This page documents the steps required to take when supplying Gene Ontology annotations to the GO Consortium (GOC). For general information on how to conduct GO annotations, please see the GO Annotation Policies Guide.
Steps to prepare GO annotations for submission to the GOC
1. Contact the Gene Ontology Consortium
Please contact the GOC before carrying out the annotation work; this will ensure that GOC mentors and trainers can be of assistance in producing data sets in agreement with the GOC annotation policies and format requirements.
2. Provide a GAF2.0 formatted file
Research groups looking to supply Gene Ontology annotations to the Consortium must submit an appropriately formatted annotation file that conforms to syntactic and semantic requirements of the Consortium. The primary GO annotation format is the Gene Association Format (GAF) 2.0, or GAF2.0. This page contains details on how to build and populate the GAF2.0 File.
Please ensure that:
- Submissions are made using this flat, tab-delimited format file: GAF2.0
- The file has the correct file header
- The file has the correct number of columns, even if some of them are not populated with data
- If the file contains column names, these must be commented out using an exclamation mark
! at the start of the line
- The file contains no leading or trailing spaces
2.1 Make annotations to UniProtKB accessions or NCBI identifiers
- Human data, MODs: The ideal object identifiers for annotations are stable database identifiers. That is, ideally, all annotations should describe the activities or locations of protein accession from the UniProt KnowledgeBase (UniProtKB) that are present in the UniProt Reference Proteome Files.
- Non-MODs: If this is not possible, research groups should first ensure that alternative identifiers are also stable, and then provide identifier mapping files (i.e. gp2protein, gp2rna; see below), where equivalent UniProtKB or NCBI identifiers should be supplied. A gp_unlocalized file should also be provided where no sequence or genomic location is known for a gene identifier.
- If mapping to UniProtKB or NCBI identifiers is not a possibility: In this case the research group should contact the GOC to explore the alternatives.
2.2 Provide a database name
Each research group must provide a database name, which will be used to acknowledge the annotation set and to appropriately credit your work. This name would be visible in the 'assigned_by' field (Column 15) of all the annotation lines that the group is contributing. This name will also be added to the list of annotation providers.
2.3 Include bibliographic references
Each annotation line must include the citation of a bibliographic reference, which details the methods and results from which the annotation was made. The reference should be either a PubMed identifier or an abstract (GO_REF) describing how the annotation was made. Please see the Gene Ontology Reference Collection for a list of all current GO references.
3. State whether or not regular updates will be submitted
For research groups conducting curation, it is not always necessary to commit to supplying regular updates for their annotations. When the research team chooses to enter 'Longer-term Annotation Contribution / Collaboration' as the submitting group, a primary point of contact must also be identified so that requests may be redirected and proper action on such requests may be taken in a timely manner. The GOC will take responsibility for corrections and updates to datasets included in non-recurring submissions or those from annotation groups that become 'inactive' annotation providers.
4. Identifier Mapping Files
Providing complete identifier mapping files is necessary for:
- Downloading sequences from UniProtKB and NCBI. These sequences are used for inferencing annotations in a phylogenetic context using the Phylogenetic Annotation and Inference Tool (PAINT).
- Searching for GO annotations in AmiGO, using other database cross-reference IDs (UniProt or NCBI).
- Helping to keep track of IDs and annotations, removing duplicates, etc.
Please be aware: when identifier mapping is carried out, due to different database release cycles, sequence identifiers that should correspond with each other may not always display the same data.
4.1 gp2protein file
- The gp2protein format specifications are described here.
- The gp2protein mapping file must contain the complete list of protein-coding genes in the respective organism (or community), including those proteins not annotated to GO.
- The first column should contain all gene or gene product identifiers (these are typically MOD-specific identifiers). The second column should contain mappings to canonical identifiers. Protein coding genes must map to UniProtKB accessions (preferably Swiss-Prot, otherwise TrEMBL). If identifiers are unavailable in UniProtKB, NCBI identifiers (NP_ and XP_) are permissible.
- If the annotation group is satisfied with identifier mappings from an external identifier type to UniProtKB accessions, as supplied by the UniProt Knowledgebase cross-references, then UniProtKB will take the responsibility of supplying the external ID -> UniProtKB mapping to the GO.
4.2 gp2rna file
- The gp2rna format specifications are similar to those of gp2protein files. The differences between the two are described here.
- If the annotation file includes non-coding RNAs (ncRNAs), then the corresponding gp2rna file must include all ncRNA genes currently identified in the genome build, including ncRNAs not annotated to GO.
- Functional ncRNAs must map to NCBI (NR_ or XR_) if available; if unavailable, leave the field blank.
4.3 gp_unlocalized file
- If your database supplies gene identifiers that have been manually curated from the literature, where no sequence or genomic location is known (such genes have been sometimes described as 'unlocalized genes', 'single heritable traits' or 'phenotypic orphans'), then you should additionally supply a complete gp_unlocalized_file.
- This file should contain a list of all the non-genome localized gene identifiers available, including those not annotated to GO.
- The file must meet the gp_unlocalized format specification, which should be similar to the gp2protein file format.
4.4 Exceptions for Macromolecular Complexes
- If the annotation file includes macromolecular complexes as the subject of the annotation, no corresponding entry is required for the gp2protein file. Only gene or gene product mappings should be included.
- Groups must regularly update their gp2protein or gp2rna files (i.e. in response to UniProtKB's feedback on inclusion of obsolete or secondary UniProtKB accessions in a group's gp2protein, or in the case NCBI identifiers are made obsolete). For groups who provide authoritative files for a species, or who are funded by the GO NIH grant, please consult the description of GO annotation activities by central GO Consortium members.