Annotation Conf. Call, May 12, 2015

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Agenda

Transferring col-16 data for ISS (Becky)

We would like to discuss some rules to transfer col-16 data for ISS annotations: [1]

  • If the annotation being transferred has an annotation extension (which may, of course, subsequently need to be modified if it contains any species-specific components), then the transfer will be allowed, even if an IDA- or IPI-evidenced annotation to the same, or descendant, GO term already exists. These annotations should only be transferred on a case-by-case basis where the curator considers there is good evidence that the C16 information would be conserved between the two entries.
  • If the annotation being transferred does *not* have an extension, then the transfer will be disallowed, as per the current rules.

Ion channels- Ontology overhaul (David)

http://wiki.geneontology.org/index.php/Ontology_meeting_2015-02-26#Issues_With_Ion_Channels

Complexes in CC

New guidelines for creating complexes in GO old def: "Any macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical." [GOC:go_curators]


new def: "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical." [GOC:go_curators]


new definition comment: "A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Interactions that should not be captured as protein complexes include:

  • enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional;
  • proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex;
  • proteins with the same function but with either no demonstrable physical link or one that can be inferred by sequence homology;
  • any complex where the only evidence is based on genetic interaction data."

Review apoptosis annotations

There are several annotations from various groups with a range of ev.codes to the following apoptosis terms.

GO:0001836 release of cytochrome c from mitochondria
GO:0008625 extrinsic apoptotic signaling pathway via death domain receptors 
GO:0008631 intrinsic apoptotic signaling pathway in response to oxidative stress 
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0097192 extrinsic apoptotic signaling pathway in absence of ligand
GO:1902510 regulation of apoptotic DNA fragmentation

In some cases it is the issue of readout vs being involved in the process. For e.g. for the term :
GO:0001836, release of cytochrome c from mitochondria
The release of cytochrome c from mitochondria is a central event in the signaling phase of the apoptotic process, and it is often used by researchers to monitor this type of cell death. Any event that induces apoptosis will at some point induce the release of cytochrome c from mitochondria. Therefore, this term should only be used to annotate gene products that are directly involved in this process. An example is Drp1 (DNM1L, UniProt symbol O00429) in PMID:20850011.

Apoptosis curation manual is available here- http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual
Can the annotations be reviewed and fixed?

Discussion

Transferring col-16 data for ISS (Becky)

  • There was agreement to Becky's proposal. We should all use curator judgement and not automatically transfer AE data.
  • What happens to ISS annotations that predates AE? Can we back fill? (fill in)

Ion channels- Ontology overhaul (David)

  • All the issues with these terms and why they were overhauled can be found in the link above.
  • There are two new classifications- selective and non-selective ion channels. We all need to go back and make sure our annotations are housed correctly. Vast majority of ion channels are specific. We are hoping the list of non-selective ion channels will be small.
  • Calcium ion channel is a channel that passes calcium. It is about the specificity, it is selective for only those ions. We tried to differentiate these from the non-selective ones in the ontology
  • Non-selective channels will let any ion go through.
  • What happens if the authors haven't tested for all the ions, but conclude it is say a calcium channel based on the limited experiments they did?
    • Good point- we want to collect such papers and decide how to annotate those.
  • anti-porters exchange ions. Are they selective porters? They are child of transmembrane transporters
  • regarding the non-selective channels- what are all the ions they can transport? is there a set? Can the ontology editors add a comment?
  • Action item Huaiyu will send a list of the non-specific (and specific?) channels, and we will take it from there. Rama will distribute the list/post it on the wiki.

Complexes in CC

  • All the details mentioned in this agenda item were sent out as an email.
  • Action itemPaola will work with IntAct group and expand the Comment field for the complex terms (acceptable and unacceptable rules for what can be called a complex). We might provide a link to the IntAct guidelines.
  • Goal is to be in line with IntAct so we are consistent

Review apoptosis annotations

  • Action itemRama will send out a break down of annotations to these terms (by group) and we will take it from there.

Next Call