To be covered:

1. What is fedora,
2. and why bother?
3. Why federate rather than unify?
4. HTTP-orientation
5. Information models
6. Making it work: a modern delivery mechanism
7. Demonstration: dayflash
8. Example servers.
9. To everything, there is a season: fedora's place

1.  What is fedora, and why bother?

• What

  • Federation of Research Assets
  • Web-like database system using HTTP communication
  • Language is the unifying communications element
  • The molecular model provides integration of chemical information

2.  What is fedora, and why bother?

• Why

  • Integration of disparate information is necessary, difficult
    Researchers are limited by fixed data models
  • Computers get better, access to information gets more difficult
    Integrating a new type of information is harder now than in 1990
  • We're not even reinventing the wheel, we're duplicating it!
    Encapsulate data once, then use it everywhere
  • Researchers need to try out new things cheaply
    Special-purpose applications don't serve researchers well

3.  Why federate rather than unify?

• Theoretically

  • Information is best represented by a native data model.
  • Each server does the best job representing its data, regardless of application.
  • Integration with other information sources is done by each server using local, native data model.
  • Servers don't have to know about each other's conventions.
  • Cheap to try new things, due to minimal side effects.

• Practically

  • Each resource can be supported/tested/administered separately.
  • Resource modularization allows efficient, specific deployment.
  • Scale independence: isolated laptop to collaborative web.
  • Potential for zero-administration implementation.

4.  HTTP-orientation

• Advantages

  • HTTP was specifically designed for collaborative computing

  • HTTP is now used for most information exchange on this planet

  • Flexible: can transport all kinds of data (not just HTML)

  • Scaleable: from laptop to workgroup to corporate LAN to WWW

  • Universal: virtually everyone already knows how to browse HTTP

• Disadvantages

  • Stateless model is harder to secure

  • Real-time applications are limited
    e.g., molecular editing, 3-D display

5.  Information models

• logpstar - observed hydrophobicity as log(P_o/w)
  • 11,053 structures, names, observed data of one kind
  • "simplest" chemical information model is still non-trivial
  • find exact/generic structure, similar structures, find by name
• wdi - World Drug Index, pharmacology of named drugs
  • 67,059 formal entries containing ~800,000 fields
  • 7 pharmacology types (100K items), 12 name types (400K items)
  • discrete structures, combination preps and unknown structures
  • full complement of structure/name/data searching methods needed

• tcm - Traditional Chinese Medicine: structures, indications and effects
  • biological entries (sources of Chinese medicinals)
  • chemical entries (structures observed in Chinese medicinals)
  • information is represented in English, Chinese (Pinyin) and SMILES
  • underlying information model is Traditional Chinese Medicine

• park - annotated photographic archive of medicinal sources
  • photographs of medicinal sources which are mostly biological
  • provides best identification available for such entities
  • complements Latin/English/Chinese names which are not reliable
  • annotations searchable in multiple languages

• dcm - Dictionary of Chinese Medicine, encyclopedic
  • 220,000+ fields in 4 languages (English, Chinese, Pinyin, Latin)
  • underlying information model is Traditional Chinese Medicine
  • identifiers are expressed as traditional Chinese characters
  • add'l info, e.g., western medical concepts, acupuncture channels
  • intrinsic queries are multilingual-multiconceptual

• zi4 - Chinese character service
  • Chinese character image and mapping services
  • Unicode, Traditional- and Simplified-Chinese characters
  • Traditional to Simplified translation
  • pragmatic utility handles non-trivial requirement

• planet - Protein-Ligand Association NETwork
  • each data object is a protein-ligand association, i.e., a relationship between one or more proteins and one or more ligands
  • e.g., observed binding, computed docking
  • large/small molecule search/similarity methods are implemented
  • robust in the face of relatively poor oxidation state information typical of crystallographic data
  • big and fast

• pathos - metabolic pathway chart
  • models a modern metabolic pathway chart
  • agents, cofactors, compounds, diseases, enzymes, landmarks, notes, pathways, regulators, steps
  • represents unified metabolism (plant, unicellular and animal)
  • a natural index: most drugs operate in this realm
  • massive image representing a massive reaction schema
  • integrated name/structure/similarity/functionality searching

• ecbook - Enzyme Commission codebook
  • EC code index is a discrete model of enzyme functionality
  • EC codes are dynamic with time
  • many-to-many relationship required due to multifunctional enzymes
  • primarily a crossreference and index to other databases

• qsar - Quantitative Struture-Activity Relationships
  • Each primary entity is an observed relationship between molecular structure and biological activity (6500+) or physical property (7600+)
  • Raw data and references are included (13,000+ authors!)
  • Search by both component (data) and relationship (QSAR) properties
  • Supports relationships of QSAR relationships (comparative QSAR)
  • However, other applications might be just as important

6.  Making it work: a modern delivery mechanism

• "Computers get better, access to information gets more difficult." -- if we are to succeed, this needs to be reversed.
• Continuing improvements in computer technology makes it possible to simplify information access, let's use it.
• HTTP-oriented services form a logical beginning: how do we implement a complete solution for research purposes?

• One attractive solution: embedded HTTP servers on flash memory devices.
  • good capacity, excellent random-access performance
  • promises zero-administration solution
  • embedded hardware licensing can simplify installation
  • provide all required resources: admin privileges not needed
  • robost, no moving parts, 10 year persistance
  • main disadvantage: this is not the way we already do things!

• This has been implemented using USB flash-memory-based drives.

7.  Demonstration: dayflash

• Notice:

  • Plug-n-play: self configuring, zero-admin
  • Truly minimal interaction, no command line
  • Nothing written to disk: no traces, no priv's needed
  • Delivers high performance network services

8.  Example servers

• Available at MUG'02

  • tcm472x: http://mainline.daylight.com:8888/
    wdidemo, tcm, dcm, park, zi4, logpstar
  • mug02: http://janus.daylight.com/
    above, plus full wdi, qsar, imagine, pathos, and some more
  • meta4x: http://meta4x.daylight.com:23456/
  
  planet, pathos, ecbook, wdidemo

9.  To everything, there is a season: fedora's place

• Excellent for wide dissemination of complex data sources
• Good for research; not perfect but better than what we have so far
• Does not compete with RDB of data with known/simple data models
• Limited number of databases to be released with Daylight 4.81
• HTTP toolkit also to be released with Daylight 4.81

• Apple ... for still being there
• Derwent ... for WDI
• Jack Delany and Yosi Tatiz, Daylight ... for making room for this work
• Nigel Wiseman and Bob Felt, Paradigm ... for DCM
• Peter Nielsen, Daylight and Bill Milne, Ashgate ... for TCM
• Dawn Abriel ... for medical expertise
• Ragu Bharadwaj, Daylight ... for JavaGrins and OS-X enthusiasm
• Roger Sayle, Metaphorics ... for rasmol and inspiration
• Scott Dixon, Metaphorics ... for planet
• Xinjian Yan, NIST ... for TCM
• Zhou Jiaju, Chinese Academy of Sciences ... for TCM
• Al Leo and Corwin Hansch, BioByte ... for c/logp and QSAR