id: http://purl.obolibrary.org/obo/go/subsets/go_subsets_metadata
description: Subsets
subsets:
  - id: goantislim_grouping
    title: GO antislim
    role: ExclusionList
    short_label: goantislim
    status: obsolete
    description: Grouping classes that can be excluded in enrichment analyses etc.
    archived_url: http://release.geneontology.org/2018-08-09/ontology/subsets/goantislim_grouping.obo
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
  - id: gocheck_do_not_annotate
    title: GO antislim
    role: ExclusionList
    short_label: Do not annotate
    status: active
    description: "Terms that are too high level to be informative for annotation."
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: gocheck_do_not_manually_annotate
    title: Terms not allowed for manual annotation
    short_label: Do not manually annotate
    status: obsolete
    replaced_by:
      - gocheck_do_not_annotate
    description: "Terms that are too high level to be informative for manual annotation; merged with gocheck_do_not_annotate."
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
  - id: gocheck_obsoletion_candidate
    title: Obsoletion candidate subset
    short_label: Obsoletion candidate subset
    role: ExclusionList
    status: active
    description: "Terms that are scheduled for obsoletion."
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: goslim_agr
    title: AGR slim
    role: Ribbon
    short_label: Animals and fungi (Opisthokonta)
    status: active
    description: "Subset for Alliance of Genome Resources (AGR). The purpose of this subsets is mainly to drive the 'ribbon' display."
    taxa:
      - id: NCBITaxon:33154
        label: Opisthokonta
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: Mary.Dolan@jax.org
        label: Mary Dolan
        orcid: orcid:0000-0001-7732-3295
  - id: goslim_aspergillus
    title: Aspergillus slim
    short_label: Aspergillus
    role: Binning
    status: obsolete
    description: "Aspergillus GO slim."
    taxa:
      - id: NCBITaxon:5052
        label: Aspergillus
    contact:
      email: candida-curator@lists.stanford.edu
      label: CDG helpdesk
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: jodils@stanford.edu
        label: Jodi Lew-Smith
        orcid: orcid:0000-0003-0784-046X
        github: jlewsmith
  - id: goslim_candida
    title: Candida slim
    short_label: Candida
    role: Binning
    status: active
    description: "Candida GO slim."
    taxa:
      - id: NCBITaxon:1535326
        label: Candida
    contact:
      email: candida-curator@lists.stanford.edu
      label: CGD helpdesk
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: jodils@stanford.edu
        label: Jodi Lew-Smith
        orcid: orcid:0000-0003-0784-046X
        github: jlewsmith
  - id: goslim_chembl
    title: ChEMBL slim
    short_label: ChEMBL
    role: Binning
    status: active
    description: "Subset for ChEMBL."  ## TODO: add more details
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    contact:
      email: bzdrazil@ebi.ac.uk
      label: Barbara Zdrazil
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: bzdrazil@ebi.ac.uk
        label: Barbara Zdrazil
        orcid: orcid:0000-0001-9395-1515
        github: BZdrazil
  - id: goslim_drosophila
    title: Drosophila subset
    short_label: Insects
    role: Binning
    status: active
    description: "GO subset for insects. This subset can be used for binning purposes, most annotations should map to a term in the subset."
    taxa:
      - id: NCBITaxon:50557
        label: Insecta
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
        - email: gocur@morgan.harvard.edu
          label: GO FlyBase curators
          orcid: orcid:0000-0003-3212-6364
          github: hattrill
  - id: goslim_euk_cellular_processes_ribbon
    title: GO ribbon for eukaroytic cellular processes
    short_label: Eukaroytic cellular processes
    role: Ribbon
    status: active
    description: "GO ribbon subset that mainly serves to drive the UniProt 'ribbon' display for cellular processes in eukaryotes."
    taxa:
      - id: NCBITaxon:2759
        label: Eukaryota
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: goslim_flyBase_ribbon
    title: FlyBase Ribbon slim
    short_label: Insects
    role: Ribbon
    status: active
    description: "Insect GO ribbon subset produced by FlyBase. The purpose of this subset is mainly to drive the Flybase and the UniProt 'ribbon' display."
    taxa:
      - id: NCBITaxon:50557
        label: Insecta
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: gocur@morgan.harvard.edu
        label: GO FlyBase curators
        orcid: orcid:0000-0003-3212-6364
        github: hattrill
  - id: goslim_generic
    title: Generic GO subset
    role: Binning
    short_label: All organisms
    status: active
    description: Generic GO subset. Applies to all species. This slim can be used for binning purposes, most annotations should map to a term in the slim.
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: goslim_goa
    title: GOA slim
    status: obsolete
    description: "The GOA slim had not been maintained since 2002, and had no terms in the 2018 version of the ontology. This subset was removed from the ontology."
    archived_url: "http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/GO_slims/archived_GO_slims/goslim_goa.2002?rev=1.4;content-type=text%2Fplain."
  - id: goslim_metagenomics
    title: Metagenomics slim
    short_label: Metagenomics
    status: active
    description: A slim for high-level visualisation of the functional profile of metagenomic samples
    see_also:
      - https://www.ebi.ac.uk/about/news/updates-from-data-resources/metagenomics-go-slim-2016/
      - PMID:29069476
    taxa:
     - id: NCBITaxon:408169
       label: metagenomes
    contact: 
      email: metagenomics-help@ebi.ac.uk
      label: MGnify helpdesk
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: 
        label: Alex Mitchell
        orcid:  https://orcid.org/0000-0001-8655-7966
        github: almitchell
  - id: goslim_mouse
    title: Mouse GO slim
    short_label: Mouse
    role: Binning
    status: active
    description: "Mouse GO subset."
    taxa:
      - id: NCBITaxon:10090
        label: Mus musculus
    contact:
      email: mgi-help@jax.org
      label: MGI helpdesk
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: Mary.Dolan@jax.org
        label: Mary Dolan
        orcid: orcid:0000-0001-7732-3295
        github: mdolanme
  - id: goslim_pir
    title: PIR slim
    short_label: PIR
    role: Binning
    status: active
    description: "PIR (Protein Information Resource) slim"  ## TODO: better describe this
    taxa:
      - id: NCBITaxon:1
        label: all organisms
    contact:
      email: dan5@georgetown.edu
      label: Darren Natale
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: dan5@georgetown.edu
        label: Darren Natale
        orcid: orcid:0000-0001-5809-9523
        github: nataled
  - id: goslim_plant_ribbon
    title: Plant Ribbon subset
    short_label: Plants
    role: Ribbon
    status: active
    description: "GO ribbon subset that mainly serves to drive the UniProt 'ribbon' display for plant and algae species."
    taxa:
      - id: NCBITaxon:33090
        label: Viridiplantae
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: goslim_plant
    title: Plant slim
    short_label: Plants
    role: Binning
    status: active
    description: "Plant GO subset."
    taxa:
      - id: NCBITaxon:33090
        label: Viridiplantae
    contact:
      email: curator@arabidopsis.org
      label: TAIR helpdesk
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: tberardi@arabidopsis.org
        label: Tanya Berardini
        orcid: orcid:0000-0002-3837-8864
        github: tberardini
  - id: goslim_pombe
    title: Schizosaccharomyces pombe slim
    short_label: Schizosaccharomyces pombe
    role: Binning
    status: active
    description: "Schizosaccharomyces pombe GO subset."
    taxa:
      - id: NCBITaxon:4896
        label: Schizosaccharomyces pombe
    contact:
      email: vw253@cam.ac.uk
      label: Valerie Wood
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: vw253@cam.ac.uk
        label: Valerie Wood
        orcid: orcid:0000-0001-6330-7526
        github: ValWood
  - id: goslim_prokaroyte_ribbon
    title: Prokaryote Ribbon slim
    short_label: Bacteria and Archaea (Prokaryotes)
    role: Ribbon
    status: active
    description: "Prokaryote GO ribbon subset that mainly serves to drive the UniProt 'ribbon' display for prokaryote organisms."
    taxa:
      - id: NCBITaxon:2
        label: Bacteria
      - id: NCBITaxon:2157
        label: Archaea
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: goslim_synapse
    title: synapse GO slim
    short_label: SynGO
    role: Binning
    status: active
    description: "Synapse GO slim provided by SynGO. This is the subset of GO terms available for annotation in the SynGO tool."
    taxa:
      - id: NCBITaxon:9606
        label: Homo sapiens
      - id: NCBITaxon:10090
        label: Mus musculus
      - id: NCBITaxon:10116
        label: Rattus norvegicus
      - id: NCBITaxon:7227
        label: Drosophila melanogaster
      - id: NCBITaxon:6239
        label: Caenorhabditis elegans
      - id: NCBITaxon:7955
        label: Danio rerio
    contact:
      email: pim.van.nierop@gmail.com
      label: Pim van Nierop
    tracker: https://github.com/geneontology/go-ontology
    contributors:
      - email: pim.van.nierop@gmail.com
        label: Pim van Nierop
        orcid: orcid:0000-0003-0593-3443
        github: Pimmelorus
      - email: frank.koopmans@vu.nl
        label: Frank Koopmans
        orcid: orcid:0000-0002-4973-5732
        github: ftwkoopmans
  - id: goslim_virus
    title: Virus slim
    short_label: Viruses
    status: active
    description: Virus-relevant terms
    role: Binning, Ribbon
    taxa:
      - id: NCBITaxon:10239
        label: Viruses
    tracker: https://github.com/geneontology/go-ontology/issues
    contact:
      - email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: go-ontology@lists.stanford.edu
        label: GO Ontology Curators
  - id: goslim_yeast
    title: Yeast slim
    short_label: Yeast
    status: active
    role: Binning
    description: "Saccharomyces cerevisiae GO slim"
    taxa:
      - id: NCBITaxon:559292
        label: Saccharomyces cerevisiae
    contact:
      email: sgd-helpdesk@lists.stanford.edu
      label: SGD helpdesk
    tracker: https://github.com/geneontology/go-ontology/issues
    contributors:
      - email: stacia@stanford.edu
        label: Stacia Engel
        orcid: orcid:0000-0001-5472-917X
        github: srengel
      - email: suzia@stanford.edu
        label: Suzi Aleksander
        orcid: orcid:0000-0001-6787-2901
        github: suzialeksander
  - id: obsolete_gosubset_prok
    title: Prokaryote subset
    status: obsolete
    description: "GO terms relevant for prokaryotes. Replaced by taxon constraints. To obtain a GO file relevant for prokaryotes, one should should exclude any term (and children) with the relationships 'never in bacteria' or 'only in eukaryotes' (and subclasses of eukaryotes). The latest version of the gosubset_prok .obo file can be found at http://purl.obolibrary.org/obo/go/releases/2018-06-01/subsets/gosubset_prok.obo"
    taxa:
      - id: NCBITaxon:2
        label: Bacteria
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
  - id: mf_needs_review
    title: MF terms to be reviewed
    status: obsolete
    description: "MF terms to be reviewed. Terms reviewed in 2018."
    archived_url: http://release.geneontology.org/2018-07-02/ontology/subsets/mf_needs_review.obo
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
    see_also:
      - https://github.com/geneontology/go-ontology/issues/16166
  - id: termgenie_unvetted
    title: Term Genie terms to be reviewed
    status: obsolete
    description: "Term Genie terms to be reviewed."
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
  - id: obsolete_virus_checked
    title: Virus checked
    status: obsolete
    description: "Terms approved by the Virus working group (2010)."
    archived_url: http://release.geneontology.org/2018-08-09/ontology/subsets/virus_checked.obo
    taxa:
      - id: NCBITaxon:10239
        label: Viruses
    contact:
      email: go-ontology@lists.stanford.edu
      label: GO Ontology Curators
    tracker: https://github.com/geneontology/go-ontology/issues
