==== Omics Data Standards WG - Minutes 07-25-2016 ====

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  * Matrix Formats and intermediate formats to facilitate module swapping (mapping, etc)
      * FASTQ is definitely needed as the initial raw data
  * Discuss over which format should be the candidate
      * Valid read-pair format may be extensible (columns can be added, e.g. cellular barcodes)
      * Discuss data structures and bits of information needed first?
        * Pair-wise contact stored as sparse array while high-order contacts may be stored as matrices
      * Read/write of said candidates should require a low threshold for the broader community
  * What columns will be required and which ones will be optional?
  * Standardize mapping procedures? (AWG?)
  * Re-cap on known formats
      * Butler file: a binary form of contact matrix for visualization purposes only, like bigWig;
      * Hdf5 file: a binary file/platform including multi-dimensional arrays that can store meta-data along with the core files, platform including indexing/compression modules that can be switched;
      * .hic format: family of formats including validpairs/mergednodups, wrapper available for query/compression, multiple contact matrices, meta-data available;
  * Factors to consider: How to use the format? Visualization,
      * Current situation of the eco-system (software support, popular tools for visualization, community usage, documentation, etc)
      * Performances (query speed, etc)
      * Analysis and visualization may have different needs (pull out the whole matrix vs rapid resolution change and querying)
        * Yet benchmarks can be heavily influenced by implementation
        * Discuss the details of the benchmarks for all three formats and design tests for them.
  * Interaction format is not finalized in ENCODE as it’s out of the core formats.

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