genes to be added to the previously identified 1,962 cancer genes.**
**Identify and annotate relationships between genes and disease for the remaining ~1,700 LF genes plus any new genes.**
**Identify and annotate relationships between genes and compounds for the remaining ~1,700 LF genes plus any new genes.**
**Deliver completed annotation packages of the databases as XML files to NCI-CBIIT.**
**Period of Performance: April 23, 2008 – April 2009 **
**Sub-Contractor(s): Sophic – includes BioMax Germany**
**Compliance Level:**
**Budget: 1, 297,414**
**FFP or Fixed Price: T & M**
**Sole Source**

## Technical Overview

**Describe the tasks and what the project ‘leave behind’ is**
**The NCI-CBIIT carried out a pilot project in 2004 and three additional projects in 2005, 2006 and 2007 (“Cancer Gene Data Curation Project”) that identified relationships between cancer genes and disease, and cancer genes and drugs.  As part of this effort, MEDLINE abstracts were searched for meaningful co-occurrence of known gene and disease terms using the NCI Thesaurus and a vocabulary proprietary to the Subcontractor that conducted the previous phases of this work.  The 2007 project identified 6,610 true cancer-related genes, of which a cumulative 4,658 gene have been manually annotated during previous project phases. There remain 1,962 true cancer-related genes that require annotation of the gene to disease and gene to drug relationships identified by text mining the medical literature.**

## Technical Status

**What has been accomplished to date**
**Decision (2):   Divide each of the HFG into 250,000 sentences for Gene-Disease and 250,000 Gene-Compound Relationship sentence relationship “batches”.   Create a gene/disease and gene/compound relationship base line set of sentences to make sure we capture ALL gene-disease and gene-compound relationships with at least 1 sentence.  Estimated average of 3 sentences per relationships based on current analysis**
**Decision (4):  The manual annotation of the 185,000 Gene-Disease Relationships and 188,000 Gene-Compound Relationships can proceed. **
**Decision (7):  Gene Disease Strategy – Explanation of HFG Gene Disease Sentence Selection based on the following statistical analysis:**
**a.  There are 84,739 gene-disease relationships for the 310 HF genes.**
**b.  68,498 gene-disease relationships are covered by approximately 185,000 with less than 10     sentences for each distinct gene-disease relationships.**
**c.  There are 16,241 gene-disease relationships to be assigned to approximate 65,000 by a rational drill down approach.**
**Decision (8):  For this approach 4 functional categories have been assigned:**
**A****	****Expression**
**B****	****Abnormality**
**C****	****Biomarker**
**D****	****Therapy**
**By NLP analysis 99% of the 16,241 gene-disease relationships are captured by sentences containing any of the 4 categories.**
** ****In order to combine maximum value of sentence and broad coverage of the categories the sentences containing any combination of the categories has been determined by NLP analysis.**
**ABCD**
**ABC**
**BCD**
**ACD**
**AB**
**AC**
**AD**
**BC**
**BD**
**CD**
**A**
**B**
**C**
**D**
**The proposed approach based on the sentence count statistics is to move in three steps.**
**1) Annotate all sentences of the top 4 category combinations.**
**2)  Pick the top 3-4 most recent publications for category combinations AB through CD for gene disease relationships not covered under 1)**
**3) Pick the top 3-4 most recent publications for category combinations A through D for gene disease relationships not covered under 1 or 2)**

## Technical -Continued

**What is the next set of milestones/deliverables**
**Focused annotation and curation of HF genes with disease and compound relationships in 6 months**
**MEDLINE repository refreshed and the identification of new HF and LF genes to be annotated and curated**
**Full annotation and curation of LF genes with disease and compound relationships in 12 months**
**Integration of the HF and LF genes in caBIO updates**
**Task 3.2Focused Annotation of Cancer Gene-Disease Relationships for HF Genes6 months from contract startTask **
**3.3Focused Annotation of Cancer Gene-Compound Relationships for HF Genes6 months from contract startTask **
**3.4Report Summarizing the Results of Refreshing theMEDLINE Abstract Corpus and Gene NameHarmonization****	****	****	****	****	****	****	****9 months from contract startTask **
**3.5Full Annotation of Cancer Gene-Disease Relationships for LF Genes12 months from contract startTask **
**3.6Full Annotation of Cancer Gene-Compound Relationships for LF Genes12 months from contract start**

## Decision Nodes

**Decision Nodes**

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## Financial Status

**Overall Budget – Spend approximately 108,266 per month**
**Amt Invoiced to Date- $349,368 August 1 26.93%)**
**Estimate at Completion- fully funded**

## Issues/Risks

**Technical or Financial Issues or Risk Items: None at this time**