Difference between revisions of "Annotation Conf. Call, July 14, 2015"

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===Next Call===
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We will discuss some of the relations (mostly used for Col-16) that have been slated for obsoletion. They are:
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<pre>in_presence_of
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in_absence_of,
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independent_of
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</pre>
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If you have examples (papers) where you have used them, please add it to the agenda for the next call.

Revision as of 14:43, 13 July 2015


Agenda

New ECO term for inferencing pipeline

The InterOntology inferencing pipeline will get new ECO terms.

  • The 2 first codes would distinguish between annotations inferred from manual and automated annotations:

- evidence based on logical inference from manual annotation used in automatic assertion - evidence based on logical inference from electronic annotation used in automatic assertion Both terms belong in the "automatic assertion" part of the ontology, and should be descendants of ECO:0000501, because the pipeline that generates the inferred annotations is an automatic one.

The third code, "evidence based on logical inference used in automatic assertion", would be a parent of the other two. Adding such a parent, though it would not be used directly in the annotations themselves, would make it easier for processing the rules in the eco-usage-constraints [1] file (which associates evidence codes with the values allowed in the with_string): we'd have only one entry in the file and the rule would be automatically propagated to the subclasses.

  • IEA will be used in regular GAFs and ECO in the GPAD. The GOID that was used for the inference will be in the With/From column for the IEAs
  • Once the ECO term is available the scripts that generate these inferences will make this change. There will be enough notice!

New Term Genie templates

Two new templates are now ready to use in the TermGenie (TG) tool to request new GO terms:

Template: macromolecular complex binding; Description: binding of a macromolecular complex

Template: cellular component organization; Description: organization of a cellular component

These templates can be found using the text search box, or expanding the 'Molecular Function' or 'Processes' tree respectively.

The TermGenie tool is available at http://go.termgenie.org/. An online manual is here: http://go.termgenie.org/help/index.html There is also a TG help desk: help@go.termgenie.org

miRNA guidelines (Rachael and others)

http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual

Note: The guidelines don't only cover annotation of miRNAs but also annotation of proteins involved in the miRNA biogenesis pathway! (e.g. Dicer, Drosha etc.)

use of 'regulation of activity' (UCL group)

'QUESTION: Would you annotate a protein involved in localisation (or regulation of localisation) of X to ‘regulation of X activity’ ?'

Case 1: ION CHANNELS

In response to stimuli, ion channels are localised within the neuron to increase synaptic transmission, membrane potential etc.

Would you annotate the GPs that regulate this localization or directly localize ion channels to:

  • regulation of cation channel activity ; GO:2001257

and/or

  • regulation of cation transmembrane transport ; GO:1904062

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Case 2: TRANSCRIPTION FACTORS

Would you annotate factors that shuttle TFs into the nucleus, or the upstream signals that regulate the shuttling to:

  • regulation of sequence-specific DNA binding transcription factor activity ; GO:0051090’

and/or:

  • regulation of transcription from RNA polymerase II promoter ; GO:0006357

See PMID: 8851662 for different mechanisms of modulating TF localisation

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Case 3: TRANSPORTERS

Would you annotate GPs that localise a transporter (or regulate localisation of a transporter) to 'regulation of transporter activity’?

GLUT4 is sequestered in intracellular vesicles. In response to insulin, GLUT4 is translocated to the plasma membrane where GLUT4 transporters are inserted and become available for transporting glucose. Thus glucose uptake is regulated by controlling the number of GLUT4 transporters on the cell surface.

Would you annotate the GPs involved in regulating GLUT4 translocation to:

  • regulation of transporter activity ; GO:0032409
  • regulation of transport ; GO:0051049

In this case, the signaling components are regulating the localisation of GLUT4.

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Case 4: KINASES

Would you annotate GPs that localise a kinase to a specific place in the cell to:

  • regulation of kinase activity ; GO:0043549

and/or:

  • regulation of phosphorylation ; GO:0042325

The regulatory subunits of some kinases, for instance (e.g. PI3K), are involved in trafficking the catalytic kinase to the site of its substates.

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Next Call

We will discuss some of the relations (mostly used for Col-16) that have been slated for obsoletion. They are:

in_presence_of
in_absence_of, 
independent_of

If you have examples (papers) where you have used them, please add it to the agenda for the next call.