diff --git a/_docs/contributing-go.md b/_docs/contributing-go.md index e66a1b83..8cbdfc37 100644 --- a/_docs/contributing-go.md +++ b/_docs/contributing-go.md @@ -10,7 +10,7 @@ While most GO annotations are produced by [members of the GO Consortium](/docs/g Researchers who notice either missing or inaccurate annotations for a gene or a GO term can [send this information to the GO Consortium](http://help.geneontology.org/){:target="blank"}. ### 1. Gather all necessary information -- Paper citation (PMID if available) +- Literature citation (PMID if available) - Description of the issue: the gene product and the term combination that you suggest be reviewed and why you believe this is incorrect - A suggestion for a solution, if possible @@ -19,7 +19,18 @@ Researchers who notice either missing or inaccurate annotations for a gene or a * Alternatively, contact the [GO helpdesk](http://help.geneontology.org/){:target="blank"} with your request. ## Contributing new GO annotations -Research groups who wish to generate GO annotations, for instance new annotations for genes of a species that is not currently annotated in GO, annotating specific genes for a given biological research domain, can contribute these annotations to the GO knowledgebase. +Our recommendation for annotating novel genomes is to [submit transcripts to NCBI](https://www.ncbi.nlm.nih.gov/). These submissions will reach [UniProt](https://www.uniprot.org/){:target="blank"}, where [InterPro2GO](https://www.ebi.ac.uk/GOA/InterPro2GO){:target="blank"} will automatically create high-quality ([IEA](/docs/guide-go-evidence-codes/)) GO annotations. These annotations will be made available in a future GO release. GO does not recommend that groups create their own IEAs with internal tools due to reproducibility and accuracy concerns. + +Research groups who wish to generate manual GO annotations from experimental data- for instance, new annotations for genes of a species that is not currently annotated in GO, or annotating specific genes for a given biological research domain- can contribute these annotations to the GO knowledgebase. **Please contact us early in your project to establish the data exchange process between your group and GO.** GO will make sure you have access to the proper documentation and training materials to ensure your annotations meet the GO guidelines. + +GO annotation files must be in [GAF 2.2](/docs/go-annotation-file-gaf-format-2.2/) and contain: +- UniProt IDs, or IDs that can be mapped to UniProt, for each annotated entity +- precise & informative valid GO terms for each entity, taking in to account taxon constraints and term restrictions +- PMID of the published literature describing the methods and findings +- a precise [evidence code](/docs/guide-go-evidence-codes/) +- other mandatory elements are listed in the [GAF 2.2 documentation](/docs/go-annotation-file-gaf-format-2.2/) + +Other information, such as mapping files, may be required in addition to the GAF. ## Contributing your expertise -The Gene Ontology Consortium welcomes contributions from experts in any area of biology to help us improve the annotations. [Contact us](mailto:help@geneontology.org) to start contributing to the GO annotations. +The Gene Ontology Consortium welcomes contributions from experts in any area of biology to help us improve the annotations. [Contact us](mailto:help@geneontology.org) to start contributing or improving GO annotations. diff --git a/_docs/go-archives.md b/_docs/go-archives.md index 40a0dd8b..9b9cf176 100644 --- a/_docs/go-archives.md +++ b/_docs/go-archives.md @@ -71,7 +71,8 @@ GO currently provides the Gene Ontology in the OBO 1.2 format (as produced by th GO currently provides annotations in GAF 2.2 as well as GPAD/GPI 2.0, and encourages anyone consuming or producing older versions to adopt the newest format. See the [annotation download page](/docs/download-go-annotations/) for more information about current annotation file formats. + [GPAD 1.0, 1.1 & 1.2](/docs/gene-product-association-data-gpad-format-1.1/): pending deprecation as of 2024. -+ [GPI 1.1 & 1.2](/docs/gene-product-information-gpi-format/): pending deprecation as of 2024. ++ [GPI 1.1 & 1.2](/docs/gene-product-information-gpi-format/): pending deprecation as of 2024. ++ GO-CAMs were briefly available as SIF (Simple Interaction Format) files and support for these ended in 2024. + [GAF 2.0](/docs/go-annotation-file-gaf-format-2.0/): deprecated in March 2021. + GAF 1.0: deprecated in June 2010.