Core Consortium annotation activities - 2012

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Activities to which contributing GO annotation groups must minimally agree

  • All GO annotation efforts who would like to supply their annotations to the Consortium must supply an appropriately formatted annotation file that conforms to the Consortium's syntaxtic and semantic requirements. The primary GO annotation format is GAF:2.0.
    • If you are a new annotation group, please see the guidance provided here.
  • All annotations must be describe the activities or locations UniProtKB identifiers located in the UniProt Reference Proteome Files, unless the group agrees to provide a complete gp2protein mapping file, or gp2rna and unlocalised_gp files, where additionally required (see below).
  • While the current primary annotation file format applies GO evidence codes to describe the category of support available in the cited reference, groups must support the Consortium's intent to transition to using Evidence Ontology identifiers in future annotation formats.
  • Curational groups do not need to commit to supplying regular updates to their annotations. In the case of non-recurring submissions or those from annotation groups which are now inactive annotation providers, responsibility for corrections and updates will revert to the GOC, please see the guidance provided here, for further details.

Complete identifier mapping files

Why do we need mapping files?

  • For downloading sequences from UniProt/NCBI. These sequences are used for AmiGO BLAST and for phylogenetic inferencing (PAINT)
  • To search for GO annotations in AmiGO using other DB cross reference IDs (UniProt or NCBI)
  • The ID mapping will help with book keeping and tracking IDs and annotations, removing duplicates etc


Complete gp2protein file

The file must meet the gp2protein format specification

The gp2protein-mapping file must contain the full list of all protein-encoding genes in the respective organism (or community), including those proteins not annotated to GO.

The first column contains all gene or gene product identifiers (these are typically MOD-specific identifiers) and the second column contains mappings to canonical identifiers. rotein coding genes must map to UniProtKB identifiers (Swiss-Prot in preference, if not then TrEMBL). If identifiers are truly unavailable in UniProtKB then NCBI identifiers (NP_ and XP_) are permissible.

If an annotation group is fully satisfied with the identifier mapping from an external identifier type to UniProtKB accessions, as supplied by the UniProt Knowledgebase cross-references, then UniProtKB is willing to take on the responsibility of supplying the external id -> UniProtKB mapping to the GO Consortium.

Complete gp2rna file

If your annotation file includes ncRNAs, then the gp2protein files must include all ncRNA-encoding genes currently identified in the genome build including those ncRNAs not annotated to GO.

Functional ncRNA must map to NCBI (NR_ or XR_) if available, blank if unavailable).

gp2rna format

Complete gp_unlocalized file

If your database supplies gene identifiers that have been manually curated from the literature, but where no sequence or genomic location is known (such genes have been variously described as 'unlocalised 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.

gp_unlocalised file format

Macromolecular complexes

If the annotation file includes macromolecular complexes as the subject of the annotation then no corresponding entry is required for the gp2protein file – only gene or gene product mappings should be included.

Updates of identifier mapping files.

Groups must regularly update their gp2protein or gp2rna file (e.g. in response to UniProt-GOA feedback on inclusion of obsolete/secondary UniProtKB accessions in a group’s gp2protein, or obsoletion of NCBI identifiers).

For groups who provide authoritative files for a species, or who are funded by the GO NIH grant, please see the following description of GO annotation activities by central GO Consortium members