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Databases מאגרי מידע - חלק ב'

Databases מאגרי מידע - חלק ב'. 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

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Databases מאגרי מידע - חלק ב'

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  1. Databases מאגרי מידע - חלק ב' אחסון שליפה

  2. 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

  3. Nucleotide & Protein Sequence DBs ~20 Years of Data Accumulation First generation vs. advanced generations More redundant vs. less redundant Repository DBs (archives) vs. topic centered Not curated vs. well curated Partially annotated vs. fully annotated

  4. First Generation Databases EMBL/GenBank/DDBJ Primary Sequence Repositories בור סוד שאינו מאבד טיפה (highly redundant) אך גם אינו מעבד טיפה (poorly annotated)

  5. 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.

  6. Unexpected information you can find in these dbs: EMBL מי חבר של פידל? כמה שנים הוא שמר את הסיגר?

  7. Advanced generations of nucleotide sequence databases Non-redundant sequence-centric database A comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. RefSeq Gene-centric databases All the sequence information relevant to a given gene is made accessible at once Gene Genome-centric databases Information about gene sequence, relative position, strand orientation, biochemical functions… Genome browsers Different entries Single entry

  8. Current tutorial Preview/index, limits History Previous and current tutorials Preview/index MeSH terms 5. Think, evaluate. The computer is just a machine. You are (hopefully) a thinking organism. 4. Access additional entries discussing same or similar entities by links to additional databases (DBXref) 1. Think – phrase your scientific question. 2. Choose appropriate database Fields 3. Phrase your query Syntax Keywords Boolean operators

  9. Evaluating Search Results Search results “scientific truth” Harder to detect (?) Easy to detect

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