Creation and Maintenance of GeneKeyDB

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Creation and Maintenance of GeneKeyDB

• Research being conducted by
• Kevin Kastner
• Under the direction of
• Dr. Erich Baker

2
The Problem

• There exists thousands of biomedical data
  sources.
• In 2006, there were 557 relevant public
  resources in molecular biology.
• This is growing rapidly.
• 203 sources in 1999
• 226 sources in 2000
• 277 sources in 2001.

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The Problem

• Traditional database approaches are too
  structured.
• Scientific objects change identification over
  time.
• Gene names change over time.
• The Human Genome Nomenclature Database (HUGO)
  contains 13,594 active symbols, 9635 literature
  aliases, and 2739 withdrawn symbols.
• SIR2L1 (w/drawn) is a synonym for SIRT1 and
  sir2-like 1.

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Scientific Object Identities
5
The Solution

• GeneKeyDB
• A gene-centered relational database developed to
  enhance data mining in biological data sets.
• GeneKeyDB relies primarily on existing database
  identifiers derived from community databases
  (NCBI, GO, Ensembl, et al.) as well as the known
  relationships among those identifiers.
• Version 1 is already out!
• http//www.biomedcentral.com/1471-2105/6/72

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Weaknesses of Version 1

• Can no longer be updated
• Complex queries must be made to the database in
  order to obtain desired information

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Complex Queries

• SELECT ll_xp_cdd.cdd_name, ll_np_cdd.cdd_name,
  organism
• FROM ll_xp_cdd, ll_np_cdd, ll_locus
• WHERE ll_xp_cdd.cdd_score ll_np_cdd.cdd_score
• AND ll_id IN
• (SELECT ll_id
• FROM ll_refseq_xm
• WHERE ll_refseq_xm_id IN
• (SELECT ll_refseq_xm_id
• FROM ll_xp_cdd, ll_np_cdd
• WHERE ll_xp_cdd.cdd_score ll_np_cdd.cdd_score
  ))
• AND ll_id IN
• (SELECT ll_id
• FROM ll_refseq_nm
• WHERE ll_refseq_nm_id IN
• (SELECT ll_refseq_nm_id
• FROM ll_xp_cdd, ll_np_cdd
• WHERE ll_xp_cdd.cdd_score ll_np_cdd.cdd_score)
  )

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Current Research

• Creation of APIs to validate data in the database
  and to enable querying to become much easier for
  the user.
• One-step updating of the database and the
  information it contains.

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API Alternative

• // fxn(search_params, desired_info), returns
  ll_id
• curated.cdd(score ,null)
• curated_score ? score
• locus_id1 ? gaa.cdd((name ,score ), score
  )
• gaa_name ? name
• gaa_score ? score
• locus_id2 ? curated.cdd(name ,score )
• curated_name ? name
• locus_id ? intersect(locus_id1 ,locus_id2
  )
• locus(organism , locus_id )
• print(gaa_name , curated_name , organism )

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External Implementations

• Some databases have APIs as well.
• Ensembl
• APIs are done in Perl.
• APIs for GeneKeyDB will be done in Java.
• More structured language.
• Easier to read.

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The Future of GeneKeyDB

• GeneKeyDB will join even more external and widely
  used databases together.
• Code for updating GeneKeyDB will tie into
  database information that will change in expected
  ways.
• Lowers the required number of code rewrites.
• GeneKeyDB will be dynamically updated.

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The Future of GeneKeyDB

• APIs made that will be written in Perl.
• Perl is used often, almost exclusively, by
  biologists.
• Can have Perl APIs tie into Java APIs, rather
  than creating all new ones.

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Comments? Questions?

• http//genereg.ornl.gov/gkdb/