Annotation Conf. Call 2017-01-24: Difference between revisions
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***Capturing the protein substrate, HIF-1. | ***Capturing the protein substrate, HIF-1. | ||
***Other players: O2, Fe2+, 2-oxoglutarate | ***Other players: O2, Fe2+, 2-oxoglutarate | ||
**To what extent do we want to tease out the different molecular functions of complex members? | |||
***VCB complex: pVHL, elongin B, elongin C, cullin-2 (Cul2), and Rbx1 | |||
= Minutes = | = Minutes = | ||
*On call: Barbara, David H., David OS, Edith, George, Giulia, Harold, Helen, Karen, Li, Midori, Moni, Paola, Pascale, Paul T., Petra, Rachael, Ruth, Sabrina, Stacia, Stan, Tanya, Terry, Val | |||
== GO Meeting == | |||
*Need more info on attendees so we can plan - will talk with Pankaj | |||
== Biocurator Meeting == | |||
*February 17th - deadline for poster abstract and early registration | |||
*Stanford - end of March | |||
== github Ticket on New Qualifiers == | |||
*Proposal to add more qualifiers for BP annotation | |||
*Need to review the use of these and have very clear documentation on their usage | |||
*causally upstream of or within may be useful for annotating results of phenotypic analysis | |||
*There may be different ways of annotating regulation, but we will want to standardize what we use | |||
*Think about how we can provide separate sets of annotations to users by employing these qualifiers | |||
*Curators will need to re-examine existing annotations to determine what the correct qualifier will be | |||
**Can we be clever about this, e.g. using evidence codes to help guide what qualifier is used? | |||
= LEGO Models = | |||
== David and Karen == | |||
*Two points: | |||
**How deep do we drill down with respect to evidence codes in a LEGO model? | |||
**How do we annotate models when information comes form more than one species? | |||
*Highlights: | |||
**MGI using PRO IDs for modified forms of a protein | |||
**Human protein annotated with three specific pieces of evidence to support kinase activity | |||
***Output in GPAD is three separate lines - one for each piece of evidence | |||
**MGI has decided, however, to instead select the one GO evidence code that supports the annotation | |||
***This will result in just one line of evidence in the GPAD file | |||
**Pascale - SIB is using these more granular evidence codes in their internal curation practices | |||
**In the case of these three evidence codes, two map to IDA and one didn't | |||
**Karen - don't really want three lines of evidence when the inference is really based on the summation of the three | |||
**Paul T. - can we still trace back to the PubMed ID? | |||
**David H. - yes | |||
**Tanya - if we were going to also add IMP, should that be a new annoton? | |||
**David H. - no, you can just add the additional evidence onto the same assertion? | |||
*Mouse protein is annotated to kinase activity with ISO evidence code, based on the human annotation | |||
*Should the human annotation be included in the same model, or can it be included in the same model? | |||
*Easier for curator to put the annotation in the same model | |||
*Karen - do we need to make strict rules on this? | |||
*Pascale - in terms of data model, thought we wanted just one model per species | |||
*Paul T. - this should be okay with the data model; curators will need to decide what they want as a curation unit | |||
*David H. - within an annoton, though, we're NOT mixing species | |||
*Species are kept together, but evidence may be based on orthology | |||
*Ruth - nice to include all of the evidence in one canvas to help track down the evidence | |||
*David H. - could scrolling over the evidence 'E' in the mouse model, somehow highlight the human annotation from which it's derived | |||
*Paul T. - could we harness the Excel sheet concept here? | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 13:23, 24 January 2017
Bluejeans URL
https://bluejeans.com/993661940
Agenda
GO Meeting Reminder
- Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June 5th
- Meeting Registration Site
- Meeting Agenda
github Tickets
- New qualifiers for biological process
- Will be discussed on the February 14th annotation call, but please look at the ticket and comment there, if needed.
LEGO Models
MGI - David and Karen
WB - Kimberly
Model: Regulation of HIF-1 under normoxic conditions
- Questions:
- How to annotate the role of substrates and co-factors wrt the hydroxylase activity of EGL-9?
- Capturing the protein substrate, HIF-1.
- Other players: O2, Fe2+, 2-oxoglutarate
- To what extent do we want to tease out the different molecular functions of complex members?
- VCB complex: pVHL, elongin B, elongin C, cullin-2 (Cul2), and Rbx1
- How to annotate the role of substrates and co-factors wrt the hydroxylase activity of EGL-9?
Minutes
- On call: Barbara, David H., David OS, Edith, George, Giulia, Harold, Helen, Karen, Li, Midori, Moni, Paola, Pascale, Paul T., Petra, Rachael, Ruth, Sabrina, Stacia, Stan, Tanya, Terry, Val
GO Meeting
- Need more info on attendees so we can plan - will talk with Pankaj
Biocurator Meeting
- February 17th - deadline for poster abstract and early registration
- Stanford - end of March
github Ticket on New Qualifiers
- Proposal to add more qualifiers for BP annotation
- Need to review the use of these and have very clear documentation on their usage
- causally upstream of or within may be useful for annotating results of phenotypic analysis
- There may be different ways of annotating regulation, but we will want to standardize what we use
- Think about how we can provide separate sets of annotations to users by employing these qualifiers
- Curators will need to re-examine existing annotations to determine what the correct qualifier will be
- Can we be clever about this, e.g. using evidence codes to help guide what qualifier is used?
LEGO Models
David and Karen
- Two points:
- How deep do we drill down with respect to evidence codes in a LEGO model?
- How do we annotate models when information comes form more than one species?
- Highlights:
- MGI using PRO IDs for modified forms of a protein
- Human protein annotated with three specific pieces of evidence to support kinase activity
- Output in GPAD is three separate lines - one for each piece of evidence
- MGI has decided, however, to instead select the one GO evidence code that supports the annotation
- This will result in just one line of evidence in the GPAD file
- Pascale - SIB is using these more granular evidence codes in their internal curation practices
- In the case of these three evidence codes, two map to IDA and one didn't
- Karen - don't really want three lines of evidence when the inference is really based on the summation of the three
- Paul T. - can we still trace back to the PubMed ID?
- David H. - yes
- Tanya - if we were going to also add IMP, should that be a new annoton?
- David H. - no, you can just add the additional evidence onto the same assertion?
- Mouse protein is annotated to kinase activity with ISO evidence code, based on the human annotation
- Should the human annotation be included in the same model, or can it be included in the same model?
- Easier for curator to put the annotation in the same model
- Karen - do we need to make strict rules on this?
- Pascale - in terms of data model, thought we wanted just one model per species
- Paul T. - this should be okay with the data model; curators will need to decide what they want as a curation unit
- David H. - within an annoton, though, we're NOT mixing species
- Species are kept together, but evidence may be based on orthology
- Ruth - nice to include all of the evidence in one canvas to help track down the evidence
- David H. - could scrolling over the evidence 'E' in the mouse model, somehow highlight the human annotation from which it's derived
- Paul T. - could we harness the Excel sheet concept here?