Supporting Reasoning within Use Case WP7b
July 12th, 2011, 12:00 - 12:50 CET
Participants: Zhisheng (VUA), Mark (UFSD), Niraj (UFSD),
- regret: Angus (UFSD),
Agenda
- Keyword Extension Reasoner Plugin
- Meaning of the GWAS parameters
- Experiments and evaluation
- MIMIR data
- Next Teleconference
Minutes
- Meaning of the GWAS parameters.
gwas:x gwas:searchInRif "false" true: use RIF data, false: use PubMed data gwas:x gwas:useUMLS "false" . true: use UMLS keyword extension, false: use UMLS keyword extension gwas:x gwas:searchMode "1" . 1: all data without considering the date constraint, 2: before the date, 3: after the date gwas:x gwas:dateConstraint "20110412"
what does snpHasScore mean? Is it prior propability? or BFDP (Baysian false-discovery probability)?
answer: it is prior probability.
If the answer is for the former, how can we get BFDP of SNPs?
answer: BFDP requires two things. prior and additional calculation
Does the keyword group change the results or not?
gwas:x gwas:hasKeywordGroup gwas:g1
Answer: newly found keywords by the keyword reasoner should be marked as the same group.
- Experiments and evaluation
how can we organize the experiments next?
Three diseases:
Breast cancer keywords
Prostate cancer keywords
Type 2 diabetes keywords
Try on all the combinations:
1) MeSH or LLD
2) Semantic Distance Measure or not
3) Google distances or others.
4) Substring match or not
5) Direct subClass or not
6) Candidate SNPs, if without any SNP in the queries, it would consider all the SNPs in the file MIMIX/mimix-indices/snp-index/indexedSNPs.txt
It may take a week to get the results.
splitting the SNP file into multiple subfiles, and test it with the same file name of all SNPs list file to test the whole set separately.
What are the criteria for the evaluation?
answer:
1) prior
2) time performance
- MIMIR data
is the existing MIMIR data enough for the experiments?
answer: got everything Sheffield has.
is it sufficient to get meaningful results?
answer: if it is possible to add more from ?PubMed.
- Next teleconference
August 2nd, 2011 12:00 - 13:00 CET