From a429a7bdd72c99f0ebf77756f418e11206150557 Mon Sep 17 00:00:00 2001 From: suzialeksander Date: Tue, 13 Dec 2022 15:41:19 -0700 Subject: [PATCH 1/3] Update contributing-go.md @pgaudet and/or @vanaukenk- I've added a few notes for new contributing groups in the "Contributing new GO annotations" section. Can you check to make sure it's correct but not over/under promising. Ideally there will be another doc (in progress) that will have more detailed instructions once they've contacted us, plus the MOU. This is just to let groups like the beetle group have an idea before they start/contact us. --- _docs/contributing-go.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/_docs/contributing-go.md b/_docs/contributing-go.md index e66a1b83..146fdab4 100644 --- a/_docs/contributing-go.md +++ b/_docs/contributing-go.md @@ -19,7 +19,14 @@ 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 ([IEA](/docs/guide-go-evidence-codes/)) GO annotations. These annotations will be made available in a future GO release. GO does not recommend groups create their own IEAs with internal tools due to reproducibility and accuracy concerns. Please contact us if you have questions. + +Research groups who wish to generate manual GO annotations- 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. At a minimum, we will need a [GAF 2.2](/docs/go-annotation-file-gaf-format-2.2/) that contains: +- UniProt IDs, or IDs that can be mapped to UniProt, for each annotated entity +- precise & informative GO terms for each entity, taking in to account taxon constraints and term restrictions +- PMID of the published literature describing the methods and findings + +Contributing groups will also be responsible for maintaining their set of annotations long-term unless we can incorporate them into another group (e.g. GOA). Please contact us early in your project to ensure we can accept your annotations and that you can commit to attending training and other required calls . ## 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. From ac21e06da9034c5a8c8076d8fa6cfda69e0be3fa Mon Sep 17 00:00:00 2001 From: suzialeksander Date: Mon, 22 Jul 2024 21:08:06 -0600 Subject: [PATCH 2/3] Update contributing-go.md --- _docs/contributing-go.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/_docs/contributing-go.md b/_docs/contributing-go.md index 146fdab4..7e01e012 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 @@ -19,14 +19,14 @@ 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 -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 ([IEA](/docs/guide-go-evidence-codes/)) GO annotations. These annotations will be made available in a future GO release. GO does not recommend groups create their own IEAs with internal tools due to reproducibility and accuracy concerns. Please contact us if you have questions. +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 groups create their own IEAs with internal tools due to reproducibility and accuracy concerns. Please contact us if you have questions. -Research groups who wish to generate manual GO annotations- 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. At a minimum, we will need a [GAF 2.2](/docs/go-annotation-file-gaf-format-2.2/) that contains: +Research groups who wish to generate manual GO annotations- 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. At a minimum, we will need a [GAF 2.2](/docs/go-annotation-file-gaf-format-2.2/) that contains: - UniProt IDs, or IDs that can be mapped to UniProt, for each annotated entity -- precise & informative GO terms for each entity, taking in to account taxon constraints and term restrictions +- 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 -Contributing groups will also be responsible for maintaining their set of annotations long-term unless we can incorporate them into another group (e.g. GOA). Please contact us early in your project to ensure we can accept your annotations and that you can commit to attending training and other required calls . +Contributing groups will also be responsible for maintaining their set of annotations long-term unless we can incorporate them into another group (e.g. GOA). Please contact us early in your project to ensure we can accept your annotations and that you can commit to attending training and other required calls. ## 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. From 9f60c1a681562d7f7c8a243225a0e984e246fe76 Mon Sep 17 00:00:00 2001 From: suzialeksander Date: Wed, 24 Jul 2024 15:39:57 -0600 Subject: [PATCH 3/3] Update contributing-go.md --- _docs/contributing-go.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/_docs/contributing-go.md b/_docs/contributing-go.md index 7e01e012..8cbdfc37 100644 --- a/_docs/contributing-go.md +++ b/_docs/contributing-go.md @@ -19,14 +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 -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 groups create their own IEAs with internal tools due to reproducibility and accuracy concerns. Please contact us if you have questions. +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- 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. At a minimum, we will need a [GAF 2.2](/docs/go-annotation-file-gaf-format-2.2/) that contains: +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/) -Contributing groups will also be responsible for maintaining their set of annotations long-term unless we can incorporate them into another group (e.g. GOA). Please contact us early in your project to ensure we can accept your annotations and that you can commit to attending training and other required calls. +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.