Annotation Conf. Call 2019-11-19: Difference between revisions
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**Examples: | **Examples: | ||
***Two DNA-binding transcription factors that compete for overlapping regulatory sequences | ***Two DNA-binding transcription factors that compete for overlapping regulatory sequences | ||
****TF-A 'enables' 'regulatory region binding' directly negatively regulates 'regulatory region binding' | |||
***A gene product that binds and sequesters an enzyme substrate | ***A gene product that binds and sequesters an enzyme substrate | ||
***Inhibitor A 'enables' 'substrate binding' directly negatively regulates 'catalytic activity' | |||
***A decoy receptor that binds and sequesters a ligand | ***A decoy receptor that binds and sequesters a ligand | ||
****decoy receptor 'enables' ligand binding directly negatively regulates 'receptor activity' | |||
****secreted frizzled-related proteins | ****secreted frizzled-related proteins | ||
Revision as of 10:24, 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
- 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'
- the annotations will be used in the future to create or check the logical definitions in the ontology
- If the inhibitor acts by competitively binding to an entity required for the activity of another gene product:
- proposal: the activity of the inhibitor (upstream) 'directly negatively regulates' the activity of the downstream gene product
- Examples:
- Two DNA-binding transcription factors that compete for overlapping regulatory sequences
- TF-A 'enables' 'regulatory region binding' directly negatively regulates 'regulatory region binding'
- A gene product that binds and sequesters an enzyme substrate
- Inhibitor A 'enables' 'substrate binding' directly negatively regulates 'catalytic activity'
- A decoy receptor that binds and sequesters a ligand
- decoy receptor 'enables' ligand binding directly negatively regulates 'receptor activity'
- secreted frizzled-related proteins
- 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: