NeSC, 25 April 2002 Why Don’t Scientists Use Databases? 1 Why Don’t Scientists Use Why Don’t Scientists Use Databases? Databases? Peter Buneman Peter Buneman Division of Informatics Division of Informatics University of Edinburgh University of Edinburgh Digital Libraries grant IIS 98-17444 (NSF,DARPA,NLM, LoC,NEH, NASA) http://db.cis.upenn.edu http://db.cis.upenn.edu/Research/ provenance.html
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NeSC, 25 April 2002 Why Dont Scientists Use Databases? 1 Why Dont Scientists Use Databases? Peter Buneman Division of Informatics University of Edinburgh.
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NeSC, 25 April 2002 Why Don’t Scientists Use Databases?
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Why Don’t Scientists Use Why Don’t Scientists Use Databases?Databases?
Peter BunemanPeter BunemanDivision of InformaticsDivision of InformaticsUniversity of EdinburghUniversity of Edinburgh
Digital Libraries grant IIS 98-17444
(NSF,DARPA,NLM, LoC,NEH, NASA)
http://db.cis.upenn.edu
http://db.cis.upenn.edu/Research/provenance.html
NeSC, 25 April 2002 Why Don’t Scientists Use Databases?
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Why Don’t Scientists Use Why Don’t Scientists Use DatabasesDatabases
MuchMuch
??RelationalRelational
Thanks to:• The ontologists and astronomers at Edinburgh• The database and bio-informatics groups at Penn• Aleri Inc.Special thanks (material stolen from)• Sanjeev Khanna, Wang-Chiew, Keishi Tajima, Susan Davidson, Fidel Salas
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Scientific Data is UbiquitousScientific Data is Ubiquitous
• 500 or so public molecular biology databases.– much discovery in silico
• Vast amounts of satellite imagery– maintaining it is very expensive
• Terabytes of astronomical data (not image data)• Linguistic corpora are essential research tools --
also in terabytes
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Relational DBs -- tabular dataRelational DBs -- tabular dataId Name Address123 H. Simpson Springfield456 L. Simpson Springfield321 A. Jones London
Id Course Grade456 Geometry A123 Algorithms D456 Voltaire A321 Geometry B321 Algorithms C
Title Dept TeacherAlgorithms CompSci Dr. DeadheadVoltaire French Prof. lePewGeometry Math Dr. Obtuse
•Useful information is obtained by combining tables.•Efficient algorithms for
– comining and indexing tables– transaction processing (updates and multiple users)
• Relational databases are a multi giga-$ industry
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Reasons for MismatchReasons for Mismatch
• Scientific data sets are too large (image data, huge analyses)
• Scientific data is too complex• Relational databases don’t work
well with arrays and scientific computation
• Schema evolution and history are important
• Databases are too expensive
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Swissprot -- Swissprot -- a curated a curated databasedatabase(1 of ~100,000 (1 of ~100,000 entries)entries)
ID 11SB_CUCMA STANDARD; PRT; 480 AA.AC P13744;DT 01-JAN-1990 (REL. 13, CREATED)DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)DE 11S GLOBULIN BETA SUBUNIT PRECURSOR.OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;OC VIOLALES; CUCURBITACEAE.RN [1]RP SEQUENCE FROM N.A.RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;RX MEDLINE; 88166744.RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;RL EUR. J. BIOCHEM. 172:627-632(1988).RN [2]RP SEQUENCE OF 22-30 AND 297-302.RA OHMIYA M., HARA I., MASTUBARA H.;RL PLANT CELL PHYSIOL. 21:157-167(1980).CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN.CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND ACC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY ACC DISULFIDE BOND.CC -!- SIMILARITY: TO OTHER 11S SEED STORAGE PROTEINS (GLOBULINS).DR EMBL; M36407; G167492; -.DR PIR; S00366; FWPU1B.DR PROSITE; PS00305; 11S_SEED_STORAGE; 1.KW SEED STORAGE PROTEIN; SIGNAL.FT SIGNAL 1 21FT CHAIN 22 480 11S GLOBULIN BETA SUBUNIT.FT CHAIN 22 296 GAMMA CHAIN (ACIDIC).FT CHAIN 297 480 DELTA CHAIN (BASIC).FT MOD_RES 22 22 PYRROLIDONE CARBOXYLIC ACID.FT DISULFID 124 303 INTERCHAIN (GAMMA-DELTA) (POTENTIAL).FT CONFLICT 27 27 S -> E (IN REF. 2).FT CONFLICT 30 30 E -> S (IN REF. 2).SQ SEQUENCE 480 AA; 54625 MW; D515DD6E CRC32; MARSSLFTFL CLAVFINGCL SQIEQQSPWE FQGSEVWQQH RYQSPRACRL ENLRAQDPVR RAEAEAIFTE VWDQDNDEFQ CAGVNMIRHT IRPKGLLLPG FSNAPKLIFV AQGFGIRGIA EAFQIDGGLV RKLKGEDDER DRIVQVDEDF EVLLPEKDEE ERSRGRYIES ESESENGLEE TICTLRLKQN IGRSVRADVF NPRGGRISTA NYHTLPILRQ VRLSAERGVL YSNAMVAPHY TVNSHSVMYA TRGNARVQVV DNFGQSVFDG EVREGQVLMI PQNFVVIKRA SDRGFEWIAF KTNDNAITNL LAGRVSQMRM LPLGVLSNMY RISREEAQRL KYGQQEMRVL SPGRSQGRRE//
...OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;OC VIOLALES; CUCURBITACEAE.RN [1]RP SEQUENCE FROM N.A.RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;RX MEDLINE; 88166744.RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;RL EUR. J. BIOCHEM. 172:627-632(1988)....
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ID 11SB_CUCMA STANDARD; PRT; 480 AA.AC P13744;DT 01-JAN-1990 (REL. 13, CREATED)DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)DE 11S GLOBULIN BETA SUBUNIT PRECURSOR.OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;OC VIOLALES; CUCURBITACEAE.RN [1]RP SEQUENCE FROM N.A.RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;RX MEDLINE; 88166744.RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;RL EUR. J. BIOCHEM. 172:627-632(1988).RN [2]RP SEQUENCE OF 22-30 AND 297-302.RA OHMIYA M., HARA I., MASTUBARA H.;RL PLANT CELL PHYSIOL. 21:157-167(1980).CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN.CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND ACC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY ACC DISULFIDE BOND.CC -!- SIMILARITY: TO OTHER 11S SEED STORAGE PROTEINS (GLOBULINS).DR EMBL; M36407; G167492; -.DR PIR; S00366; FWPU1B.DR PROSITE; PS00305; 11S_SEED_STORAGE; 1.KW SEED STORAGE PROTEIN; SIGNAL.FT SIGNAL 1 21FT CHAIN 22 480 11S GLOBULIN BETA SUBUNIT.FT CHAIN 22 296 GAMMA CHAIN (ACIDIC).FT CHAIN 297 480 DELTA CHAIN (BASIC).FT MOD_RES 22 22 PYRROLIDONE CARBOXYLIC ACID.FT DISULFID 124 303 INTERCHAIN (GAMMA-DELTA) (POTENTIAL).FT CONFLICT 27 27 S -> E (IN REF. 2).FT CONFLICT 30 30 E -> S (IN REF. 2).SQ SEQUENCE 480 AA; 54625 MW; D515DD6E CRC32; MARSSLFTFL CLAVFINGCL SQIEQQSPWE FQGSEVWQQH RYQSPRACRL ENLRAQDPVR RAEAEAIFTE VWDQDNDEFQ CAGVNMIRHT IRPKGLLLPG FSNAPKLIFV AQGFGIRGIA EAFQIDGGLV RKLKGEDDER DRIVQVDEDF EVLLPEKDEE ERSRGRYIES ESESENGLEE TICTLRLKQN IGRSVRADVF NPRGGRISTA NYHTLPILRQ VRLSAERGVL YSNAMVAPHY TVNSHSVMYA TRGNARVQVV DNFGQSVFDG EVREGQVLMI PQNFVVIKRA SDRGFEWIAF KTNDNAITNL LAGRVSQMRM LPLGVLSNMY RISREEAQRL KYGQQEMRVL SPGRSQGRRE//
RN [1]RP SEQUENCE FROM N.A.RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;RX MEDLINE; 88166744.RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;RL EUR. J. BIOCHEM. 172:627-632(1988).RN [2]RP SEQUENCE OF 22-30 AND 297-302.RA OHMIYA M., HARA I., MASTUBARA H.;RL PLANT CELL PHYSIOL. 21:157-167(1980).
Hierarchical data.Order important.
DT 01-JAN-1990 (REL. 13, CREATED)DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)
Record (inadequate)of history
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ID 11SB_CUCMA STANDARD; PRT; 480 AA.AC P13744;DT 01-JAN-1990 (REL. 13, CREATED)DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)DE 11S GLOBULIN BETA SUBUNIT PRECURSOR.OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;OC VIOLALES; CUCURBITACEAE.RN [1]RP SEQUENCE FROM N.A.RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;RX MEDLINE; 88166744.RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;RL EUR. J. BIOCHEM. 172:627-632(1988).RN [2]RP SEQUENCE OF 22-30 AND 297-302.RA OHMIYA M., HARA I., MASTUBARA H.;RL PLANT CELL PHYSIOL. 21:157-167(1980).CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN.CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND ACC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY ACC DISULFIDE BOND.CC -!- SIMILARITY: TO OTHER 11S SEED STORAGE PROTEINS (GLOBULINS).DR EMBL; M36407; G167492; -.DR PIR; S00366; FWPU1B.DR PROSITE; PS00305; 11S_SEED_STORAGE; 1.KW SEED STORAGE PROTEIN; SIGNAL.FT SIGNAL 1 21FT CHAIN 22 480 11S GLOBULIN BETA SUBUNIT.FT CHAIN 22 296 GAMMA CHAIN (ACIDIC).FT CHAIN 297 480 DELTA CHAIN (BASIC).FT MOD_RES 22 22 PYRROLIDONE CARBOXYLIC ACID.FT DISULFID 124 303 INTERCHAIN (GAMMA-DELTA) (POTENTIAL).FT CONFLICT 27 27 S -> E (IN REF. 2).FT CONFLICT 30 30 E -> S (IN REF. 2).SQ SEQUENCE 480 AA; 54625 MW; D515DD6E CRC32; MARSSLFTFL CLAVFINGCL SQIEQQSPWE FQGSEVWQQH RYQSPRACRL ENLRAQDPVR RAEAEAIFTE VWDQDNDEFQ CAGVNMIRHT IRPKGLLLPG FSNAPKLIFV AQGFGIRGIA EAFQIDGGLV RKLKGEDDER DRIVQVDEDF EVLLPEKDEE ERSRGRYIES ESESENGLEE TICTLRLKQN IGRSVRADVF NPRGGRISTA NYHTLPILRQ VRLSAERGVL YSNAMVAPHY TVNSHSVMYA TRGNARVQVV DNFGQSVFDG EVREGQVLMI PQNFVVIKRA SDRGFEWIAF KTNDNAITNL LAGRVSQMRM LPLGVLSNMY RISREEAQRL KYGQQEMRVL SPGRSQGRRE//
FT SIGNAL 1 21FT CHAIN 22 480 11S GLOBULIN BETA SUBUNIT.FT CHAIN 22 296 GAMMA CHAIN (ACIDIC).FT CHAIN 297 480 DELTA CHAIN (BASIC).FT MOD_RES 22 22 PYRROLIDONE CARBOXYLIC ACID.FT DISULFID 124 303 INTERCHAIN (GAMMA-DELTA) (POTENTIAL).FT CONFLICT 27 27 S -> E (IN REF. 2).FT CONFLICT 30 30 E -> S (IN REF. 2).
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ID 11SB_CUCMA STANDARD; PRT; 480 AA.AC P13744;DT 01-JAN-1990 (REL. 13, CREATED)DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)DT 01-NOV-1990 (REL. 16, LAST ANNOTATION UPDATE)DE 11S GLOBULIN BETA SUBUNIT PRECURSOR.OS CUCURBITA MAXIMA (PUMPKIN) (WINTER SQUASH).OC EUKARYOTA; PLANTA; EMBRYOPHYTA; ANGIOSPERMAE; DICOTYLEDONEAE;OC VIOLALES; CUCURBITACEAE.RN [1]RP SEQUENCE FROM N.A.RC STRAIN=CV. KUROKAWA AMAKURI NANKIN;RX MEDLINE; 88166744.RA HAYASHI M., MORI H., NISHIMURA M., AKAZAWA T., HARA-NISHIMURA I.;RL EUR. J. BIOCHEM. 172:627-632(1988).RN [2]RP SEQUENCE OF 22-30 AND 297-302.RA OHMIYA M., HARA I., MASTUBARA H.;RL PLANT CELL PHYSIOL. 21:157-167(1980).CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN.CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND ACC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY ACC DISULFIDE BOND.CC -!- SIMILARITY: TO OTHER 11S SEED STORAGE PROTEINS (GLOBULINS).DR EMBL; M36407; G167492; -.DR PIR; S00366; FWPU1B.DR PROSITE; PS00305; 11S_SEED_STORAGE; 1.KW SEED STORAGE PROTEIN; SIGNAL.FT SIGNAL 1 21FT CHAIN 22 480 11S GLOBULIN BETA SUBUNIT.FT CHAIN 22 296 GAMMA CHAIN (ACIDIC).FT CHAIN 297 480 DELTA CHAIN (BASIC).FT MOD_RES 22 22 PYRROLIDONE CARBOXYLIC ACID.FT DISULFID 124 303 INTERCHAIN (GAMMA-DELTA) (POTENTIAL).FT CONFLICT 27 27 S -> E (IN REF. 2).FT CONFLICT 30 30 E -> S (IN REF. 2).SQ SEQUENCE 480 AA; 54625 MW; D515DD6E CRC32; MARSSLFTFL CLAVFINGCL SQIEQQSPWE FQGSEVWQQH RYQSPRACRL ENLRAQDPVR RAEAEAIFTE VWDQDNDEFQ CAGVNMIRHT IRPKGLLLPG FSNAPKLIFV AQGFGIRGIA EAFQIDGGLV RKLKGEDDER DRIVQVDEDF EVLLPEKDEE ERSRGRYIES ESESENGLEE TICTLRLKQN IGRSVRADVF NPRGGRISTA NYHTLPILRQ VRLSAERGVL YSNAMVAPHY TVNSHSVMYA TRGNARVQVV DNFGQSVFDG EVREGQVLMI PQNFVVIKRA SDRGFEWIAF KTNDNAITNL LAGRVSQMRM LPLGVLSNMY RISREEAQRL KYGQQEMRVL SPGRSQGRRE//
CC -!- FUNCTION: THIS IS A SEED STORAGE PROTEIN.CC -!- SUBUNIT: HEXAMER; EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND ACC BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR AND LINKED BY ACC DISULFIDE BOND.CC -!- SIMILARITY: TO OTHER 11S SEED STORAGE PROTEINS (GLOBULINS).
Structure in comments= schema evolution
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To turn Swissprot into tables To turn Swissprot into tables requires:requires:
• 20 - 30 tables – nothing extraordinary by relational
standards, but– huge query to reconstruct original form
• Invented keys • Queries on order and arrays• Recursive query processing• Also need to deal with schema evolution
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Curated DatabasesCurated Databases
• Useful scientific databases are often curated : they are created/ maintained with a great deal of “manual” labour.
select xyzfrom pqrwhere abc
Database people’s idea of what happens
What really happens
DB1 DB2
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Database Inter-dependence is Database Inter-dependence is ComplexComplex
GERD
TRRD
GenBank
Swissprot
EpoDB
TransFac
GAIA
BEAD
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Three new topicsThree new topics
• Annotation– how do I annotate a data element, and how
is this passed through queries?• Archiving
– how do we keep all the old versions of a database?
• Vertical partitioning.– combining databases and vector processing.
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Data AnnotationData Annotation(Khanna, Tan)(Khanna, Tan)
• Some databases (e.g. biology and linguistics) are designed to accommodate annotations
• Also a need for ad hoc (unanticipated) annotations.– How are annotations communicated?– How are they passed through queries?
• No general techniques or principles.
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Restaurant Cost Type
Peacock Alley
Bull & Bear
PacificaSoho Kitchen & Bar
$$$ French
$$$ Seafood
$ Chinese$ American
Restaurant Cost Type
PacificaSoho Kitchen & Bar
$ Chinese$ American
All Restaurants (View 1) Cheap Restaurants (View 2)
Yummy chicken curry!!
NYRestaurants (Source Table)
Restaurant Cost Type
Peacock Alley
Bull & Bear
PacificaSoho Kitchen & Bar
Zip
$$$ French 10022
$$$ Seafood 10022
$ Chinese 10013$ American10022
Serves fine French Cuisine in elegant setting. Jackets required.
Extensive wine list!
Sharing annotationsSharing annotations(courtesy of Wang-Chiew Tan)(courtesy of Wang-Chiew Tan)
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Annotation Annotation lookslooks simple but ... simple but ...
• Computing how an annotation should move through a query is intractable
• Equivalent queries may not carry annotations in the same way
• New insights are needed!
NeSC, 25 April 2002 Why Don’t Scientists Use Databases?
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How do we Build Archival Databases?How do we Build Archival Databases?[Khanna, Tajima, Tan][Khanna, Tajima, Tan]
• Many scientific database keep archives. It’s important to preserve the state of knowledge as it was in the past
• Archive frequently: space consuming
• Archive infrequently: delay in getting recent information published.
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The dangers of electronic documentsThe dangers of electronic documents
APPENDIX I: SAMPLE QUESTIONS FOR A FEDERATED DATABASEContinued HGP progress will depend in part upon the ability of genome databases to answer increasingly complex queries that span multiple community databases.
Some examples of such queries are given in this appendix. Note, however, until a fully atomized sequence database is available (i.e., no data stored in ASCII text fields), none of the queries in this appendix can be answered. ...
APPENDIX I: SAMPLE QUESTIONS FOR A FEDERATED DATABASEContinued HGP progress will depend in part upon the ability of genome databases to answer increasingly complex queries that span multiple community databases.
Some examples of such queries are given in this appendix. Note, however, until a fully atomized sequence database is available (i.e., no data stored in ASCII text fields), none of the queries in this appendix can be answered. ...
APPENDIX I: SAMPLE QUESTIONS FOR A FEDERATED DATABASEContinued HGP progress will depend in part upon the ability of genome databases to answer increasingly complex queries that span multiple community databases.
Some examples of such queries are given in this appendix. Note, however, until a fully relationalized sequence database is available, none of the queries in this appendix can be answered. ...
APPENDIX I: SAMPLE QUESTIONS FOR A FEDERATED DATABASEContinued HGP progress will depend in part upon the ability of genome databases to answer increasingly complex queries that span multiple community databases.
Some examples of such queries are given in this appendix. Note, however, until a fully relationalized sequence database is available, none of the queries in this appendix can be answered. ...
Now:Now:
Then:Then:
Report of a DOE “bioinformatics summit” ca. 1994
(No archive/edition! No footnote!)
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Examples from BioinformaticsExamples from Bioinformatics
• Swissprot. New version produced every four months. – Old versions are kept.– Difficult to get at most recent data
• OMIM. New version produced every day– Old versions are not kept– Impossible to reconstruct past states of the
data
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Current approaches use “diff”Current approaches use “diff”
Columns are stored contiguously. Order is preserved(Vertical partitioning)
disk pages
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Advantages of Vertical PatitioningAdvantages of Vertical Patitioning• Faster queries.
– A query that reads 2 columns in 100 does 2% of the i/o (i/o cost dominates)
– A few columns can often reside in memory.• Computation on order• Can use both SQL and vector processing languages• Downside: deletions are horribly expensive.
– but deletions are uncommon in scientific DBs• Vertical partitioning can also be performed on
hierarchical structures -- like Swissprot -- and XML
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Many other issuesMany other issues• Heterogeneous data integration
– a perennial problem– can it be done by the end-users?
• Distributed query evaluation against redundant, constrained data.
• Data provenance• Data streams• and many more
All these involve hard, fundamental All these involve hard, fundamental problems in Computer Scienceproblems in Computer Science