Open Source Solutions for Tissue Banking Informatics

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Open Source Solutions forTissue Banking
Informatics

• Jules J. Berman, Ph.D., M.D.
• INFORMATICS FOR REPOSITORIES
• Wednesday, May 21, 2008
• 330 pm 405 pm

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Approaches to finding open source solutions

• 1. Generalize (don't specialize). Wherever
  possible, don't think of your tissue repository
  problems as being unique. Try to think of your
  problems as instances of very general informatics
  problems.
• In most cases, the same open source solutions
  that work for bioinformaticians, astronomers, and
  factory inventories will likely work for you

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Approaches to finding open source solutions

• 2. Learn a popular open source programming
  language that is easy to learn and that is
  supplemented by an enthusiastic biomedical
  community
• Perl
• Python
• Ruby

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Approaches to finding open source solutions

• 3. Use open source, unencumbered nomenclatures,
  codes, syntactic formats. Otherwise, can't share
  or post data through web
• MESH (standard, open source, free)
• UMLS (standard, encumbered)
• SNOMED (standard, encumbered)
• Neoplasm Classification (non-standard, open
  source, free, standard syntax XML, RDF)
• http//www.julesberman.info/

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Approaches to finding open source solutions

• 4. Use an open source and general data syntax
• HTML (formatting and linking)
• XML (describing data)
• RDF (getting meaning from described data)

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All data can be specified using RDF, developed by
the W3C. RDF files are collections of
statements expressed as data triples ltidentified
subjectgtltmetadatagtltdatagt Jules Berman blood
glucose level 85 Mary Smith eye color
brown Samuel Rice eye color blue Jules
Berman eye color brown When you bind a
key/value pair to a specified object, you're
moving from the realm of data structure (i.e.,
XML) into the realm of data meaning.
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RDF permits data to be merged between different
files
Medical file Jules Berman blood glucose
level 85 Mary Smith eye color
brown Samuel Rice eye color blue Jules
Berman eye color brown
Merged Jules Berman database Jules Berman
blood glucose level 85 Jules Berman eye
color brown Jules Berman hat size 9
Hat file Sally Frann hat size 8 Jules
Berman hat size 9 Fred Garfield hat size
9 Fred Garfield hat_type bowler
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Approaches...

• 5. Use open source utilities not software
  applications (open source or otherwise)l
• Utilities are simple programs that do one type of
  job, very well. Often work from command-line
  (i.e., no GUI)
• Once you've mastered a dozen or so utilities, you
• can handle most informatics task that you'll come
  across.
• Applications are often complex and seldom provide
  the functionality you need (now or future).

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Approaches ...

• 6. Learn the algorithms for your discipline.
• Algorithms are process descriptions that work
  every time.
• Most informatics algorithms can be implemented in
  under ten lines of software code
• You can think of software applications as many
  algorithms working under a GUI
• If you really understand algorithms, you can make
  important contributions to your field.

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Approaches...

• 7. De-emphasize standards.
• Most standards are difficult to understand, and
  there are many of them, often covering obscure
  domains. Many standards are just bad.
• Data kept in a standard today may be non-standard
  legacy data tomorrow.
• Unlike physical standards, standards are
  transformable (so why fuss over any one
  standard?).
• Standards can be encumbered

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• Specifications often a better solution than
  Standards
• Specifications are just descriptions of your
  data.
• A specification requires a common language for
  describing data (so that you and your computer
  can understand what it's trying to convey).
• Specifications give you enormous freedom to
  create and describe new and unconventional data
  objects.
• Usually done in RDF
• If you've specified your data well, you can port
  between standards when you need to.

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• Example Pathology image annotation

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• Important descriptors of an image might include
• File information
• Image capture information
• Image format information
• Specimen information
• Patient information
• Pathology information
• Region of interest information

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• JPEG is an image format that is used by millions
  of people in all types of professions, including
  the medical profession
• JPEG can now be used without worrying about IP
  issues
• You can put any information you want into the
  header of a JPEG image (including an RDF
  document) so that specified clinical/pathological
  information can be conveyed with the image
• Because images non-physical, it is usually easy
  to interconvert image formats

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By annotating our images, we can ensure that the
image conveys meaning and value By using RDF, we
can ensure that the individual triples can be
integrated with heterogeneous data sources beyond
those of images. By using pre-existing
international general standards for describing
any kind of data, we attain interoperability and
avoid the confusion and complexity that occurs
whenever a new standard is created. See
http//www.julesberman.info/spec2img.htm
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• Would you like to write a
• Tissue Respository/Tissue Informatics
• book?
• jjberman_at_alum.mit.edu