maize-GAMER - Mixed-Method Pipeline Data

Raw output from mixed-method pipelines have been converted to GAF 2.0 format.
Each pipeline used in the project outputs data in a specific format, and custom
R code was used to convert these into the standard GO Annotation Format 2.0.

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*                                                                             *
*   Please note, most of the data files contained in this DOI are             *
*   compressed into GZip files (.gz extension).                               *
*   Mac and Linux OS's can extract this file type natively.                   *
*   Windows OS requires software to extract the archive.  7-Zip               *
*   (http://www.7-zip.org) is free and open source software that will         *
*   allow windows PCs to open and decompress the archive.                     *
*                                                                             *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *


/a._mm_gaf: This directory contains 3 files
File Name                  | Description
---------------------------+---------------------------------------------------
 1 _readme.txt             |
                           |
 2. argot2-0.0.gaf.gz      | The raw output from Argot2 converted into
                           | GAF format.
                           |
 3. fanngo-0.0.gaf.gz      | The raw output from FANN-GO converted into
                           | GAF format.
                           |
 4. pannzer-0.0.gaf.gz     | The raw output from PANNZER tool converted
                           | into GAF format.



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*                                                                             *
*   A slight change to the GAF format was made to accomodate the score for    *
*   annotations from mixed method pipelines. The column "With" has been       *
*   used to store the score for each annotation.                              *
*                                                                             *
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Column Name                | Column Description
---------------------------+---------------------------------------------------
  DB                       | Database from which the identifier in DB object ID
                           | is drawn
                           |
  DB Object ID             | A unique identifier from the database in DB for
                           | the item being annotated
                           |
  DB Object Symbol         | A (unique and valid) symbol to which DB object ID
                           | is matched
                           |
  Qualifier                | Flags that modify the interpretation of an
                           | annotation
                           |
  GO ID                    | The GO identifier for the term attributed to the
                           | DB object ID
                           |
  DB:Reference             | One or more unique identifiers for a single
                           | source cited as an authority for the attribution
                           | of the GO ID to the DB object ID
                           |
  Evidence Code            | Evidence codes for GO annotation this field
                           | is mandatory
                           |
***************************|***************************************************
  With                     | Used to assign score from the mixed-method
                           | pipeline
***************************|***************************************************
                           |
  Aspect                   | Refers to the namespace or ontology to which the
                           | GO ID
                           | (column 5) belongs
                           |
  DB Object Name           | Name of gene or gene product
                           |
  DB Object Synonym        | Gene symbol
                           |
  DB Object Type           | A description of the type of gene product being
                           | annotated
                           |
  Taxon                    | Taxonomic identifier
                           |
  Date                     | Date on which the annotation was made
                           |
  Assigned By              | The database which made the annotation
                           |
  Annotation Extension     | Contains cross references to other ontologies
                           | that can
                           | be used to qualify or enhance the annotation
                           |
  Gene Product Form ID     | Allows the annotation of specific variants of that
                           | gene or gene product.

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*                                                                             *
*   Please note, data files contained in this DOI are                         *
*   compressed into GZip files (.gz extension).                               *
*   Mac and Linux OS's can extract this file type natively.                   *
*   Windows OS requires software to extract the archive.  7-Zip               *
*   (http://www.7-zip.org) is free and open source software that will         *
*   allow windows PCs to open and decompress the archive.                     *
*                                                                             *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *