maize-GAMER raw datasets for maize.B73.AGPv4.r1

Raw datasets before any cleanup from the maize-GAMER component datasets, public
maize GO datasets, and gold standard dataset from MaizeGDB.

Argot2, FANN-GO, and PANNZER datasets were run through a filtering step to
remove the low confident annotations. Outputs from InterProScan and
sequence-similarity based maize GO datasets were converted from default output
formats to GAF 2.0. Gramene provided the annotations in GAF format, but both
Phytozome and AgriGO maize GO datasets had to be converted to GAF 2.0.


* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*                                                                             *
*   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.   *
*                                                                             *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *


/b._raw_gaf: This directory contains 7 files
File Name                                 | Description
------------------------------------------+------------------------------------
 1. _raw_gaf-desc.txt                     | Detailed description of the
                                          | contents of data files in
                                          | this folder
                                          |
 2. maize.B73.AGPv4.arabidopsis.gaf.gz    | GO annotations in GAF format for
                                          | maize from sequence similarity
                                          | method used with TAIR datasets
                                          |
 3. maize.B73.AGPv4.argot2.5.gaf.gz       | A subset of GO annotations selected
                                          | from maize.B73.AGPv4.argot2.5.gaf.gz
                                          | after removing low confidence
                                          | annotations based on annotation
                                          | scores
                                          |
 4. maize.B73.AGPv4.fanngo.gaf.gz         | A subset of GO annotations selected
                                          | from maize.B73.AGPv4.fanngo.gaf.gz
                                          | after removing low confidence
                                          | annotations based on annotation
                                          | scores
                                          |
 5. maize.B73.AGPv4.Interproscan5.gaf.gz  | Output from InterProScan pipeline
                                          | for Maize RefGen_v3 covereted into
                                          | GAF format
                                          |
 6. maize.B73.AGPv4.pannzer.gaf.gz        | A subset of GO annotations selected
                                          | from maize.B73.AGPv4.pannzer.gaf.gz
                                          | after removing low confidence
                                          | annotations based on annotation
                                          | scores
                                          |
 7. maize.B73.AGPv4.uniprot.plants.gaf.gz | GO annotations in GAF format for
                                          | maize from sequence similarity
                                          | method used with UniProt datasets


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                         | This field is used to hold an additional
                              | identifier for annotations using certain
                              | evidence codes
                              |
 Aspect                       | Refers to the namespace or ontology to
                              | which the GO ID belongs to
                              |
 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