Ontology Development: Difference between revisions
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= Group Leader = | = Group Leader = | ||
David Hill (MGI) | David Hill (MGI); GitHub: @ukemi | ||
=Communication= | =Communication= | ||
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= Documentation= | = Documentation= | ||
==[[ | ==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]== | ||
==[[Installing and Using git]]== | ==[[Installing and Using git]]== | ||
==[[Ontology Editors Daily Workflow]]== | ==[[Ontology Editors Daily Workflow]]== | ||
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!colspan="2" | New terms | !colspan="2" | New terms | ||
|- | |- | ||
|rowspan=" | |rowspan="9"|[[Principles for creating a GO term]] (being reviewed) | ||
|[[Guidelines for creating a GO term]] | |[[Guidelines for creating a GO term]] | ||
|- | |- | ||
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|[[Guidelines for GO textual definitions]] (being reviewed) | |[[Guidelines for GO textual definitions]] (being reviewed) | ||
|- | |- | ||
|[[Guidelines for equivalence axioms]] (being reviewed) | |[[Guidelines for equivalence axioms]] (being reviewed) --- Also [[Logical_Definitions]] (being reviewed) | ||
|- | |- | ||
|[[Guidelines for new Molecular Functions]] (new) | |[[Guidelines for new Molecular Functions]] (new) | ||
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==[[Relations]] General Relations Documentation Draft To be reviewed== | ==[[Relations]] General Relations Documentation Draft To be reviewed== | ||
==Website - to be moved to the wiki?== | ==Website - to be moved to the wiki?== | ||
* | * [http://www.geneontology.org/page/biological-process-ontology-guidelines Biological-process-ontology-guidelines] | ||
=[[Identifiers]] To be reviewed= | =[[Identifiers]] To be reviewed= | ||
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=Content Development = | =Content Development = | ||
==Projects | ==Ongoing Projects== | ||
*[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T) | *[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T) | ||
*[[Cell Cycle]] (Val, Pombe experts, GOEds) | *[[Cell Cycle]] (Val, Pombe experts, GOEds) | ||
*[[Enzymes and EC mappings]] | *[[Enzymes and EC mappings]] | ||
*[[Non-symbiotic multi-organism processes]] (Jane, David OS) | *[[Non-symbiotic multi-organism processes]] (Jane, David OS) | ||
* Signaling: [[2017 Cambridge GOC Signalling Workshop]] | |||
* [[Protein_Complexes:_who,_what,_where]] | |||
===Low priority=== | ===Low priority=== | ||
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*[[microbial ontology development and annotation]] | *[[microbial ontology development and annotation]] | ||
=== | ===Completed projects=== | ||
*[[ | *[[Adding missing CHEBI xps]] | ||
*[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS) | |||
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]] | *Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]] | ||
**[[ | *[http://wiki.geneontology.org/index.php/Extensions/x-metazoan-anatomy Uberon alignment] (DavidH) | ||
**[[ | *[[:Category:Content MENGO|MENGO collaboration]] (Jane) | ||
*[[:Category:Content PAMGO|PAMGO collaboration]] (Jane) | |||
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 1 | |||
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007) | |||
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013 | |||
*Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts) - [https://www.ncbi.nlm.nih.gov/pubmed/29455577 Denny et al 2018] | |||
*[[ASCB 2009]] | |||
*[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points | |||
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan) | |||
*[[Cardiovascular physiology/development]] - implemented Oct 2007 | |||
*[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others) - started summer 2008 | |||
*[[Central Nervous System Development]] | |||
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009) | |||
*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 | |||
*[[Electron transport]] | |||
*Extracellular RNA-containing vesicles (Paola, Aleks and community experts) [https://www.ncbi.nlm.nih.gov/pubmed/27076901 Cheung et al 2016] | |||
*[[FP-regulates| regulates links between function and process]] (David, Tanya) | |||
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820]) | |||
*[[Function-Process Links]] | |||
*[[Heart_Development_workshop|Heart Development]] (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky) | |||
*[[Lung_Development]] (David, Jen, community experts) | |||
*[[Immunology Revisions]] | |||
*[[Isa-complete_BP|is_a complete biological process]] | |||
*[[Kidney Development]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group) | |||
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group) | |||
*[[Morphogenesis]] (David, Tanya) | |||
*[[Muscle Biology]] - Started Feb. 2007; meeting July 2007; Done Oct 2007 | |||
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS) | |||
*[[Plant_term]] - March 28, 2007 | |||
*[[plasma lipoprotein particle ontology]] - done Sept. 2010 | |||
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008 | |||
*[[Regulation Main Page]] live March 2008 | |||
*[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya) | |||
*[[RNA processing]] | |||
*[[SDB 2009]] | |||
*[[Sensu Main Page|Sensu revamp]] | |||
*[[Signaling |Signaling overhaul]] (Becky, signaling WG) | *[[Signaling |Signaling overhaul]] (Becky, signaling WG) | ||
*[https://github.com/geneontology/synapse Synapse project] (Synapse experts, DavidOS, Becky Foulger) - completed 2018 | |||
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012 | |||
*[[Transporters]] (Jen and community experts) - Started Feb. 2007 | |||
*[[Utilization]] - done March 2010 | |||
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others) | *[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others) | ||
*[[ | *Generic [[GO slim overhaul]] (Jane & Val) | ||
* | *Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex') | ||
* | *regulates links- Dec 2008 (David, Tanya) | ||
*Correct disjointness violations | |||
* | |||
*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). | *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). | ||
===Proposed content work=== | ===Proposed content work=== | ||
A list of topics that we propose to address, but for which a timeline has not been set | A list of topics that we propose to address, but for which a timeline has not been set | ||
* [[protein and peptidyl amino acid modification / protein processing]] | * [[protein and peptidyl amino acid modification / protein processing]] | ||
* [[Response to drug]] | * [[Response to drug]] | ||
* [[Polyketide synthases]] | * [[Polyketide synthases]] | ||
=Quality Control= | =Quality Control= | ||
==SPARQL checks on the ontology== | ==SPARQL checks on the ontology== | ||
[https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries SPARQL checks on the ontology] | |||
==Ontology release pipeline== | ==Ontology release pipeline== | ||
* [[Release Pipeline]] | |||
* [http://current.geneontology.org/reports/gorule-report.html GO Rules rrrors reports] | |||
'''TO BE REPLACED''' | '''TO BE REPLACED''' | ||
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya) | *Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya) | ||
[[Category:Ontology]][[Category:GO Editors]] | [[Category:Ontology]][[Category:GO Editors]] |
Revision as of 06:11, 23 July 2019
Group's focus
This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology. With the help of the software team the group create rules to ensure the ontology's integrity.
Group Leader
David Hill (MGI); GitHub: @ukemi
Communication
Editor's Conference calls
When
- 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.
- Reminder emails are sent out to the go-ontology mailing list (see Internal_email_lists to register).
Agenda and Minutes
- 2019
- Past Annotation Call Minutes: 2005-2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 |
Documentation
Protégé 5.5 setup
Installing and Using git
Ontology Editors Daily Workflow
Editing the Ontology
Relations General Relations Documentation Draft To be reviewed
Website - to be moved to the wiki?
Identifiers To be reviewed
Guidance for organizing content meetings
(old doc, but basic principles still apply)
Content Development
Ongoing Projects
- Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
- Cell Cycle (Val, Pombe experts, GOEds)
- Enzymes and EC mappings
- Non-symbiotic multi-organism processes (Jane, David OS)
- Signaling: 2017 Cambridge GOC Signalling Workshop
- Protein_Complexes:_who,_what,_where
Low priority
- Neuro Behaviour Ontology (NBO)-GO alignment (Jane, George Gkoutos, Chris, DavidOS)
- microbial ontology development and annotation
Completed projects
- Adding missing CHEBI xps
- Cell cross-products, Cell-type specific GO terms (Jane, Paola, Alex, Chris, DavidOS)
- Addition of cross-products - see Category:Cross_Products and Cross_Product_Guide
- Uberon alignment (DavidH)
- MENGO collaboration (Jane)
- PAMGO collaboration (Jane)
- PAMGO collaboration, phase 1
- PAMGO collaboration, phase 2 (as of Jan. 2007)
- Apoptosis (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
- Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts) - Denny et al 2018
- ASCB 2009
- Binding discussion - mainly annotation issues, but with some ontology content points
- Cardiac conduction (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
- Cardiovascular physiology/development - implemented Oct 2007
- Cellular component processes (Jane, David, Midori, Val, ad hoc others) - started summer 2008
- Central Nervous System Development
- Chaperones(completed by working group at Cambridge GOC meeting Sept. 2009)
- Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts) Roncaglia et al 2017
- Collaboration with MIT GO-Engineering - Manuscript written
- Electron transport
- Extracellular RNA-containing vesicles (Paola, Aleks and community experts) Cheung et al 2016
- regulates links between function and process (David, Tanya)
- Gene expression (SF 1418820)
- Function-Process Links
- Heart Development (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
- Lung_Development (David, Jen, community experts)
- Immunology Revisions
- is_a complete biological process
- Kidney Development (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Kidney Physiology (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Morphogenesis (David, Tanya)
- Muscle Biology - Started Feb. 2007; meeting July 2007; Done Oct 2007
- Neurobiology Project (David, Tanya, Jane, Paola, DavidOS)
- Plant_term - March 28, 2007
- plasma lipoprotein particle ontology - done Sept. 2010
- Peptidase & protease activity overhaul begun June 2008; essentially completed August 2008
- Regulation Main Page live March 2008
- Regulator, activator and inhibitor MF terms (David, Tanya)
- RNA processing
- SDB 2009
- Sensu revamp
- Signaling overhaul (Becky, signaling WG)
- Synapse project (Synapse experts, DavidOS, Becky Foulger) - completed 2018
- Transcription & transcription factor activity overhaul (Karen, David) - 2012
- Transporters (Jen and community experts) - Started Feb. 2007
- Utilization - done March 2010
- Virus-related term overhaul, Phage Terms (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
- Generic GO slim overhaul (Jane & Val)
- Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')
- regulates links- Dec 2008 (David, Tanya)
- Correct disjointness violations
- Rework disjoint terms as concluded in discussion on GO list (Jane).
Proposed content work
A list of topics that we propose to address, but for which a timeline has not been set
- protein and peptidyl amino acid modification / protein processing
- Response to drug
- Polyketide synthases
Quality Control
SPARQL checks on the ontology
Ontology release pipeline
TO BE REPLACED
- Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)