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| = Group Leader = | | = Group Leader = |
| David Hill (MGI); GitHub: @ukemi
| | Pascale Gaudet (GO Central); GitHub: @pgaudet |
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| | == Ontology editors== |
| | Pascale Gaudet, Raymond Lee, Val Wood |
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| | ==Software support== |
| | Jim Balhoff |
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| | == Other group members== |
| | Tanya Berardini, Peter D'Eustachio, Steven Marygold, Li Ni, Kimberly VanAuken |
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| | ==PIs== |
| | Chris Mungall, Paul Thomas |
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| =Communication= | | =Communication= |
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| === When === | | === When === |
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| * Calls are held weekly on Mondays, 12:00PM-1:00PM EST | | * Calls are held weekly on Mondays, 12:00PM-1:00PM EST |
| * Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it. | | * Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it. |
| * Reminder emails are sent out to the go-ontology mailing list (see [[Internal_email_lists]] to register). | | * Reminder emails are sent out to the go-ontology mailing list (see [[Internal_email_lists]] to register). |
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| === Agenda and Minutes === | | === Agenda and Minutes === |
| * [[Ontology editors' conference call minutes 2019|2019]] | | * [[Ontology editors' conference call minutes 2024|2024]] |
| * Past Annotation Call Minutes: [[Ontology Development reports 2005-2010|2005-2010]] | [[Ontology editor's conference call minutes 2011|2011]] | [[Ontology editor's conference call minutes 2012|2012]] | [[Ontology editor's conference call minutes 2013|2013]] | [[Ontology editor's conference call minutes 2014|2014]] | [[Ontology editor's conference call minutes 2015|2015]] | [[Ontology editor's conference call minutes 2016|2016]] | [[Ontology editor's conference call minutes 2017|2017]] | [[Ontology editor's conference call minutes 2018|2018]] | | | * Past Ontology Editors' Calls: [[Ontology Development reports 2005-2010|2005-2010]] | [[Ontology editor's conference call minutes 2011|2011]] | [[Ontology editor's conference call minutes 2012|2012]] | [[Ontology editor's conference call minutes 2013|2013]] | [[Ontology editor's conference call minutes 2014|2014]] | [[Ontology editor's conference call minutes 2015|2015]] | [[Ontology editor's conference call minutes 2016|2016]] | [[Ontology editor's conference call minutes 2017|2017]] | [[Ontology editor's conference call minutes 2018|2018]] | [[Ontology editors' conference call minutes 2019|2019]] | [[Ontology editors' conference call minutes 2020|2020]] | [[Ontology editors' conference call minutes 2021|2021]] | [[Ontology editors' conference call minutes 2022|2022]] | [[Ontology editors' conference call minutes 2023|2023]] |
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| = Documentation=
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| ==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]==
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| ==[[Installing and Using git]]==
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| ==[[Ontology Editors Daily Workflow]]==
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| ==Editing the Ontology==
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| {| class="wikitable"
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| !colspan="2" | [[General Gene Ontology Principles]]
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| !colspan="2" | New terms
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| |rowspan="7"|[[Principles for creating a GO term]] (being reviewed)
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| |[[Guidelines for creating a GO term]]
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| |[[Guidelines for creating relationships between terms]] (being reviewed)
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| |-
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| |[[Guidelines for creating disjoint terms]] (to be written)
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| |[[Guidelines for creating a Regulation Term]]
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| |[[Guidelines for GO textual definitions]] (being reviewed)
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| |[[Guidelines for equivalence axioms]] (being reviewed) --- Also [[Logical_Definitions]] (being reviewed)
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| |-
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| |[[Guidelines for new Molecular Functions]] (new)
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| |- | |
| |[[Guidelines for new Biological Processes]] (new)
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| |-
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| |[[Guidelines for new Cellular Components]] (new) | |
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| !colspan="2" |Modifying existing terms
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| |rowspan="4"|[[Principles for Modifying an Existing Ontology Term]] (to be reviewed)
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| |[[Deleting Asserted Subclasses]]
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| |[[Adding Term Comments]]
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| |[[Adding a Term to a GO Subset (Slim)]]
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| |-
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| |[[Adding Taxon Restrictions]]
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| !colspan="2" |Term obsoletion
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| |rowspan="2" |[[Principles for term obsoletion]]
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| |[[Obsoleting an Existing Ontology Term]] | |
| |- | |
| |[[Restoring an Obsolete Ontology Term]]
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| !colspan="2" |Term merges
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| |[[Principles for merging terms]] (being reviewed) | |
| |[[Merging Ontology Terms]]
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| !colspan="2" |Subsets
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| |Subset documentation (to add)
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| |[[Adding and Removing GO Subsets (Slims)]] | |
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| !colspan="2" |Import Files
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| | Principles for [[GO import files]]
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| |[[Adding Terms and Regenerating the Import Files]]
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| |}
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| ==[[Relations]] General Relations Documentation Draft To be reviewed==
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| ==Website - to be moved to the wiki?==
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| * [http://www.geneontology.org/page/biological-process-ontology-guidelines Biological-process-ontology-guidelines]
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| =[[Identifiers]] To be reviewed=
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| =[[Content Meeting Documentation|Guidance for organizing content meetings]]=
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| (old doc, but basic principles still apply)
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| | ===GO ontology in GitHub=== |
| | * The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track ontology issues. |
| | * The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-ontology here]. |
| | * Contact information for each group that contributes to the consortium is available [https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv here] |
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| =Content Development = | | ===GO ontology on slack=== |
| ==Ongoing Projects== | | *The GO consortium uses [https://geneontologyworkspace.slack.com/home GO Slack] as an informal chat service: [https://app.slack.com/client/T01NYRYPN6T/C01PAGWQM7X go-ontology slack channel]. |
| *[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T)
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| *[[Cell Cycle]] (Val, Pombe experts, GOEds)
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| *[[Enzymes and EC mappings]]
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| *[[Non-symbiotic multi-organism processes]] (Jane, David OS)
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| * Signaling: [[2017 Cambridge GOC Signalling Workshop]]
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| * [[Protein_Complexes:_who,_what,_where]]
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| ===Low priority===
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| *[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
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| *[[microbial ontology development and annotation]]
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| ===Completed projects=== | |
| *[[Adding missing CHEBI xps]]
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| *[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
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| *Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
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| *[http://wiki.geneontology.org/index.php/Extensions/x-metazoan-anatomy Uberon alignment] (DavidH)
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| *[[:Category:Content MENGO|MENGO collaboration]] (Jane)
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| *[[:Category:Content PAMGO|PAMGO collaboration]] (Jane)
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| *[[:Category:Content PAMGO|PAMGO collaboration]], phase 1
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| *[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)
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| *[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
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| *Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts) - [https://www.ncbi.nlm.nih.gov/pubmed/29455577 Denny et al 2018]
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| *[[ASCB 2009]]
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| *[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points
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| *[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
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| *[[Cardiovascular physiology/development]] - implemented Oct 2007
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| *[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others) - started summer 2008
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| *[[Central Nervous System Development]]
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| *[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)
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| *Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts) [https://www.ncbi.nlm.nih.gov/pubmed/29177046 Roncaglia et al 2017] | |
| *[[Collaboration with MIT GO-Engineering]] - Manuscript written
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| *[[Electron transport]]
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| *Extracellular RNA-containing vesicles (Paola, Aleks and community experts) [https://www.ncbi.nlm.nih.gov/pubmed/27076901 Cheung et al 2016]
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| *[[FP-regulates| regulates links between function and process]] (David, Tanya)
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| *Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
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| *[[Function-Process Links]]
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| *[[Heart_Development_workshop|Heart Development]] (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
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| *[[Lung_Development]] (David, Jen, community experts)
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| *[[Immunology Revisions]]
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| *[[Isa-complete_BP|is_a complete biological process]]
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| *[[Kidney Development]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
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| *[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
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| *[[Morphogenesis]] (David, Tanya)
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| *[[Muscle Biology]] - Started Feb. 2007; meeting July 2007; Done Oct 2007
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| *[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)
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| *[[Plant_term]] - March 28, 2007
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| *[[plasma lipoprotein particle ontology]] - done Sept. 2010
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| *[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008
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| *[[Regulation Main Page]] live March 2008
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| *[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya)
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| *[[RNA processing]]
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| *[[SDB 2009]]
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| *[[Sensu Main Page|Sensu revamp]]
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| *[[Signaling |Signaling overhaul]] (Becky, signaling WG)
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| *[https://github.com/geneontology/synapse Synapse project] (Synapse experts, DavidOS, Becky Foulger) - completed 2018
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| *[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
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| *[[Transporters]] (Jen and community experts) - Started Feb. 2007
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| *[[Utilization]] - done March 2010
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| *[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
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| *Generic [[GO slim overhaul]] (Jane & Val)
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| *Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')
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| *regulates links- Dec 2008 (David, Tanya)
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| *Correct disjointness violations
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| *Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list] (Jane).
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| ===Proposed content work===
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| A list of topics that we propose to address, but for which a timeline has not been set
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| *Peripheral nervous system development
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| *Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
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| *Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)
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| * [[Recombination and DNA repair]]
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| * [[RNA processes]]
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| * [[Bile formation and secretion processes]]
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| * [[protein and peptidyl amino acid modification / protein processing]]
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| * [[Response to drug]]
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| * [[Polyketide synthases]]
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| * [[cell growth/proliferation/division]]
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| * [[oxidoreductases]]
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| =Quality Control=
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| ==SPARQL checks on the ontology==
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| [https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries SPARQL checks on the ontology]
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| ==Ontology release pipeline== | | ==Ontology release pipeline== |
| * [[Release Pipeline]] | | * [[Release Pipeline]] |
| * [http://current.geneontology.org/reports/gorule-report.html GO Rules rrrors reports]
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| '''TO BE REPLACED'''
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| *Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
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| [[Category:Ontology]][[Category:GO Editors]] | | [[Category:Ontology]][[Category:GO Editors]] |