Annotation Conf. Call 2019-11-19
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: