Fedora
Federation Of Research Assets
MUG'03, Dave Weininger, Metaphorics

Index

1. Fedora servers form a federation of services
2. Why federate rather than unify?
3. Fedora servers provide HTTP services
4. Things to do with federated databases
5. Fedora commercial release

1.  Fedora services

• Fedora servers form a federation of services

  • No unifying data model
    • Each information base can be represented in its most natural form
    • Services are useful in isolation or in any combination
  • Generic linguistic links, e.g.,
    • molecules and reactions via SMILES
    • enzyme functionality via ECN
  • Specific linguistic links, e.g.,
    • English (common names, pharmacology)
    • Latin (diseases, taxonomy)
    • Chinese (medicinals)
  • All problems are treated as "small" problems
    • Generally can be stored in memory
    • Generally no need to store "data about data"

2.  Why federate rather than unify?

• Main advantage of federation: synergy

  • navigate through dramatically different realms
    • Allopathic (wdi) vs. Traditional Chinese Medicine (tcm)
    • Biochemistry (empath) vs. molecular biology (planet)
    • Chemistry (wdi) vs. biochemistry (empath)

  • Linkages are made via information models rather than data models
  • What do you know about this molecular structure?
  • What do you know about this enzyme functionality?
• Main disadvantage of federation: anarchy
  • No rules about how one sets up a database (fewer, anyway)
  • Results are often unexpected
  • Machines/humans are both producers/consumers of information
• Main disadvantage of unification: committees
  • Unifying data models is a long, drawn-out process
  • Result is often not as useful as it might be, driving a square peg into a round hole
  • Motivation is often efficiency, but what kind of efficiency?

3.  Fedora servers provide HTTP services

• Fedora services look like HTTP webservers

  • Looks like a normal web server
    each fedora server provides a specific service on a specific port
  • Works like a normal web server
    Existing client software (browsers) and skills (web surfing) are used
  • There are some differences under the covers
    there are (usually) no files at all, fedora services can talk to each other
• Minimal number of unifying capabilities
  • Each fedora service should do a good job at individual task
  • Fedora GUI - hyperlink everything
  • Establishes identity/similarity relationships
  • Provides similar and related links
  • No GUI tricks are used (Java beans, active controls, etc.)
• Related presentations

  • HTTP toolkit (MUG '02) and HTTP toolkit (MUG '01)
    development of the HTTP toolkit underlying fedora
  • The online.daylight.com experiment (EMUG'01)
    describes experiment deploying fedora on WWW
  • TCM -- Traditional Chinese Medicines (EMUG '00)
    an early fedora exploring alternative information models

4.  Things to do with federated databases

• Pharmacological information surfing

  • Start with drug name, e.g., lipitor in wdi
    Note not many very similar. Enzyme is not listed. [Surprising, since Lipitor is world's best selling drug.]
  • What's related (to the small molecule)? planet has one complex 1HWK and two (roughly) similar ones
    Note importance of similarity comparison: carboxyillic acid vs. lactone
    Note that rather distant similarities (0.45) are useful
  • Planet provides protein sequence, and complexes with similar sequences
    There are a bunch with the same sequence.
    Complexes with atorvastatin (original) are rediscovered.
    Finds complexes with structurally distant natural ligand HMG/CoA
    Also finds complexes with rosuvastatin, cerivastatin, fluvastatin, simvastatin, compactin
  • This protein is an enzyme: what related information is available?
    The enzyme is "human HMG-COA reductase".
    The EC Number is 1.1.1.34
    Enzyme Commission name is: hydroxymethylglutaryl-CoA reductase (NADPH2)
    Empath shows the metabolic action of this enzyme,
    ... as well as metabolic regulators, biological scope, direction, reversibility, stoichiometry, etc.
    Empath also shows the activating and deactivating steps for this enzyme
  • Given function in metabolic context, discover new relationships
    Next step in the anabolic pathway is phosphorylation of mevalonate via the enzyme mevalonate kinase. These enzymes are related metabolically rather than structurally.
    Is anything known about mevalonate kinase (ECN-2.7.1.36)? Yes, e.g., 1KVK in planet.
    Also, 1AQY
    Back to empath, there is a similar metabolic relationship with the (anabolic) synthesis of the precursor, S-3-hydroxy-3-methyl-Glutaryl-CoA via the enzyme hydroxymethyl-glutaryl-CoA synthase.
    Note how difficult this would be using paper charts, etc.
• Some other fun starting points

  • Folic acid and ascorbyl palmitate in medusa
  • Luteolin and N-Acetyl-D-glucosamine in tcm
  • 1HH7, 1CLQ, 1G7X, 3LBD in planet
  • beta-lactamase and Estradiol 17beta-dehydrogenase in empath

• Warning, this can be addictive

      Date: Wed, 19 Feb 2003 01:22:18 -0800
      From: Scott Dixon 
      To: Dave Weininger 
      Subject: planet
  
      Hi, Dave-
      I've spent a few more hours just wandering through planet at random.  
      It is really fascinating to see what is there.  After all the years of 
      using the PDB, I think I learned more about what is in there in the 
      last few hours than I ever knew before.  I can't wait to see what 
      happens when we hook up the other servers.  Should be amazing.
      ...
      Cheers,
      Scott
    

5.  Fedora commercial release

• Fedora servers are available from Metaphorics
  • Servers at MUG'03 will be available as products
  • Demo servers will be available on website soon after MUG
  • Sales of corporate packages be ready RSN
  • Fedora servers are licensed on a per-network basis
  • See Yosi.
• Metaphorics is a Daylight partner
  • Metaphorics servers use the Daylight Toolkits (including HTTP)
  • All software and database licensing is provided with products.
  • We're scheduling site and meeting visits, talk with us!
• Specifics and caveats
  • planet -- ready for v2.81 (requires good server hardware)
  • empath -- almost ready for v2.81 (licensing is close)
  • ecbook -- ready for v2.81
  • wdi -- ready to go, special deal for WDI licensees
  • tcm/dcm/zi4 -- offered as package, ready for v2.81
  • Exceptions: medusa (not a product), park (alpha free with tcm)
• Future fedora's
  • ACD
  • QSAR
  • Wombat