Annotation Conf. Call 2019-11-19: Difference between revisions
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=== 'activated by' and 'inhibited by' === | === 'activated by' and 'inhibited by' === | ||
*If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator: | *If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator: | ||
**remove the 'activated by' or 'inhibited by' annotation extension | **remove the ''activated by'' or ''inhibited by'' annotation extension | ||
**create a new 'binding' annotation with an annotation extension of: 'directly positively regulates' or 'directly negatively regulates' the regulated activity of the gene product | **create a new 'binding' annotation with an annotation extension of: ''directly positively regulates'' or ''directly negatively regulates'' the regulated activity of the gene product | ||
*If the annotation is to a binding term, and the extension is 'activated by' the chemical or molecular entity bound: | **Example: | ||
**remove the 'activated by' annotation extension and replace with 'has input' | ***GP ''enables'' | ||
**the annotations | *If the annotation is to a binding term, and the extension is ''activated by'' the chemical or molecular entity bound: | ||
**remove the ''activated by'' annotation extension and replace with ''has input'' | |||
**Example: | |||
***GP ''enables'' '(1->3)-beta-D-glucan binding' ''has input'' '(1->3)-beta-D-glucan' | |||
**the annotations can be used in the future to create or check term logical definitions in the ontology | |||
*If the inhibitor acts by competitively binding to an entity required for the activity of another gene product: | *If the inhibitor acts by competitively binding to an entity required for the activity of another gene product: | ||
** | **The activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the next (downstream) gene product | ||
**Examples: | **Examples (with standard annotations): | ||
***Two DNA-binding transcription factors that compete for overlapping regulatory sequences | ***Two DNA-binding transcription factors that compete for overlapping regulatory sequences | ||
***A gene product that binds and sequesters an enzyme substrate | ****TF-A ''enables'' 'RNA polymerase II regulatory region sequence-specific DNA binding' ''directly negatively regulates'' 'RNA polymerase II regulatory region sequence-specific DNA binding' | ||
***A gene product that binds and sequesters an enzyme's substrate | |||
***Inhibitor ''enables'' 'protein binding' ''directly negatively regulates'' 'catalytic activity' | |||
***A decoy receptor that binds and sequesters a ligand | ***A decoy receptor that binds and sequesters a ligand | ||
****secreted frizzled-related proteins | ****Decoy receptor ''enables'' 'protein binding' ''directly negatively regulates'' 'receptor activity' | ||
*****secreted frizzled-related proteins | |||
* Spreadsheet for activated_by: https://docs.google.com/spreadsheets/d/1bUQ7uSHaLbr8uvYu04Jbmr76bn-ja01hJxbcGnx-U6I/edit#gid=0 | |||
* Spreadsheet for inhibited_by: https://docs.google.com/spreadsheets/d/17SV7E7MUlJzyfc5c8DKss2yqPAIgXIXN1xMXNioWc-U/edit#gid=0 | |||
==Noctua Form 2.0 Demo== | ==Noctua Form 2.0 Demo== | ||
*Demonstration of the newly redesigned Noctua curation form | *Demonstration of the newly redesigned Noctua curation form | ||
*[https://docs.google.com/document/d/1DZu25YKdH_D3Ics5BSmyvN8IGfGlTcCcwQ4HzviZeWM/edit#heading=h.e6msjvy4rdk9 User Guide] | |||
*[https://geneontology.github.io/noctua-form/ Draft User Guide with short video] | |||
= Minutes = | = Minutes = | ||
*Present: | *Present: Bill, Bob, Colin, David H, Dave F, Dmitry, Doug, Dustin, Giulia, Harold, Karen, Kimberly, Leyla, Li, Midori, Niels, Patrick, Penelope, Petra, Rob, Ruth, Pascale, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi A, Tanya | ||
== Progress Reports == | |||
*Annotation groups should copy and complete the template (linked above) | |||
*Include all FTEs working on GO, even if not paid by the grant | |||
*Annotation stats will be produced by the GOC pipeline scripts, but it would be good if curators review them | |||
*Groups should fill out other sections, e.g. annotation strategy, publications, highlights (e.g. web display, special annotation projects) | |||
== Annotation Extension Relations == | |||
=== 'activated by' and 'inhibited by' === | |||
*Re-annotation of standard annotations using these relations for extensions should focus on the relevant activities and their causal relation | |||
*Curators should also focus on the relevant regulatory activities where the mechanism for the regulation is known | |||
*If the mechanism is not known, we would no longer capture this information in a GO annotation | |||
*We will review/add some more examples to the documentation and curators should bring these examples to annotation calls for discussion | |||
**Midori asked about enzymes that require a metal ion in order to function; if these are considered co-factors we would not be annotating that information | |||
==Noctua Form 2.0 Demo== | |||
*Noctua Form 2.0 will be going into production soon, so we had a demo of its new functionality and workflow | |||
*We'll send an email out to curators when the form is officially in production | |||
*Please provide feedback on the geneontology/noctua-form github tracker | |||
==Next Annotation Call== | |||
*We will have our next call on Tuesday, November 26th | |||
[[Category:Annotation Working Group]] |
Latest revision as of 15:56, 19 November 2019
Agenda
Progress Reports
- Reminder: due mid-December
- Annotation Group Template
- GO will generate annotation stats
Annotation Extension Relations
'activated by' and 'inhibited by'
- If the chemical or molecular entity performing the activation or inhibition acts directly on the gene product by binding to it and is believed to be an endogenous regulator:
- remove the activated by or inhibited by annotation extension
- create a new 'binding' annotation with an annotation extension of: directly positively regulates or directly negatively regulates the regulated activity of the gene product
- Example:
- GP enables
- If the annotation is to a binding term, and the extension is activated by the chemical or molecular entity bound:
- remove the activated by annotation extension and replace with has input
- Example:
- GP enables '(1->3)-beta-D-glucan binding' has input '(1->3)-beta-D-glucan'
- the annotations can be used in the future to create or check term logical definitions in the ontology
- If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
- The activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the next (downstream) gene product
- Examples (with standard annotations):
- Two DNA-binding transcription factors that compete for overlapping regulatory sequences
- TF-A enables 'RNA polymerase II regulatory region sequence-specific DNA binding' directly negatively regulates 'RNA polymerase II regulatory region sequence-specific DNA binding'
- A gene product that binds and sequesters an enzyme's substrate
- Inhibitor enables 'protein binding' directly negatively regulates 'catalytic activity'
- A decoy receptor that binds and sequesters a ligand
- Decoy receptor enables 'protein binding' directly negatively regulates 'receptor activity'
- secreted frizzled-related proteins
- Decoy receptor enables 'protein binding' directly negatively regulates 'receptor activity'
- Two DNA-binding transcription factors that compete for overlapping regulatory sequences
- Spreadsheet for activated_by: https://docs.google.com/spreadsheets/d/1bUQ7uSHaLbr8uvYu04Jbmr76bn-ja01hJxbcGnx-U6I/edit#gid=0
- Spreadsheet for inhibited_by: https://docs.google.com/spreadsheets/d/17SV7E7MUlJzyfc5c8DKss2yqPAIgXIXN1xMXNioWc-U/edit#gid=0
Noctua Form 2.0 Demo
- Demonstration of the newly redesigned Noctua curation form
- User Guide
- Draft User Guide with short video
Minutes
- Present: Bill, Bob, Colin, David H, Dave F, Dmitry, Doug, Dustin, Giulia, Harold, Karen, Kimberly, Leyla, Li, Midori, Niels, Patrick, Penelope, Petra, Rob, Ruth, Pascale, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi A, Tanya
Progress Reports
- Annotation groups should copy and complete the template (linked above)
- Include all FTEs working on GO, even if not paid by the grant
- Annotation stats will be produced by the GOC pipeline scripts, but it would be good if curators review them
- Groups should fill out other sections, e.g. annotation strategy, publications, highlights (e.g. web display, special annotation projects)
Annotation Extension Relations
'activated by' and 'inhibited by'
- Re-annotation of standard annotations using these relations for extensions should focus on the relevant activities and their causal relation
- Curators should also focus on the relevant regulatory activities where the mechanism for the regulation is known
- If the mechanism is not known, we would no longer capture this information in a GO annotation
- We will review/add some more examples to the documentation and curators should bring these examples to annotation calls for discussion
- Midori asked about enzymes that require a metal ion in order to function; if these are considered co-factors we would not be annotating that information
Noctua Form 2.0 Demo
- Noctua Form 2.0 will be going into production soon, so we had a demo of its new functionality and workflow
- We'll send an email out to curators when the form is officially in production
- Please provide feedback on the geneontology/noctua-form github tracker
Next Annotation Call
- We will have our next call on Tuesday, November 26th