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Removing yaml links to download page / subset #194

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Removing yaml links to download page / subset #194

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30 changes: 15 additions & 15 deletions _docs/download-ontology.md
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Expand Up @@ -47,29 +47,29 @@ GO slims are subsets of terms in the ontology. GO subsets give a broad overview
The GO subsets in this list are maintained as part of the GO flat file. The files available below for download are generated by script from that file.


|**Subset name**|**Maintainer**|**File name**|**OBO format**|**OWL format**|**json format**|**yaml format**|
|**Subset name**|**Maintainer**|**File name**|**OBO format**|**OWL format**|**json format**|
|------------------|-------------|-------------|-------------|------------|-------------|------------|
|**GO slim AGR subset**|Developed by GO Consortium for the [Alliance of Genomes Resources](https://www.alliancegenome.org/){:target="blank"} |goslim_agr |[obo](http://current.geneontology.org/ontology/subsets/goslim_agr.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_agr.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_agr.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_agr.yaml) |
|**Generic GO subset**|GO Consortium |goslim_generic|[obo](http://current.geneontology.org/ontology/subsets/goslim_generic.obo)| [owl](http://current.geneontology.org/ontology/subsets/goslim_generic.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_generic.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_generic.yaml) |
|*__Aspergillus__* **subset**|[_Aspergillus_ Genome Data](http://www.aspgd.org/){:target="blank"} |goslim_aspergillus|[obo](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.yaml) |
|*__Candida albicans__* **subset**|[_Candida_ Genome Database](http://www.candidagenome.org/){:target="blank"} |goslim_candida|[obo](http://current.geneontology.org/ontology/subsets/goslim_candida.obo)|[owl](http://current.geneontology.org/ontology/subsets/goslim_candida.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_candida.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_candida.yaml) |
|**Chembl Drug Target subset**|[ChEMBL](https://www.ebi.ac.uk/chembl/){:target="blank"} |goslim_chembl|[obo](http://current.geneontology.org/ontology/subsets/goslim_chembl.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_chembl.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_chembl.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_chembl.yaml) |
|**Metagenomics subset**|[InterPro](http://www.ebi.ac.uk/interpro/){:target="blank"} group|goslim_metagenomic|[obo](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.obo) | [owl](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.yaml) |
|**Mouse GO slim**|[Mouse Genome Informatics](http://www.informatics.jax.org/){:target="blank"} |goslim_mouse|[obo](http://current.geneontology.org/ontology/subsets/goslim_mouse.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_mouse.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_mouse.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_mouse.yaml) |
|**Plant subset**|[The _Arabidopsis_ Information Resource](https://www.arabidopsis.org/){:target="blank"} |goslim_plant|[obo](http://current.geneontology.org/ontology/subsets/goslim_plant.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_plant.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_plant.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_plant.yaml) |
|**Protein Information Resource subset**|[PIR](https://pir.georgetown.edu/){:target="blank"} |goslim_pir|[obo](http://current.geneontology.org/ontology/subsets/goslim_pir.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_pir.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_pir.json){:target="blank"} | [yaml](http://current.geneontology.org/ontology/subsets/goslim_pir.yaml) |
|*__Schizosaccharomyces pombe__* **subset**|[PomBase](https://www.pombase.org/){:target="blank"} |goslim_pombe|[obo](http://current.geneontology.org/ontology/subsets/goslim_pombe.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_pombe.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_pombe.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_pombe.yaml) |
|**Yeast subset**|[_Saccharomyces_ Genome Database](https://www.yeastgenome.org/){:target="blank"} |goslim_yeast|[obo](http://current.geneontology.org/ontology/subsets/goslim_yeast.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_yeast.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_yeast.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/goslim_yeast.yaml) |
|**GO slim AGR subset**|Developed by GO Consortium for the [Alliance of Genomes Resources](https://www.alliancegenome.org/){:target="blank"} |goslim_agr |[obo](http://current.geneontology.org/ontology/subsets/goslim_agr.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_agr.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_agr.json){:target="blank"} |
|**Generic GO subset**|GO Consortium |goslim_generic|[obo](http://current.geneontology.org/ontology/subsets/goslim_generic.obo)| [owl](http://current.geneontology.org/ontology/subsets/goslim_generic.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_generic.json){:target="blank"} |
|*__Aspergillus__* **subset**|[_Aspergillus_ Genome Data](http://www.aspgd.org/){:target="blank"} |goslim_aspergillus|[obo](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_aspergillus.json){:target="blank"} |
|*__Candida albicans__* **subset**|[_Candida_ Genome Database](http://www.candidagenome.org/){:target="blank"} |goslim_candida|[obo](http://current.geneontology.org/ontology/subsets/goslim_candida.obo)|[owl](http://current.geneontology.org/ontology/subsets/goslim_candida.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_candida.json){:target="blank"} |
|**Chembl Drug Target subset**|[ChEMBL](https://www.ebi.ac.uk/chembl/){:target="blank"} |goslim_chembl|[obo](http://current.geneontology.org/ontology/subsets/goslim_chembl.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_chembl.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_chembl.json){:target="blank"} |
|**Metagenomics subset**|[InterPro](http://www.ebi.ac.uk/interpro/){:target="blank"} group|goslim_metagenomic|[obo](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.obo) | [owl](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_metagenomics.json){:target="blank"} |
|**Mouse GO slim**|[Mouse Genome Informatics](http://www.informatics.jax.org/){:target="blank"} |goslim_mouse|[obo](http://current.geneontology.org/ontology/subsets/goslim_mouse.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_mouse.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_mouse.json){:target="blank"} |
|**Plant subset**|[The _Arabidopsis_ Information Resource](https://www.arabidopsis.org/){:target="blank"} |goslim_plant|[obo](http://current.geneontology.org/ontology/subsets/goslim_plant.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_plant.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_plant.json){:target="blank"} |
|**Protein Information Resource subset**|[PIR](https://pir.georgetown.edu/){:target="blank"} |goslim_pir|[obo](http://current.geneontology.org/ontology/subsets/goslim_pir.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_pir.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_pir.json){:target="blank"} |
|*__Schizosaccharomyces pombe__* **subset**|[PomBase](https://www.pombase.org/){:target="blank"} |goslim_pombe|[obo](http://current.geneontology.org/ontology/subsets/goslim_pombe.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_pombe.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_pombe.json){:target="blank"} |
|**Yeast subset**|[_Saccharomyces_ Genome Database](https://www.yeastgenome.org/){:target="blank"} |goslim_yeast|[obo](http://current.geneontology.org/ontology/subsets/goslim_yeast.obo) |[owl](http://current.geneontology.org/ontology/subsets/goslim_yeast.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/goslim_yeast.json){:target="blank"} |

### Download GO "*__anti-slims__*"

For internal checking purposes, GO maintains two "anti-slims", terms to which annotations should not be made. "Anti-slim" terms should never be used when creating a subset.


|**Subset name**|**Usage** |**File name** |**OBO format** |**OWL format** |**json format** |**yaml format** |
|**Subset name**|**Usage** |**File name** |**OBO format** |**OWL format** |**json format** |
|------------------|----------|----------|----------|----------|----------|----------|
|**Do not annotate**|The set of high level terms that are useful for grouping, but should have no direct annotations| gocheck_do_not_annotate |[obo](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.obo)| [owl](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.yaml)|
|**Do not manually annotate**|The set of high level terms that are useful for grouping, but should have no direct annotations except from automated tools| gocheck_do_not_manually_annotate|[obo](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.obo)|[owl](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.json){:target="blank"} |[yaml](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.yaml)|
|**Do not annotate**|The set of high level terms that are useful for grouping, but should have no direct annotations| gocheck_do_not_annotate |[obo](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.obo)| [owl](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/gocheck_do_not_annotate.json){:target="blank"} |
|**Do not manually annotate**|The set of high level terms that are useful for grouping, but should have no direct annotations except from automated tools| gocheck_do_not_manually_annotate|[obo](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.obo)|[owl](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.owl){:target="blank"} |[json](http://current.geneontology.org/ontology/subsets/gocheck_do_not_manually_annotate.json){:target="blank"} |


## Cross-references of GO to other classification systems
Expand Down