Annotation Conf. Call, June 9, 2015

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Agenda

github accounts

As Chris mentioned in an email SF, ontology will be moving to github (software is already in github). Please get an account in github. More details to follow. https://github.com/geneontology/go-site/wiki/GitHub-pointers-for-GO-Consortium-members

GAF 2.1 release (pipe/comma)

Ontology updates

ion channels

Update on ion channels. Background: http://wiki.geneontology.org/index.php/Annotation_Conf._Call,_May_12,_2015#Ion_channels-_Ontology_overhaul_.28David.29_2

Based on discussion at the previous annotation call and among editors, below is a revised proposal. This hasn't been implemented in the ontology yet.

1) The recently created terms:

  • non-selective anion channel activity
  • non-selective cation channel activity

will be obsoleted (reason: added in error). Unless (see very end of proposal).

2) All existing terms under 'ion channel activity' will be meant to be agnostic to the notion of selectivity or non-selectivity, that is, their definitions will simply state that the channel is capable of passing a given ion, regardless as to whether only that specific ion can pass through, or whether other ions can pass as well:

  • we will remove 'selective' from the definition (as in "Enables the selective, facilitated diffusion of...");
  • we will remove synonyms containing the 'specific' string (e.g. 'chloride-specific channel activity');
  • we will add 'non-selective anion channel activity' as a narrow synonym to 'anion channel activity';
  • we will add 'non-selective cation channel activity' as a narrow synonym to 'cation channel activity'.

3) We will create new terms for selective channels. This should be done on a case-by-case basis. We could either draw a list of known selective channels, or use the list of non-selective channels that Huaiyu had offered to provide. Also see point 4) below about annotations.

  • These new terms would be called e.g. 'selective calcium channel activity' and
  • would be given exact synonyms e.g. 'calcium-specific channel activity'.
  • The definitions would read "Enables the selective, facilitated diffusion of...".

4) Annotations:

If we go this route, all current annotations would be correct, though some of them (the ones to selective channels) would not be as granular as they could. These are the ones we'd want to re-annotate. General rules for annotating ion channels should be:

  • If a paper gives evidence that a channel is selective for a given ion (or if the curator knows from prior knowledge), the channel component(s) should be annotated to a selective term, e.g. 'selective calcium channel activity'. If the term doesn't exist, the curator should request it.
  • If a paper shows that a channel passes a given ion, but does not specify if the channel is selective for that ion or not (or if the curator does not know from prior knowledge), the channel component(s) should be annotated to one of the existing term as appropriate, e.g. 'calcium channel activity'.
  • If a paper shows that a channel passes more than one ion and is therefore non-selective (e.g. TRP channels let sodium, potassium and calcium through), the channel component(s) should be annotated to as many existing terms as appropriate (e.g. all three 'sodium channel activity', 'potassium channel activity' and 'calcium channel activity' provided the paper shows experiments for all of them!).

5) End results:

  • Selective channel proteins could be pulled out as such => gain of information;
  • Non-selective channels would not be pulled out as such; the assumption would be that if selectivity isn't specified, the channel is either non-selective or of unknown specificity. If this is unwelcome, we could leave the recently created terms 'non-selective anion channel activity' and 'non-selective cation channel activity' in the ontology, and ask curators to move their existing annotations there if they belong to the list of non-selective channels provided by Huaiyu.

Any comments please?

UPDATE:

This proposal was circulated by email after the last annotation call. There were two favorable comments, but we’re not sure if everyone else had had a chance to review or not. The pending issues are:

- Non-selective anion/cation channel activity: obsolete or keep? [Paola leans towards keeping them as they could be immediately useful to add granularity, see below]

- To assist re-curation, we need a list of known selective channels, and possibly of known non-selective channels (e.g. TRP channels) as well if we opt to keep the existing terms above. How do we strategise this? Huaiyu had provided a list of calcium channel proteins obtained as follows:

“I generated a list of genes manually annotated to calcium channel. Here is how I generated it. I used the Amigo site, searched for the term calcium channel (GO:0005245), and filtered the results with only molecular function terms and experimental evidence used in manual curation. Then I removed the genes annotated to calcium channel regulator activity. [Note from Paola: if you use QuickGO, the default behavior to retrieve annotations includes is_a, part_of and occurs_in relationships only, i.e. no regulation children.] As you can see, most of the annotations are correct. The main problem is in the annotation of TRPs. There are similar problems in K channel annotation, e.g., ABC transporters, serotonin receptors and TRPs are annotated as K channels.”

What additional information could we provide curators to aid reannotation? Can anyone suggest an up-to-date review or book chapter about selective and non-selective channels?

transcription terms

Proposal to rename transcription terms:

  • Move the mechanism to the end of the term, after a comma:

transcription factor binding transcription factor activity
transcription factor activity, transcription factor binding

RNA polymerase II transcription factor binding transcription factor activity
transcription factor activity, RNA polymerase II transcription factor binding

RNA polymerase II activating transcription factor binding transcription factor activity
transcription factor activity, RNA polymerase II activating transcription factor binding

  • use transcriptional repressor/activator in place of 'transcription factor activity involved in negative regulation of transcription' and 'transcription factor activity involved in positive regulation of transcription':

RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription
transcriptional repressor activity, RNA polymerase II transcription factor binding

RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription
transcriptional activator activity, RNA polymerase II transcription factor binding

3. Change 'X region sequence-specific DNA binding' to 'X binding', in cases where it is obvious from the name that this is a case of 'sequence specific DNA binding'. e.g.:

bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity'
transcription factor activity, bacterial-type RNA polymerase core promoter proximal region binding

Protein Complexes in CC

No more merges in the ontology

Terms will be made Obsolete instead with a the replace tag.

cell lines and cell types in col-16

Report from MGI

Cell type

  • Various situations that involve cell lines:
    • primary cell lines
      - As non-transformed cells taken directly from a specific tissue, these are clearly biologically relevant.
      - We DO indicate the cell type in this situation using a term from the cell type ontology.
    • immortalized cell lines
      • that model specific cell types, e.g. C2C12 myoblast cells, IMCD (a kidney, medulla/collecting duct cell line), etc.
        - Although immortalized, these types of cell lines generally have some specialized property or characteristic that reflects the cell type from which it was derived and are generally considered to be biologically relevant models for those cell types.
        - We DO we indicate the cell type in this situation using a term from the cell type ontology (CL).
      • that are used generally, e.g. HeLa cells, NIH3T3 cells (a fibroblast line)
        - These types of cell lines are most frequently used as cellular test tubes, e.g. for transcription assays where a reporter construct is co-transfected, and are rarely biologically relevant.
        - We generally do NOT indicate the cell type when a cell line of this type is used.
  • relationships to use
    • occurs in for GO terms in BP or MF
    • part of for GO terms in CC

Cell line
MGI also records information about named cell lines, such as those mentioned above. However, we do this in a notes field in the MGI interface that is not transmitted to the GAF. There is no relationship that is appropriate to attach this information to the GO annotation since this is an experimental detail, while the biologically relevant information, if any, is the cell type. Thus, based on my experience with the Protein2GO interface, I think it is not possible to capture the name of the cell line in the Annotation Extension field since P2GO only allows a defined set of approved relationships.

If you are writing a GO-related paper

If you are working on a paper related to GO, please circulate a version to the GOC or to the PIs minimally. We want to make sure the message is consistent.

June Consistency paper

UCL has picked a paper for this month's exercise. Please send Ruth your annotations in an excel sheet. http://www.ncbi.nlm.nih.gov/pubmed/?term=23954377