# Presentation: 036100

## NCI Cancer Gene Index Completion Project OverviewcaBIG ICR Meeting

- Pat Blake
- May 28, 2008

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

## Project Goal – Pilot Phase

- Goal – Use automated and manual text mining to identify all genes related to cancer.  Annotate all gene/disease and gene/compound-treatment relationships for each cancer gene and manually verify role codes and evidence codes.
- NCI Thesaurus  extended to include Medline terms.  Used Controlled Vocabulary for Annotations of Role Codes and Evidence Codes
- NLP used to identify cancer genes and expand dictionaries.
- Pilot Phase - June 2004 – 8.8M Medline Abstracts - 7,867 suspect cancer genes – 4,685 manually verified “true” cancer genes – manually annotated 1,000

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

## Index Automated & Manual Annotation Process Overview

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

*Automatic** **Textmining*

- Candidate DB

- Cancer TermDictionary

- Gene NameDictionary

- Medline Abstracts

*Manual Screening Steps*
*Manual** Annotation*
*Evidence Codes*
*Role Codes*

- Cancer / Gene / Drug

- DrugTermDictionary

**BioLT**Linguistic text analysis
- of Medline

## Cancer Gene Index Manual Annotation

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

-  Evidence codes – based on GO evidence codes
-  Role codes – based on NCI Thesaurus
-  Role details – project specific extensions of role codes
-  Organism – defined vocabulary
-  Negation – yes/no
-  Celline – yes/no
-  Comments – free text

- Annotators read each sentence and annotate the following features

## 3 Year Project and Atlas Project

- Base Year - June 2005 – Updated Medline abstracts -12M Medline Abstracts – 10,000 suspect cancer genes – 5,800 manually verified “true” cancer genes – manually annotated 1,500 cancer genes.
*Sentences - 300,000*
- Option Year 1 - June 2006 –– No Medline update - manually annotated 1,175 cancer genes.
*Sentences - 235,000*
- Option Year 2 June 2007 – Medline updated 1 April 2007 – 14M Abstracts - Atlas Project – 6,610 manually verified “true” cancer genes – manually annotated 1,175 cancer genes.
*Sentences – 210,000*
- Atlas Project - June 2007 – Automated and manual annotation of abnormality/metastasis process for all Brain, Ovarian and Lung Cancer Genes.  Manually annotated 577 disease specific cancer genes
*Sentences – 16,000*

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

## Cancer Gene Index caBIG Community Review

- The Cancer Gene Index Completion Project will take 12 Months – 5/08 – 5/09
- Current State – 16M Abstracts (4/1/07)
- 			Total Cancer Genes      6,610
- 			Genes Annotated        - _4,658_
- 			Genes to Annotate        1,952 *
**Includes 310 High Frequency Sentence Count Genes (>1,000 sentences)**
**Phase I - Annotate 310 High Frequency Genes & Phase II Annotate 1,652 Low Frequency Genes**
- 250,000 Gene-Disease Relationship Sentences and  250,000 Gene Compound Relationship Sentences
- Est. 84,000 Gene Disease Relationships – 80% - 20% Strategy
- NLP Analysis shows that 80% of the 310 HFGs are represented in 185,000 sentences showing gene-disease relationships with less than 10 sentences per relationship so the manual annotation is work-in-process.  (Approximately 185,000 sentences.)
- NLP Analysis 20% 310 HFGs.  NLP analysis shows that 20% or 16,000 relationships of the HFG gene-disease are represented in 65,000 sentences that need to be selected.
- NLP filter categories for identifying representative  of the 20% HF Gene – Disease Relationship sentences.
**Gene – Disease Categories****	****	****	****Gene – Compound Categories**
- A – Expression				A - Binding
- B – Abnormality				B - Regulation
- C – Biomarker				C - Resistance
- D – Therapy
**Vocabulary Review Condensed Categories – See PDF**

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

## 20% HFG Category & Drill-down Strategy

**Sophic**

***Integrated Life Science Solutions***

**Biomax**

- Q-1
- ABCD – 341 Sentences

- Q-2
- ABC – 2,583 Sentences
- BCD – 574  Sentences
- ACD – 2,298 Sentences

- Q-3
- AB - 44,040 Sentences
- AC - 23,259 Sentences
- AD - 42,263 Sentences
- BC - 7,440 Sentences
- BD - 5,696 Sentences
- CD - 7,764 Sentences

- Q-3
- A – 433,8099 Sentences
- B – 149,398 Sentences
- C – 44,655 Sentences
- D – 100,690 Sentences

*          **HFG – Gene-Disease Annotation Drill-down Strategy*
- Q-1 & Q-2 – Annotate all sentences.
- Q-3 – Select top 3-4 most recent  publications for each Gene-Disease relationship not in Q-1 & Q-2.
- Q-4 – Select top 3-4 most recent publications for category combinations A through D for each Gene-Disease relationship not covered in Q1-2 & 3.

## Feedback Please

- Ideas on HFG Gene-Disease Relationship Annotation Strategy?
- Review Gene-Disease Category Vocabulary.
- Review Compound-Disease Category Vocabulary.
- Any ideas or feedback to improve the project strategy and add value?
- Email feedback and comments to -
- 			Juli - _[klemmj](mailto:klemmj@mail.nih.gov)__[@mail.](mailto:klemmj@mail.nih.gov)__[nih](mailto:klemmj@mail.nih.gov)__[.](mailto:klemmj@mail.nih.gov)__[gov](mailto:klemmj@mail.nih.gov)_
- 			Pat – _[pat@](mailto:pat@sophicalliance.com)__[sophicalliance](mailto:pat@sophicalliance.com)__[.com](mailto:pat@sophicalliance.com)_
- Thank You!

**Sophic**

***Integrated Life Science Solutions***

**Biomax**