Annotation Conf. Call 2019-09-24

Agenda

October GOC Meeting - Berkeley

• Logistics and Sign-Up
• Agenda

Pipeline

• There have been some glitches with the GOC pipeline.
• New ontology terms may not be available for use yet.
• Software team is aware of the issues and working on restoring the pipeline to its regular schedule.
• Any updates here?

GO-CAMs and Annotation Extensions

• After USC hackathon in June, we formed a small working group to fully articulate the GO-CAM model specifications
• This will allow for consistent GO-CAM curation using Noctua workbenches, import projects (e.g. Reactome and MOD imports)
• Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation
  • On today's call, we will review the annotation extension relations that need further discussion, starting with happens_during
  • Google summary spreadsheet of MF extensions

happens_during

• Google spreadsheet for happens during
• Current recommendations are that 'happens during' is used to define a biological phase or life stage during which a molecular function occurs
• However, happens_during is not defined in the relations ontology
• There is a comment, however:
  • X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
  • This implies that the start and end of the molecular function and phase are known
  • For things like cell cycle phases or development stages this seems fairly straightforward
• But what about annotations that referred to a function that 'happens during' a biological process, such as 'response to oxidative stress'?
• What do we mean when we make these statements?
  • WB had seven MF annotations with 'happens during' extensions that needed review.
    • One used a WBls term, so that was okay.
    • The remaining six used 'response to' terms and in reviewing them, I changed the extension relation to 'part of' the 'response to' term. The MFs were all transcription-related functions that mediated the transcriptional response to unfolded protein, or hypoxia, or heat.
  • (Pascale): If we want to allow happens_during for 'response to' terms, then we should treat them as 'biological phases', and disallow direct annotations. Are there cases where using 'part_of' versus 'happens_during' makes sense ?
• Updated documentation on 'happens during' usage: http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:happens_during

Ontology Updates and Annotation Reviews

Cellular Component

• 'cell part' and child terms
  • creation of new term ' cellular anatomical entity'

Protein multimerization terms

• How are the reviews going?
• Next terms up: protein homodimerization, protein heterodimerization (non-IPI evidence codes)

Transcription terms

• Any issues or questions here?

Minutes

• Present: Colin, David, Dmitry, Dustin, Edith, Giulia, Helen, Harold, Karen, Kimberly, Laurent-Philippe, Michelle, Midori, Pascale, Paul T., Sabrina, Seth, Stacia, Tanya, Petra

GO-CAMs and Annotation Extensions

happens_during

• We discussed review and use of 'happens during' as an annotation extension relation for MF terms.
• Use of 'happens during' with a biological phase of life cycle stage is allowed.
• Use of 'happens during' with a 'response to x' BP term is still under review.
  • If the MF is an integral part of the 'response to' term, then the curator should update the annotation extension relation to 'part of'.
  • Other 'response to' extensions will need to be examined in more detail to better understand what information we were trying to capture and how it would be modeled in a GO-CAM.
  • PomBase has a number of these annotations and will get back to us on their thoughts.
• We will also address Barbara's questions about use of 'happens during' on a future call.

occurs_at

• We will not use SO terms with the 'occurs at' relation to capture the type of sequence or motif at which an MF occurs, e.g. 'occurs at' n_terminal_region (SO:0100014)