2010 GO camp Meeting Logistics

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Revision as of 03:38, 18 March 2010 by Yasmin Alam-Faruque (talk | contribs) (Posters being presented at the camp)

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Dates

The 3rd GO annotation camp (3 days) will be held from June 16-18, 2010 (Wednesday-Friday).

Objectives

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.

  • 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.


Venue

Swiss Institute for Bioinformatics (SIB)
Centre Médical Universitaire (CMU)
1, rue Michel Servet
CH-1211 Geneva 4
Switzerland

Registration

Register by entering your name in the Attendees section below (2010_GO_camp_Meeting_Logistics#Attendees)

We anticipate a minimal registration fee to cover lunch and coffee breaks but the amount is still to be announced (depends on funding).

Lodging Information

Hotel Adriatica Hotel Adriatica
21 rue Sautter
1205 Genève - SUISSE
Tel: +41-22-703 53 83
Fax: +41-22-703 53 88

15 single rooms from 15-19 june 2010 (04 nights)
Special prize CMU 2010, single room with breakfast: CHF 190.00 (instead of CHF 256.00).
Special prize CMU 2010, double room, double occupancy with breakfast: CHF 265.00 (instead de CHF 367.00).
this offer is valid until the 31 of March 2010
3 min. walking distance from the SIB


Hotel Le Prince Hotel le Prince
16 rue des Voisins
1205 Genève - SUISSE
Tel: +41-22-807 05 00
Fax: +41-22-320 28 70

4 rooms left from the 15-19 june 2010 (04 nights)
2 double rooms: CHF 130.00
2 twin rooms: CHF 115.00
10 min. walking distance from the SIB


Hotel Les Hauts de Rive Hotel Les Hauts-de-Rive
48, Boulevard des Tranchées
1206 Genève - SUISSE
Tel: +41-22-346 29 33
Fax: +41-22-346 22 11

6 single/double rooms left from the 15-19 june 2010 (04 nights)
double rooms with breakfast: CHF 150.00
single rooms with breakfast: CHF 120.00
11 min. walking distance from the SIB


Maps and Transportation

How to find the CMU

If you arrive by plane (Cointrin airport)
BUS:
You will have to take only one bus. The bus stop is in front of the airport on the check-in level. You must have your ticket before getting onto the bus. Beware, the ticket inspectors are heartless! There are machines at every bus stop. Only one ticket is needed: choose the option "tout genève" (cost: CHF 3.- or € 1.90.-, you need the exact change).
Geneva Airport is now offering a free public transport tickets valid for 80 minutes to new arrivals. This free ticket can be taken from a machine in the baggage claim area. This ticket is only valid with your flight ticket to prove that you have arrived on that day.
So, take BUS NUMBER 5 (direction: "HÔPITAL"). The bus ride takes about 30 minutes. Get off at the bus terminus ("HÔPITAL").

All visitors staying at a hotel, can benefit from the Geneva Transport Card, with no additional cost. This personal and non-transferable pass is established upon the visitor’s check-in in the hotel, enabling its holder to use of the entire public transportation network without restriction (bus, train and boat), with validity for the entire duration of his (her) stay including the departure day.

Geneva map (Adress: 1, rue Michel Servet)


To do

Welcome to Geneva

The annual massive, city-wide festival which spans 3 days, with hundreds of musical performances will take place on the 18-20 of June. You can find a short article on the last year festival here: Geneva's Fête de la Musique 2009.

Fête de la Musique 2010 The program is not yet available.

Agenda

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#Focused annotation issues

The agenda is not yet finalized.


Focused annotation issues

Please enter your name for participation in the working groups here: 2010_GO_camp_working_groups_composition

1. Binding and complexes

1.a. Binding documentation

The binding group presented annotation policy suggestions at the last GO Consortium meeting [1] These annotation guidelines should be finalized, and a full set of annotation guidelines on how annotation data is curated and presented in GAF files should be fully documented. For instance determine:

  • that binding annotations, especially those where the GO term does not specify a particular binding partner, should where possible, indicate the interacting partner in the 'with' column
  • fully describe the usage of pipes etc in the 'with' column.
  • ask that protein binding annotations should be reciprocal - that if protein A is annotated as binding protein B, the reverse annotation should be provided

The use of column 16 to identify protein/gene targets of an molecular function GO annotation, could benefit this binding discussion.

Working group (tentative) Emily, Donghui, Yasmin, Susan, Pascale, Ruth, Fiona, Lakshmi, Li, Serenella Please confirm here: 2010_GO_camp_working_groups_composition


1.b. Annotation of complexes

  1. Can IPI be used to annotate molecular function? For example ribosomal subunits are annotated to 'structural constituent of ribosome' (a function)
  2. 'Structural components activity' function terms: some ribosome proteins are annotated to 'structural constituent of ribosome' by IDA (for example SGD:S000005760); but the paper (PMID: 18782943) only shows purification of the complex.
  3. Chromatin? See NIPBL discussion from Feb 22 jamboree. The general question is when is a protein part of a complex or organelle or when it binds to it?
  4. (Rama:) Interpretation of author statements: Authors very often use the word complex when two proteins are interacting, but there may not be enough evidence to show the existence of a stable complex. Should curators not add another layer of critiquing and request/annotate to the complex? How far should curators go with interpreting evidence and when should we let go thinking the reviewers are okay with that language, let us go with that.


Working group (tentative) Pascale, Stan, Manu, Li, Serenella

Please confirm here: 2010_GO_camp_working_groups_composition



2. Use of regulation

  • This would include process beginning/end (maybe in the context of the new signaling terms)
  • How to decide whether to annotate to 'regulates process x' or 'process x'?

Notes: How do groups decide on when to annotate to 'regulates process x' or 'process x'? For instance does SLIT regulate axon guidance or involved in the process of axon guidance? Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process. When should annotations be inherited up the regulates relationship?

Notes: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.

(Comment from Val: This is largely overlapping with the regulation issue. Where a process begins and ends is central to the decision to annotate directly to a process or to the regulation of a process )

(Comment from Pascale: 'regulation' and 'process beginning/end' have been merged now)

(Comment from Ruth: Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)

Working group (tentative) Emily, Donghui,Val, Stan, Pascale, Yasmin, Jane, Rachael, Susan, Rama, Ruth, Fiona, Lakshmi, Jodi, Serenella

Please confirm here: 2010_GO_camp_working_groups_composition


3.a Response to terms, how will these relate to signaling terms and to final cellular effect

  • Question (Pascale): Can you have a 'response to' annotation with an IDA evidence?

Working group (tentative) Varsha, Yasmin, Ruth, Becky, Manu

Please confirm here: 2010_GO_camp_working_groups_composition


3.b. How is a downstream effect defined (i.e when not to capture phenotypes )

from 22nd Feb Jamboree call [2], Tanya: It's not uncommon for the initial publications to describe a mutant phenotype, with a developmental defect, and then later publications to describe much more explicit functions or processes. You should always annotate based on whatever evidence is available. Once you've done that, the question becomes, "When do we keep or remove the phenotype-based annotations?" At TAIR, their policy is to keep the developmental terms if they think that their users would expect to see them. Some participants suggested that one would expect all orthologs to have the same development-type annotations, across organisms. Others disagreed with this expectation.

Working group (tentative) Donghui, Val, Rachael, Rama, Ruth, Fiona, Ranjana, Jodi

Please confirm here: 2010_GO_camp_working_groups_composition


Other suggestions for agenda items

  1. What is the bottle neck for manual annotations (with experimental evidence)? How can we step up manual curation? (Rama)
  2. How are the various annotating groups keeping with all the ontology development/changes (new relationships specifically)? (Rama)
  3. How to define the limits of ISS propagation from phylogenetic studies ? (Manu)
  4. How to distinguish between large-scale experiments (LSE) and specific experiments derived GO annotation ? PubMed list of LSE, additional tags ?!? (Manu)

Posters being presented at the camp

Name Organisation Title of Poster
Varsha Khodiyar BHF-UCL Process-centric annotation can lead to large-scale ontology development
Yasmin Alam-Faruque EBI The Renal Gene Ontology initiative

Attendees

Name Organization Arrival Date/Time to Airport Departure Date/Time from Airport
Rachael Huntley GOA June 15 16.35 June 18 20.05
Yasmin Alam-Faruque GOA June 15 16.35 June 18 20.05
Pascale Gaudet dictyBase
Susan Tweedie FlyBase June 15 16.35 June 18 20.05
Ruth Lovering BHF-UCL June 15 19:55 June 18 20.05
Rama Balakrishnan SGD, Stanford University
Mike Cherry SGD, Stanford University
Suzi Lewis Berkeley
Judy Blake Jackson Laboratory
Varsha Khodiyar BHF-UCL
Doug Howe ZFIN
Paul Thomas Panther

Remote Attendees

Name Organization email (needed to set up your remote access) Time Zone
Lakshmi Pillai AgBase pillai@cvm.msstate.edu
Fiona McCarthy AgBase fmccarthy@cvm.msstate.edu
Michelle Giglio Institute for Genome Sciences (IGS) mgiglio@som.umaryland.edu

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