9 FEB 2010 RefGen Phone Conference (Archived)

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ALL GROUPS: Please fill three sections here:

  1. Annotation Status of lung curation targets9_FEB_2010_RefGen_Phone_Conference#Lung_curation_targets
  2. Who captures the 'comprehensive annotation' status?9_FEB_2010_RefGen_Phone_Conference#Plan_for_annotation_status_reporting_tool
  3. Please describe How_is_your_group_Publicizing_Ref.Genome annotation here: Ideas_for_publicizing_Ref.Genome_Annotation_Data#How_is_your_group_Publicizing_Ref.Genome_Data


  • GOA:
  • BHF-UCL:
  • MGI:
  • RGD:
  • Flybase:
  • dictyBase:
  • TAIR:
  • AgBase:
  • SGD:
  • pombe
  • Ecoli:
  • Wormbase:
  • ZFIN:
  • PPOD:
  • Berkeley:

Lung curation targets

  1. Discuss the priorities (Dec, Jan, and fgf10 from November) and goal (March 1st)
  2. Please answer prior to the call: Can everyone have the curation targets annotated by then? If not, can you write down which families are problematic?
  • GOA: We will have a good stab at getting most of them done, the most problematic will be those with many publications; DAG1, GSTT1, SerpineE1 and E2. We will try to get at least some annotations for each aspect on all of them by March 1st though.
  • BHF-UCL:
  • MGI:
  • RGD: The genes on the lists have been curated.
  • FlyBase: The Dec genes BMP4, CTNNB1 and HOXA5 are a problem for me as the fly orthologs (decapentaplegic, Antennapedia, bicoid and armadillo) are among the most intensively studied fly genes having 500 to <1000 pubs each. I'll do my best to curate the key features. I haven't started the Jan targets yet but there doesn't seem to be much info for most of the 32 genes so I hope it will possible to complete these by March 1st The other problem we have is that it takes a month or two for my annotations to make it into the public version of FlyBase and then into the ga file so even if the annotations are done by March 1st they won't necessarily be visible to the paint annotators.
  • dictyBase: We expect that we will be able to complete the lung targets by March 1st.
  • TAIR: We expect that we will be able to complete the lung targets by March 1st.
  • AgBase:
  • SGD:The HMGB2 targets may not be done by then. The curators who are working on them have said that even if they are not done by March 1st, they will be done within a week or two after that.
  • pombe
  • Ecoli: EcoliWiki didn't have any lung targets, so we are catching up on our other RefGenome genes.
  • Wormbase: We expect that we will be able to complete the lung targets by March 1st.
  • ZFIN: It is unlikely that I will get ALL the curation done by the end of Feb. I will most likely be able to have a reasonable amount done on all the genes in the set though if I cherry pick the papers carefully.

PAINT demo

Ed Lee, Berkeley

Plan for annotation status reporting tool

Kara and her group have started to work on a tool that would display the annotation status of the Panther families. There will be a regularly updated web page that will show the following information:

  1. Panther family ID
  2. Date selected for concurrent annotation
  3. Date Panther family last annotated (tree annotations)
  4. Number of members
  5. Number of RefG members
  6. Number of members with EXP
  7. Date more recent member last annotated
  8. We could add 'date comprehensively annotated' for groups that can provide this information:

Please answer prior to the call: who currently captures the 'date comprehensively annotated' and could generate a file with such information.

  • GOA: Yes
  • BHF-UCL:
  • MGI: We capture this status and can generate a file with such information.
  • RGD: We don't capture that information.
  • Flybase:
  • dictyBase: Yes (we capture curation status for the entire 'gene' curation, but could use that for now)
  • TAIR: We have just started to capture this status but do not yet generate a file at this time.
  • AgBase:
  • SGD: We capture this date, but cannot generate a file at this time. We would be able to provide this date eventually.
  • pombe
  • Ecoli: EcoliWiki keeps track of the complete list of RefGenome genes in E. coli, the number of annotations for BP, MF & CC separately as well as the completion status (List). We have a category tag that goes on all genes from the RefGenome list as well (Category).
  • Wormbase:We capture the date at which we've comprehensively annotated experimental data for RefGenome genes.
  • ZFIN: I have 'comprehensively curated' dates for the ref. genome genes. However, this is becoming a less useful date since we recently stopped trying to curate ALL the papers we enter into our DB..so until we get a literature indexer (job search on now) who will associate pubs with genes, I can't really know the true status of the literature for a gene...I can only know the status of the literature we have already associated with the gene. It's still a useful date I guess, just not as air tight as it used to be.

  • Alerts:
    • Tree curators should be alerted when the Date in Column 7 (protein annotations by MODs) is more recent than the date in Column 3 (tree annotation).
    • When the Panther families are modified (once-twice per year), there should be a check to verify that the members are still the same. If there are additions or deletions: there should be an alert for curators annotations. We may be able to automate part of the required modifications to annotations.
  • Annotations to nodes: All the previous part of the script is just a report based on the trees and the GAF files. However in some cases we annotate to nodes rather to entire trees. There needs to be a way to request a report for a specific tree node. This will be done as a second step.

Branding Ref.genome annotation data in GOC and within each group

Rama started a wiki page to collect ideas. Use this page to describe how your group is branding reference genomes and to provide suggestions.
Please also take a look at ref.genome annotation data in AmiGO and provide feedback to improve those.


GO annotation camp

  1. Overview: The annotation camp will take place over 3 days, from June 16-18 (Wednesday-Friday).
  2. Goals: This annotation camp will be focused on updating and refining skills of existing GO biocurators including new GO biocurators in existing annotation groups and including the Swiss-Prot curation team. We hope members of each MOD will be represented.
  3. Structure: There will be three (3) ‘focused annotation sessions’ where specific annotation issues will be discussed. Suggestion for discussion topics should be added to the GO camp agenda: 2010_GO_camp_Meeting_Logistics#Suggestions_for_annotation_issues_to_be_discussed
  4. Deliverables: (1) final annotation documentation for each of the three annotation topics.
    • There will be a special emphasis on the reference genome project. Deliverable: (2) annotation propagation rules for the reference genome project.
  5. Registration: If you already know whether you'll be able to attend or not, please fill the wiki meeting logistics page: 2010_GO_camp_Meeting_Logistics

Back to Reference Genome Conference_Calls Page