08 MAR 2011 RefGen Phone Conference (Archived)

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  • dictybase: Pascale,
  • GOA; Emily, Rachael, Becky,
  • PPOD: Mike,
  • pombase: Val,
  • MGI: Mary Dolan, Li, Dmitry
  • BHF-UCL: Ruth Vasha
  • BBOP: Suzy
  • Ecohub: Brenley
  • Wormbase: Ranjana, Kimberly
  • TAIR: Donghui
  • AgBase: Lakshmi
  • FlyBase: Susan
  • ZFIN: Doug
  • RGD: Stan, Shur-Jen

Action items

  • Rama: Document cron job for trees
  • All: Apoptosis Annotation Project: For next month: Discussion of the BCL family of proteins Apoptosis_Reference_Genome_Targets#BCL_family_Proteins
  • Rama: Everyone needs to communicate to the software team to upload the MF-BP inferences on the FTP site (ADD LINK TO DOCUMENTATION).

New Annotation Project

Apoptosis_Reference_Genome_Targets Project leaders: UniProtKB GOA team, Emily Dimmer

Content meeting at EBI on Apoptosis on June 1st.

Next reference genome call will discuss the BCL family of proteins Apoptosis_Reference_Genome_Targets#BCL_family_Proteins

PAINT and M2P Inferenced annotations

  • Are all the groups familiar with where the PAINT and MF-BP inferences are on the FTP site? Are there any technical questions? -Rama
  • GOA has started to provide mf2bp inferences in the UniProt file for all sources/species (as we need to ensure we have a complete and consistent data set) Edimmer
  • Are the annotating groups ready to load the mf-Bp inferences.

o SGD has looked at some of these annotations and we have some concerns. o For example yeast ADK1 is a adenylate kinase and we already have an annotation to ADP biosynthetic proces. The MF-BP inference is to the term nucleotide phosphorylation. o In another example, yeast AGE1 is annotated to GTPase activator activity and an inference has been made to 'regulation of catalytic activity'. This is a high level term and not something we would capture in our manual curation pipeline. o But it is hard for us to review all these annotations to decide which to keep etc. I would like to know how other groups are dealing with these annotations.

  • GOA only includes RefGenome annotations from PAINT for human, chicken and other species. Should we take more files directly from GO - or wait for individual MODs to include the annotations and take them from the MOD GAFs? Edimmer
  • I believe GOA has already started to provide the PAINT annotations through the files and they come with ISS evidence code. In talking to Mike Cherry about this he thinks apart from the fact that these annotations are made from the Ref.genome project, the new evidence codes is the novelty part of these annotations. If the GOC adds documentation on these evidence codes (they are available in the ECO) can the annotating groups use these new evidence codes?

Uploading PAINT annotations

(Emily): GOA will upload them unless groups objects (pombase, MGI, SGD, ZFIN does not want GOA to upload the PAINT annotations for them)