Date post: | 22-Dec-2015 |
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Databases
- חלק ב'מאגרי מידע
אחסון
שליפה
What are we looking for in a GOOD database?
• Large amount of data Numerous entries Well defined fields
• Non-redundancy• Reliable data (periodic updating) • Informative links to other DBs
• Efficient and user-friendly associated tools (software) necesary for db access/query, db information insertion, db information deletion
Curated vs. non-curated DBs
Repository DBs (archives) vs. topic centered
First generation vs. advanced generations
Not curated vs. well curated Partially annotated vs. fully annotated
Nucleotide & Protein Sequence DBs ~20 Years of Data Accumulation
More redundant vs. less redundant
Primary Sequence Repositories
בור סוד שאינו מאבד טיפה
(highly redundant)
אך גם אינו מעבד טיפה
(poorly annotated)
First Generation Databases EMBL/GenBank/DDBJ
EMBL/GenBank/DDBJ
Sort of sequence museum, where sequences are preserved for eternity as they were determined, interpreted and published
originally by their authors
)primary sequence repository(
The authors have full authority over the content of the entries they submit!
)editorial control of the content belongs to the authors(
Redundancy, insufficient annotation .
Unexpected information you can find in these dbs:
מי חבר של פידל?
EMBL
כמה שנים הוא שמר את הסיגר?
Advanced generations of nucleotide sequence databases
Non-redundant sequence-centric databaseA comprehensive, integrated, non-redundant set of
sequences, including genomic DNA, transcript (RNA), and protein products.
RefSeq
Gene-centric databasesAll the sequence information relevant to a given gene
is made accessible at onceGene
Genome-centric databasesInformation about gene sequence, relative position,
strand orientation, biochemical functions…Genome browsers
Different entries
Single entry
Boolean operatorsKeywords
Fields
Syntax
4. Access additional entries discussing same or similar entities by links to additional databases (DBXref)
2 .Choose appropriate database
3.
5 .Think, evaluate. The computer is just a machine.
You are (hopefully) a thinking organism.
1. Think – phrase your scientific question.
Phrase your query
Current tutorial
Preview/index
Preview/index, limits
MeSH terms
Previous and current tutorials
History
Not found (-)
Found (+)
RelatedFalse negative
True positive
UnrelatedTrue negative
False positive
Search results“sci
entific
trut
h”
Evaluating Search Results
Easy to detectHarder to detect (?)