LSM2241 Practical 2

Part 1
Formulating Advanced Search Queries
Objectives of Part 1
Gene Record
Search and retrieval
Formulating advanced search queries
Search and Retrieval
http://ncbi.nlm.nih/gov/gene
Two approaches
Advanced Search
Query with logical operators
Advanced NCBI Database Search
Boolean AND OR NOT
Wildcard *
Nested Operators
Quotation marks
Protein kinases vs protein kinases
Fielded Searches
Query Mapping
Filters
Boolean Operators
p q p OR q p AND q NOT p
T T T T F
T F T F F
F T T F T
F F F F T
QUICK QUIZ TIME
p q r q OR (NOT r) p AND (q OR (NOT r))
T T T
T T F
T F T
T F F
F T T
F T F
F F T
F F F
Wildcards
Applicable in most databases
Fielded Search
Search term restricted to specific type of
data
Which fields?
Query Mapping and Search Translation
Search system maps terms to database
MeSH: controlled vocabulary of terms for
NCBI databases
Filters (MyNCBI)
Define filters to refine results
http://www.youtube.com/watch?
v=BWbQrrYbGiY
Accessing Related Gene Information
Literature related to the gene
Genome records having the gene annotated on corresponding genomic
reference sequence
Related OMIM entries- Linked on MIM numbers included in summary or
phenotype
Structures related to the gene and its product
Interactions of the gene product
RefSeqs: A RefSeq is created for a completely sequenced genome and
that record contains annotated genes
SNP records: Single Nucleotide Polymorphism data
Other specific resources (for common genes)
Pathway information, etc