Friday, April 6, 2007

Tissue Microarray Data Exchange Specification

The Tissue Microarray Data Exchange Specification (TMA Specification) was developed by the Association for Pathology Informatics (API) and is available as an open access document, published in 2003.

TMAs, first introduced in 1998, are collections of hundreds of tissue cores arrayed into a single paraffin histology block (see Figure).

Each TMA block can be sectioned and mounted onto glass slides, producing hundreds of nearly-identical slides. TMAs permit investigators to use a single slide to conduct controlled studies on large cohorts of tissues, using a small amount of reagent. The source of tissue is only restricted by its availability in paraffin and ranges from cores of embedded cultured cells to tissues from any higher organism. In a typical TMA study, every TMA core is associated with a rich variety of data elements (image, tissue diagnosis, patient demographics or other biomaterial description, quantified experimental results). Under ideal circumstances, a single paraffin TMA block can be sectioned into nearly identical glass slides dispensed to many different laboratories. These laboratories may use different experimental protocols. They may capture data using different instruments, different databases, different data architectures, different data elements and immensely different formats. These laboratories would vastly increase the value of their experimental findings if they merged their findings with those of the other laboratories that used the same TMA block. Unfortunately, the practice of merging TMA data sets obtained at different laboratories using different information systems was infrequently practiced. A key barrier to this process was the incompatibility of the individual data sets. There simply was no community-based specification for exchanging TMA data. Without such a specification, TMA data files could not be effectively shared or merged among laboratories using different TMA applications.

Since publication of the TMA Specification week, the TMA Specification was downloaded from the BioMed Central site 7,424 times (April 2007).

At Google Scholar, the TMA specification paper was listed as being cited by 36 papers.

The TMA Specification has been adopted into several TMA database applications.

The common data elements for the specification are freely available.

An implemenation of the specification by an NCI-funded research consortium is also available.

-Jules Berman
My book, Principles of Big Data: Preparing, Sharing, and Analyzing Complex Information was published in 2013 by Morgan Kaufmann.

I urge you to explore my book. Google books has prepared a generous preview of the book contents.

tags: big data, metadata, data preparation, data analytics, data repurposing, datamining, data mining