Merge branch 'master' of https://github.com/geneontology/geneontology…

….github.io

_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. 

_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. <br>