Ontology Development: Difference between revisions
m (→Documentation) |
|||
(34 intermediate revisions by 2 users not shown) | |||
Line 10: | Line 10: | ||
=== When === | === When === | ||
* 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. | ||
Line 15: | Line 16: | ||
=== How to Join === | === How to Join === | ||
* Recurring meeting URL: https://stanford.zoom.us/j/828418143 | * Recurring meeting URL: https://stanford.zoom.us/j/828418143 | ||
*to join via phone: enter Meeting ID 828418143# after dialing in | *to join via phone: enter Meeting ID 828418143# after dialing in | ||
Line 23: | Line 25: | ||
* 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]] | | * 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]] | | ||
= Documentation= | = Documentation= | ||
==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]== | ==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]== | ||
==[[Installing and Using git]]== | ==[[Installing and Using git]]== | ||
==[[Ontology Editors Daily Workflow]]== | |||
==Editing the Ontology== | ==Editing the Ontology== | ||
==[[General Gene Ontology Principles]]== | {| class="wikitable" | ||
!colspan="2" | [[General Gene Ontology Principles]] | |||
|- | |||
!colspan="2" | New terms | |||
|- | |||
|rowspan="7"|[[Principles for creating a GO term]] (being reviewed) | |||
|[[Guidelines for creating a GO term]] | |||
|- | |||
|[[Guidelines for creating a Regulation Term]] | |||
|- | |||
|[[Guidelines for GO textual definitions]] (being reviewed) | |||
|- | |||
|[[Guidelines for equivalence axioms]] (being reviewed) | |||
|- | |||
|[[Guidelines for new Molecular Functions]] (new) | |||
|- | |||
|[[Guidelines for new Biological Processes]] (new) | |||
|- | |||
|[[Guidelines for new Cellular Components]] (new) | |||
|- | |||
!colspan="2" |Modifying existing terms | |||
|- | |||
|rowspan="4"|[[Principles for Modifying an Existing Ontology Term]] (to be reviewed) | |||
|[[Deleting Asserted Subclasses]] | |||
|- | |||
|[[Adding Term Comments]] | |||
|- | |||
|[[Adding a Term to a GO Subset (Slim)]] | |||
|- | |||
|[[Adding Taxon Restrictions]] | |||
|- | |||
!colspan="2" |Term obsoletion | |||
|- | |||
|rowspan="2" |[[Principles for term obsoletion]] | |||
|[[Obsoleting an Existing Ontology Term]] | |||
|- | |||
|[[Restoring an Obsolete Ontology Term]] | |||
|- | |||
!colspan="2" |Term merges | |||
|- | |||
|[[Principles for merging terms]] (being reviewed) | |||
|[[Merging Ontology Terms]] | |||
|- | |||
!colspan="2" |Subsets | |||
|- | |||
|Subset documentation (to add) | |||
|[[Adding and Removing GO Subsets (Slims)]] | |||
|- | |||
!colspan="2" |Import Files | |||
|- | |||
| Principles for [[GO import files]] | |||
|[[Adding Terms and Regenerating the Import Files]] | |||
|} | |||
==[[General Relations Documentation Draft]] To be reviewed== | |||
==[[New Ontology Editor Training]] To be reviewed== | ==[[New Ontology Editor Training]] To be reviewed== | ||
Line 134: | Line 164: | ||
=Other Ontology Development Group Activities= | =Other Ontology Development Group Activities= | ||
[[Category:Ontology]][[Category:GO Editors]] | [[Category:Ontology]][[Category:GO Editors]] |
Revision as of 10:38, 14 September 2018
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)
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-editors mailing list
How to Join
- Recurring meeting URL: https://stanford.zoom.us/j/828418143
- to join via phone: enter Meeting ID 828418143# after dialing in
- from US: +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll)
Agenda and Minutes
Documentation
Setting up Protege for GO editors
Installing and Using git
Ontology Editors Daily Workflow
Editing the Ontology
General Gene Ontology Principles | |
---|---|
New terms | |
Principles for creating a GO term (being reviewed) | Guidelines for creating a GO term |
Guidelines for creating a Regulation Term | |
Guidelines for GO textual definitions (being reviewed) | |
Guidelines for equivalence axioms (being reviewed) | |
Guidelines for new Molecular Functions (new) | |
Guidelines for new Biological Processes (new) | |
Guidelines for new Cellular Components (new) | |
Modifying existing terms | |
Principles for Modifying an Existing Ontology Term (to be reviewed) | Deleting Asserted Subclasses |
Adding Term Comments | |
Adding a Term to a GO Subset (Slim) | |
Adding Taxon Restrictions | |
Term obsoletion | |
Principles for term obsoletion | Obsoleting an Existing Ontology Term |
Restoring an Obsolete Ontology Term | |
Term merges | |
Principles for merging terms (being reviewed) | Merging Ontology Terms |
Subsets | |
Subset documentation (to add) | Adding and Removing GO Subsets (Slims) |
Import Files | |
Principles for GO import files | Adding Terms and Regenerating the Import Files |
General Relations Documentation Draft To be reviewed
New Ontology Editor Training To be reviewed
Website - to be moved to the wiki?
- Editorial-type sections copied over from the GO website ontology documentation: MF
- [Biological-process-ontology-guidelines]
Identifiers To be reviewed
Guidance for organizing content meetings
(old doc, but basic principles still apply)
Content Development
Projects
High Priority/Ongoing
- Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
- Cell Cycle (Val, Pombe experts, GOEds)
- Enzymes and EC mappings
- Synapse project (Synapse experts, DavidOS, Becky Foulger)
- Extracellular RNA-containing vesicles (Paola, Aleks and community experts)
- Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts)
- Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts)
Medium Priority
- Non-symbiotic multi-organism processes (Jane, David OS)
Low priority
- Neuro Behaviour Ontology (NBO)-GO alignment (Jane, George Gkoutos, Chris, DavidOS)
- microbial ontology development and annotation
Recently completed projects
- Uberon alignment (DavidH)
- Addition of cross-products - see Category:Cross_Products and Cross_Product_Guide
- Cell cross-products, Cell-type specific GO terms (Jane, Paola, Alex, Chris, DavidOS)
- Adding missing CHEBI xps
- Signaling overhaul (Becky, signaling WG)
- Virus-related term overhaul, Phage Terms (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
- Neurobiology Project (David, Tanya, Jane, Paola, DavidOS)
- Apoptosis (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
- Transcription & transcription factor activity overhaul (Karen, David) - 2012
- Kidney Physiology (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Cardiac conduction (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
- Rework disjoint terms as concluded in discussion on GO list (Jane).
- MENGO collaboration (Jane)
Proposed content work
A list of topics that we propose to address, but for which a timeline has not been set
- Peripheral nervous system development
- Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
- Overhaul translation, similar to what's being done for transcription. SF 1891512 is closed, but notes some issues for consideration. (midori 2010-10-04)
- Recombination and DNA repair
- RNA processes
- Bile formation and secretion processes
- protein and peptidyl amino acid modification / protein processing
- Response to drug
- Polyketide synthases
- cell growth/proliferation/division
- oxidoreductases
Completed ontology content work
Quality Control
SPARQL checks on the ontology
[|SPARQL checks on the ontology]
Ontology release pipeline
http://wiki.geneontology.org/index.php/Release_Pipeline Errors: http://current.geneontology.org/ontology/reports/index.html
TO BE REPLACED
- Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)