Annotation Conf. Call April 23, 2013
- Apoptosis curation manual and re-curation effort
- Jenkins checks
- Update on GOC meeting
Curation manual can be found here: http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual
- If you have questions about any of the new terms, please post them on SourceForge.
- Davids question about a paper (Pablo, Paola please add this example to the manual)
- Karen- it will be useful to add some of the common apoptotic drug targets. Pablo will provide a link to a good review in the manual.
- David- although we shouldn't be annotating to the top level terms, it is okay to annotate to the broad terms if that is the best you can do.
- Li- differentiate between hormone induced apoptosis and extrinsic apoptotic signaling pathway in the absence of ligand
- Pablo will add his comments to the manual
- Li- cell type specific apoptosis- should we create a new term or use col-16?
- paola- precompose a new term. if the cell type is not in the cell type ontology, then the ontology editors will work with cell type folks to add it.
- groups will be reminded once a month to check their JENKINS report.
- there are lot of IEAs that are flagged. This should be fixed now. The ontology tag (use_for_manual_curation) will be used to flag manual annotations only.
- if a new ontology tag is added, that doesn't automatically trigger a GAF check.
- if you check in a file and you want to force run the validator, ask Heiko to restart Jenkins
- Jenkins runs only on files that are checked in
- Minutes are available on Google docs (link available from the GOC wiki- http://gocwiki.geneontology.org/index.php/2013_Cambridge_GOC_Meeting_Agenda).
- AmiGO 2 (http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo) is ready for testing. Please report your bugs at: http://github.com/kltm/amigo/issues or send them to Seth/Chris
- New website is being worked on (check the new logo). http://beta.geneontology.org
- Galaxy environment has been set up (http://galaxy.berkeleybop.org/). It will be integrated with the new website.
- Annotation extension column (propagating/inferring)
1. Subsets for annotation extension relations - for use in curator tools to make it easier for curators to choose between relations. e.g. subset of relations for use with cell or tissue types or for use with targets of activities.
2. Transfer of annotation extension information by ISS, ISO. Annotation extensions are intended for expressing in vivo/normal situations for the gene product. Therefore it was agreed transfer by ISS shouldn't be done blindly, but on a case-by-case basis with the curator considering whether this extension is appropriate for the gene product the annotation is being transferred to. In the case of targets in the annotation extension, e.g. an annotation to protein kinase activity with the target protein in the annotation extension, it was agreed that if the curator wished to transfer the target information, it would be appropriate for the curator to determine the in vivo target and replace the identifier in column 16 of the ISS annotation.
- Misused terms (http://gocwiki.geneontology.org/index.php/Misused_terms - we will be going through them in future annotation calls)
- discussion on read-out vs actual involvement in the process
- Create Orcid account http://orcid.org/ (for Termgenie login) and send your username to Jane. This will be used for Xref (not for logging into TermGenie)
- Cell cycle changes
- Curators should avoid annotating to cell cycle terms for the time being. Jane should be able to finish the overhaul soon.