Extension of disease-related pathway using text mining 2006.04.24 분자유전체의학 정희준...
-
Upload
regina-elliott -
Category
Documents
-
view
214 -
download
1
Transcript of Extension of disease-related pathway using text mining 2006.04.24 분자유전체의학 정희준...
Extension of disease-related pathway using text mining
2006.04.24분자유전체의학
정희준
2006 B4GM Term Project
Introduction• Disease process 는 disease 의 이해와 치료에 있어서 중요• MeSH
• MeSH is NLM’s controlled vocabulary used for indexing articles for MEDLINE/PuMed
• MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts
• OMIM• OMIM archives mature, high-quality data of high significance, the standard in rare
mendelian disorders• ArrayXPath
• ArrayXPath have 3,088 genes or gene products• It has repository of meta-information for public pathway databases, GenMAPP, K
EGG, BioCarta and PharmGKB• If input disease name is matched to the corresponding MeSH heading or entry ter
m, PathMeSH outputs the list of the pathways containing the disease-related gene product
Problem
• OMIM 은 질병에대한 유전적 요인의 유전자를 정리
Concept diagram
Disease Gene pathway
MeSH hierarchies
OMIM MorbidMap New GRIP
PubMed
Method
• Step 1. Collect PubMed’s abstract• MeSH heading 과 유전자 symbol 을 입력하여
검색되는 PubMed 의 abstract 수집
• Step 2. Build Gene/Gene product dictionary• Entrez Gene, HGNC, SWISSPROT 에서 제공하는 symbol,
gene name 의 dictionary 구축
• Step 3. Extract gene/gene product in abstract• Step 1 에서 모은 각 질병의 abtract 에서 gene/gene pro
duct 를 추출
• Step 4. Apply filtering• Step 3 에서 추출한 gene/gene product 에 대한 유이성
검사• Filter 를 통과한 gene/gene product 를 disease-gene
관계에 포함