maize-GAMER - Mixed-Method Pipeline Data for maize.B73.AGPv4.r1

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, 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 such as 7-Zip (free and open source          *
*   available from http://www.7-zip.org)to open and decompress the archive.   *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *


/a._mm_gaf: This directory contains 4 files
File Name                                 | Description
------------------------------------------+------------------------------------
 1. _mm_gaf-desc.txt                      | Detailed description of the
                                          | contents of data files in
                                          | a._mm_gaf folder
                                          |
 2. maize.B73.AGPv4.argot2.5.gaf.gz       | The raw output from Argot2.5
                                          | converted into GAF format
                                          |
 3. maize.B73.AGPv4.fanngo.gaf.gz         | The raw output from FANN-GO
                                          | converted into GAF format
                                          |
 4. maize.B73.AGPv4.pannzer.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