https://wiki.geneontology.org/api.php?action=feedcontributions&user=Edith&feedformat=atomGO Wiki - User contributions [en]2024-03-28T18:19:28ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Obsoleting_an_Existing_Ontology_Term&diff=86561Obsoleting an Existing Ontology Term2024-02-12T16:34:55Z<p>Edith: /* 3. Subset usage */</p>
<hr />
<div> See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.<br />
<br />
<br />
==Check and notification procedure prior to obsoletion==<br />
<br />
===1. Annotation usage===<br />
Check if the term (or any of its children) is being used for annotation:<br />
* Go to AmiGO, search for the term, either by label or ID.<br />
* Use filters on the left to look at direct annotations, EXP annotations, ISS annotation, InterPro2GO annotations, UniProtKW, and UniRule annotations. <br />
<br />
===2. Create an [[Annotation_Review_Request]] ticket===<br />
* Create New issue in the [[https://github.com/geneontology/go-annotation go-annotation GitHub repo]]<br />
* In the body of the new issue, paste the GO term(s) IDs (1 or many) that need to be reviewed<br />
** '''Select report type using the labels:''' ( NOTE: If you dont add the label AT ISSUE CREATION it wont create the report)<br />
*** "direct_ann_to_list_of_terms": all direct EXP annotations to the terms entered<br />
*** "reg_ann_to_list_of_terms": all EXP annotations to the term entered, plus all children (including regulates children)<br />
** Wait for the report to be ran, a new link will appear in the ticket, linking the annotation report file <br />
** Copy to clipboard - best to do it from "edit" mode (for Pascale - mac + firefox)<br />
** Make a copy of the [https://docs.google.com/spreadsheets/d/1z496xuif_6RrooHLW4kKl0ob-GiZ_JPc0qd7Vv19RyE/edit#gid=0 New Annotation Review Template]<br />
** Paste annotations<br />
** And add the link to the spreadsheet in the Annotation GitHub ticket<br />
** More details about [[Annotation Review Request]]<br />
<br />
<br />
===2. Ontology usage===<br />
Check if the term is used elsewhere in the ontology:<br />
* In Protégé, go to the <code>Class Usage</code> tab to see if that ID is used elsewhere. Search for the term name or the term IRI (ie with underscore between GO and the numerical part of the ID, for example: 'GO_0030722'<br />
*If the term is a parent to other terms or is used in logical definitions, replace those uses by another term as appropriate. <br />
* Be sure that the term has not been used with a <code>replaced_by</code> or <code>consider tag</code>. If it has, update these, if possible, or remove them.<br />
===3. Subset usage===<br />
Check if the term is used in a subset: <br />
* In Protégé, look for any annotations with the <code>in_subset</code> tag. Report the information in the GitHub ticket. We don't need to announce that terms are present in the 'antislims' (do not annotate)<br />
<br />
===4. Taxon Constraints===<br />
Check to see if the term has been used in a taxon constraint:<br />
* If it has, the source file needs to be modified and the taxon constraint imports need to be regenerated. See: [[Adding_Taxon_Restrictions]]. Consider moving the taxon constraint to a parent term. <br />
===5. Cross-references===<br />
* Check if there are cross-references to Reactome, RHEA, EC, MetaCyc xref to the term. If there are, notify the various groups in the obsoletion email. <br />
* These cross-references should be removed. <br />
* There is no need to edit Reactome xrefs are imported automatically from a file supplied by Reactome.<br />
* Definition cross-references to RHEA, EC, MetaCyc should be also be removed. Replace by GOC:curators if no reference is left,<br />
<br />
===6. Notification email and go-announcement repo===<br />
* Send an email notification to <code>go-friends@mailman.stanford.edu</code><br />
* Obsoletion email template:<br />
* SUBJECT: <br />
Obsoletion notice: [GO:ID] [GO term label]<br />
* BODY: <br />
Dear all, <br />
The proposal has been made to obsolete: [GO:ID] [GO term name]. The reason for obsoletion is [ [http://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term#Possible_reasons_for_obsoletion SPECIFY] ]. <br />
There are X experimental annotations to this term by (list of impacted groups and their respective numbers of EXP and ISS annotations), see [link to Annotation Review Ticket]. <br />
There are X InterPro2GO/UniRule/UniProtKW mappings to this term. <br />
This term is included in the XXX subset(s).<br />
New or existing terms that are suggested for transferring annotations (optional).<br />
Any comments can be added to the issue: [link to GitHub ticket]. <br />
Unless objections are received by [DATE], we will assume that you agree to this change.<br />
* This last sentence is not included if there are no annotations; we then obsolete immediately. <br />
* We usually leave 7 days before obsoleting a term if there are annotations. If all annotations are fixed before the end of the 7-days period, we can go ahead with the obsoletion. <br />
* If the obsoletion involves a lot of reannotation, in this case we can leave a longer period for reannotation.<br />
* Paste the email in the corresponding GitHub ticket.<br />
* Also create a ticket in the [https://github.com/geneontology/go-announcements go-announcements GitHub repo]. Copy and paste the email notification message, and link to the original go-ontology ticket. Close the go-announcements ticket when you close the go-ontology ticket.<br />
<br />
===Possible reasons for obsoletion===<br />
<br />
# The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent. <br />
# The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model. <br />
# The reason for obsoletion is that this term represent an assay and not a GO process.<br />
# The reason for obsoletion is that this represents a phenotype. <br />
# The reason for obsoletion is that this term is equivalent to [appropriate GO term].<br />
#The reason for obsoletion is that this term represents a molecular function.<br />
# The reason for obsoletion is that this term represents a gene product.<br />
# The reason for obsoletion is that this term refers to a class of proteins. <br />
# The reason for obsoletion is that this term was added in error.<br />
# The reason for obsoletion is that more specific terms were created.<br />
# The reason for obsoletion is that this term was an unnecessary grouping term.<br />
# The reason for obsoletion is that the meaning of the term is ambiguous.<br />
# The reason for obsoletion is that is not known to be catalyzed by any gene product.<br />
# The reason for obsoletion is that it more specific than the specificity of any known gene product.<br />
# The reason for obsoletion is that there is no evidence that this function/process/component exists. <br />
<br />
<br />
====Examples====<br />
# GO:0030818 negative regulation of cAMP biosynthetic process.<br />
# GO:0072317 glucan endo-1,3-beta-D-glucosidase activity involved in ascospore release from ascus; GO:0100060 negative regulation of SREBP signaling pathway by DNA binding.<br />
# GO:0035826 rubidium ion transport<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# -<br />
# GO:0019562 L-phenylalanine catabolic process to phosphoenolpyruvate; GO:0097605 regulation of nuclear envelope permeability’; GO:0015993 molecular hydrogen transport.<br />
<br />
==Obsoletion Process in Protégé versions 5.5 and later==<br />
<br />
# Navigate to the term to be obsoleted.<br />
# [[Adding_References_to_GitHub_tickets |Add a link to the GitHub go-ontology ticket]]<br />
# Go to the menu <code>Edit</code> > <code>Deprecate entity</code><br />
# Protege will prompt you to choose a deprecation profile. Select the <code>Gene Ontology (GO)</code> option. <br />
# Protege will prompt you to enter an obsoletion comment. <br />
# Protege will prompt you to add a <code>replace_by</code> term. This is optional. <br />
# If you skip the previous step, Protege will prompt you to add one or more <code>consider</code> terms. <br />
# Protege will perform all operations required for the obsoletion.<br />
# If there is an annotation for <code>dcterms:conformsTo</code>, remove it by clicking the <code>x</code> in the top-right corner.<br />
# '''BUG''' As of July 10, the 'OBSOLETE' inserted in front of the '''term definition''' is missing the period. It needs to be added manually. (This has been reported to the Protege team [https://github.com/protegeproject/protege/issues/909]; '''temporary fix instructions are here:''' [[Protege5_5_setup_for_GO_Eds#Fix_Deprecate_Entity_functionality |Fix Protege Deprecate Entity Functionality]]).<br />
<br />
==Manual Protégé Obsoletion Process==<br />
<br />
'''There should be no need to use this procedure.'''<br />
<br />
# Navigate to the term to be obsoleted.<br />
#'''Make the status of the term obsolete:'''<br />
## In the ‘Annotations’ window, click on the + sign next to ‘Annotations’.<br />
## In the resulting pop-up window, select <code>owl:deprecated</code> from the left-hand menu.<br />
## Make sure the <code>Literal</code> tab view is selected from the right-hand tab list. Type "true" in the text box.<br />
## In the <code>Type</code> drop-down menu underneath the text box, select <code>xsd:boolean</code><br />
## Click <code>OK</code>. You should now see the term crossed out in the <code>Class hierarchy</code> view.<br />
# '''Remove equivalence axiom''': In the <code>Description</code> window, under <code>Equivalent To</code>, click the <code>x</code> on the right-hand side to delete the logical definition.<br />
# '''Remove ‘SubClass Of’ relations''': In the <code>Description</code> window, under the <code>SubClass Of</code> entry, click the <code>x</code> on the right-hand side to delete the SubClass Relation.<br />
# '''Edit Term label''': Add 'obsolete’ at the beginning of the term label: In the <code>Annotations</code> window, click on the <code>o</code> on the right-hand side of the <code>rdfs:label</code> entry to edit the term string. In the resulting window, in the <code>Literal</code> tab, in front of the term name, type: obsolete For example: 'obsolete gamma-glutamyltransferase activity'. Note the case-sensitivity. Make sure to have a space (and no other character) between ‘obsolete’ and the term label.<br />
# '''Definition''': Add ‘OBSOLETE.’ to the term definition: In the <code>Description</code> window, click on the <code>o</code> on the right-hand side of the definition entry. In the resulting window, in the <code>Literal</code> tab, at the beginning of the definition, type: 'OBSOLETE.'. For example: 'OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid.' Note the case-sensitivity.<br />
# '''Remove ‘Slims''': In the <code>OBO annotation</code> window, under the <code>Subset</code> entry, remove any slims that include the term. If there is a <code>replaced_by</code> tag on the obsolete term, add the target term to those slims. See also [[Adding_a_Term_to_a_GO_Subset_(Slim)]].<br />
# '''Obsoletion comment:''' Add a statement about why the term was made obsolete: In the <code>Annotations</code> window, select <code>+</code> to add an annotation. In the resulting menu, select <code>rdfs:comment</code> and select <code>Type: Xsd:string</code>. Standard comments should be adapted from the notification email ([[Obsoleting_an_Existing_Ontology_Term#Possible_reasons_for_obsoletion |Possible reasons for obsoletion]]), starting with 'This term was made obsolete because', and the reason. <br />
# '''Alternatives for Obsolete Terms''': <br />
#* '''Replace by''': If the obsoleted term is replaced by another term in the ontology: In the <code>Annotations</code> window, select <code>+</code> to add an annotation. In the resulting menu, select <code>term replaced by</code> and '''enter the term ID''' of the replacement term.<br />
#** '''Note''': Only one <code>replaced by</code> term can be used per obsoleted term.<br />
#* '''Consider''': If there is no single term term replacing the obsolete term, but there are terms that might be appropriate for annotation, add those term IDs in the <code>consider</code> tag: In the <code>Annotations</code> window, select <code>+</code> to add an annotation. In the resulting menu, select <code>consider</code> and '''enter the term ID''' of the replacement term.<br />
#** '''Note''': Add as many <code>consider</code> terms as needed.<br />
# Save changes.<br />
# The stanza looks like this: <br />
[Term]<br />
id: GO:0000005<br />
name: obsolete ribosomal chaperone activity<br />
namespace: molecular_function<br />
def: "OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function." [GOC:jl, PMID:12150913]<br />
comment: This term was made obsolete because it refers to a class of gene products and a biological process rather than a molecular function.<br />
synonym: "ribosomal chaperone activity" EXACT []<br />
is_obsolete: true<br />
consider: GO:0042254<br />
consider: GO:0044183<br />
consider: GO:0051082<br />
<br />
<br />
See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
== Review Status ==<br />
Last reviewed: November 22, 2022<br />
Reviewed by: Pascale Gaudet<br />
<br />
[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]<br />
<br />
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-01-08&diff=86372Ontology meeting 2024-01-082024-01-08T17:10:52Z<p>Edith: </p>
<hr />
<div>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul<br />
* '''Present:''' Pascale, Raymond, Chris, Jim, Steven, Edith, Peter, Paul T.<br />
* '''Regrets:'''<br />
<br />
=Announcements= <br />
No call next week - MLK day<br />
<br />
=Discussion points= <br />
==Objectives & Priorities for 2024==<br />
===Review design patterns===<br />
Repo: https://github.com/geneontology/go-ontology/tree/master/docs/patterns<br />
* [https://github.com/geneontology/go-ontology/labels/design%20pattern Tickets relevant to design patterns]<br />
* Fix terms that do not comply<br />
* Many issues: <br />
** transport: easiest? Can we aim to add a LD to all terms, that matches the DP of its superclass? <br />
** [https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/signaling_receptor_activity_by_input.tsv signaling receptor activity by input] >> ligand incorrectly identified as the input ([https://github.com/geneontology/go-ontology/issues/26217 GH ticket])<br />
*** Broader question: do we want all ligands as MF? Or should these move to x signal transduction, and keep a single activity, 'signaling receptor activity'? <br />
**** Noting that most 'signal transduction' (BP) children have no logical definition. How about, for example: <br />
GO:0038027 apolipoprotein A-I-mediated signaling pathway<br />
'cell surface receptor signaling pathway'<br />
and ('starts with' some 'signaling receptor activity')<br />
and ('has small molecule activator' some 'apolipoprotein A-I')<br />
* Noting also that there is no 'small molecule' in ChEBI; so any PRO is a ChEBI:chemical entity<br />
* [https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/involved_in_x_y.tsv involved_in_x_y] >> many terms should be obsoleted; which terms should remain?<br />
<br />
===Other tickets/projects===<br />
* Obsoletion single-step processes & regulation of MF<br />
* Obsoletion of MF/BP involved in BP<br />
* [https://github.com/geneontology/go-ontology/projects/40 Signaling cassettes]<br />
* Multi-organisms processes: <br />
** remove 'viral terms'<br />
** keep 'symbiont-mediated' and 'venom-mediated' xxx<br />
** finish [https://github.com/geneontology/go-ontology/projects/38 alignment with PathGO] (~ 75% done)<br />
<br />
===New term requests===<br />
<br />
<br />
[[Category:Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2023-08-28&diff=85787Ontology meeting 2023-08-282023-08-21T16:08:07Z<p>Edith: </p>
<hr />
<div>* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul<br />
* '''Present:''' Chris, Edith, Raymond, Jim, Tanya, Peter, Paul<br />
* '''Regrets:''' <br />
<br />
=Tickets to discuss= <br />
* [https://github.com/geneontology/go-ontology/issues/25933 Cell cell-signaling terms]<br />
These would replace regulates_o_occurs in? How are these modeled currently? ie how were these modeled during the MGI import into Noctua? <br />
** To replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, please add: epiblast cell-extraembryonic ectoderm cell signaling<br />
*** Single EXP to PMID:14511481<br />
** To replace "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation GO:0021937, please add: cerebellar Purkinje cell-granule cell precursor cell signaling (def: Any process that mediates the transfer of information from Purkinje cells to granule cell precursors.)<br />
*** [https://amigo.geneontology.org/amigo/term/GO:0021937 9 EXP]<br />
<br />
==[https://github.com/geneontology/go-ontology/projects/42#card-89996973 BP refactoring- development - GitHub Project]==<br />
* [https://github.com/geneontology/go-ontology/issues/22994#issuecomment-1642944291 NTR animal/ plant gross anatomical part developmental process] - Raymond<br />
* [https://github.com/geneontology/go-ontology/issues/23445 remove link between reproductive structure development and uberon reproductive structure] - Jim<br />
* [https://github.com/geneontology/go-ontology/issues/20469 missing children of post-embryonic animal organ development] <br />
<br />
==Other tickets==<br />
* [https://github.com/geneontology/go-ontology/issues/25087 GO:0044405 Detection of host - is it in scope for GO?]<br />
* [https://github.com/geneontology/go-ontology/issues/23268 proteinogenic] and [https://github.com/geneontology/go-ontology/issues/23269 non-proteinogenic amino acid biosynthesis]<br />
<br />
[[Category:Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2023-07-31&diff=85740Ontology meeting 2023-07-312023-07-31T16:08:19Z<p>Edith: </p>
<hr />
<div>* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul<br />
* '''Present:''' Raymond, Edith, Chris, Peter, David, Jim, Kimberly, Tanya<br />
* '''Regrets:''' Val, Pascale<br />
<br />
<br />
<br />
=Announcements=<br />
Pascale away: <br />
* July 31<br />
* Aug 7 (no GO calls week)<br />
* Aug 14th<br />
<br />
=Tickets to discuss= <br />
==[https://github.com/geneontology/go-ontology/projects/42#card-89996973 BP refactoring- development - GitHub Project]==<br />
* [https://github.com/geneontology/go-ontology/issues/22994#issuecomment-1642944291 NTR animal/ plant gross anatomical part developmental process] - Raymond<br />
* [https://github.com/geneontology/go-ontology/issues/23445 remove link between reproductive structure development and uberon reproductive structure] - Jim<br />
* [https://github.com/geneontology/go-ontology/issues/20469 missing children of post-embryonic animal organ development] <br />
<br />
==Other tickets==<br />
* [https://github.com/geneontology/go-ontology/issues/25087 GO:0044405 Detection of host - is it in scope for GO?]<br />
* [https://github.com/geneontology/go-ontology/issues/23268 proteinogenic] and [https://github.com/geneontology/go-ontology/issues/23269 non-proteinogenic amino acid biosynthesis]<br />
<br />
[[Category:Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Guidelines_for_database_cross_references&diff=85716Guidelines for database cross references2023-07-21T17:24:08Z<p>Edith: /* Adding database cross-reference types */</p>
<hr />
<div>We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General database cross-references. <br />
<br />
==Database cross-references==<br />
General database cross-references are links to external resources. Main resources GO links to are: <br />
<br />
* '''Cross references relevant for any term'''<br />
** Wikipedia<br />
<br />
* '''Cross references specific for Molecular Function terms'''<br />
** RHEA for enzymes (preferred). Note that RHEAs IDs that are not yet public cannot be used in definition cross-references. <br />
** EC<br />
** KEGG reaction <br />
** MetaCyc reaction<br />
** TCDB (for transporters)<br />
<br />
* '''Cross references specific for Biological Process terms'''<br />
** MetaCyc pathway<br />
** KEGG pathway<br />
<br />
<br />
<br />
* EC: GO editors can use provisional ECs. Preliminary ECs have a letter in the last section of the EC number, for e.g., 3.5.1.n3. Preliminary EC numbers can be sued as cross references and definition cross references, since they are unique like the complete ones. When they are turned into real EC numbers they are "transferred", so the new ID is traceable.<br />
* KEGG<br />
* MetaCyc<br />
* Reactome<br />
* RHEA: GO editors can use new (not yet public) RHEA IDs as database cross-references. These are filtered out from the public version of the ontology until they are available. Note that they cannot be used as definition xrefs.<br />
* TCDB for transporters (abbreviated as 'TC')<br />
<br />
=How to=<br />
==Adding a database cross-reference==<br />
* To add a cross-reference: <br />
*# In Protege, navigate to the term to which you wish to add to a database cross references'.<br />
*# In the Annotation window on the right, click on the <code>+</code> to the right of <code>Annotations</code> at the very top of the window.<br />
*# In the pop-up window that appears, select 'database_cross_reference' in the left hand window, and 'Literal' tab on the right side.<br />
*# Add cross reference ID and select 'xsd:string' as Datatype.<br />
*# Click on OK to save your edits.<br />
*# See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
==Adding database cross-reference types==<br />
Database cross-references may have a <code>type</code> (optional). Note that these do not apply to definition cross-references. The type needs to be added to have multiple cross-references from the same source.<br />
* The db xref types are derived from the [https://www.w3.org/TR/skos-reference/#mapping W3.org standards]. The types of <code>skos:mappingRelation</code> used by GO are: exactMatch, broadMatch, narrowMatch and relatedMatch.<br />
* To edit a cross-reference type:<br />
** Click on the <code>@</code> sign next to the cross-reference. <br />
** Click on the <code>+</code> sign on the right to add an annotation.<br />
** Select <code>source</code> in the left-hand menu, and <code>Literal</code> in the right-hand menu. Add the cross-reference type:<br />
*** <code>skos:exactMatch</code>: GO term meaning is exactly the same as the cross-referenced term; single EXACT or RELATED match allowed per term for any xref type<br />
*** <code>skos:broadMatch</code>: GO term meaning is narrower than that of the cross-referenced term. More than one BROAD xref is allowed per term, and BROAD xref can be mapped to multiple terms; need to add this to have multiple RHEA cross refs<br />
*** <code>skos:narrowMatch</code>: GO term meaning is more general than that of the cross-referenced term. More than one NARROW xref is allowed per term, but a given NARROW xref can only be mapped to a single term<br />
*** <code>skos:relatedMatch</code>: GO term meaning is not exactly the same as the cross-referenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type<br />
<br />
* Most Rhea cross-references are <code>skos:exactMatch</code>; but exceptions are allowed<br />
* Most EC and MetaCyc cross-references are <code>skos:narrowMatch</code> by default but can be upgraded to <code>skos:exactMatch</code> if there is a 1:1 correspondence. <br />
* Only one <code>skos:exactMatch</code> for each cross-reference source is allowed.<br />
* See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
== Review Status ==<br />
Last reviewed: August 4, 2021<br />
<br />
[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]<br />
<br />
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Guidelines_for_database_cross_references&diff=85715Guidelines for database cross references2023-07-21T17:22:22Z<p>Edith: /* Adding a database cross-reference */</p>
<hr />
<div>We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General database cross-references. <br />
<br />
==Database cross-references==<br />
General database cross-references are links to external resources. Main resources GO links to are: <br />
<br />
* '''Cross references relevant for any term'''<br />
** Wikipedia<br />
<br />
* '''Cross references specific for Molecular Function terms'''<br />
** RHEA for enzymes (preferred). Note that RHEAs IDs that are not yet public cannot be used in definition cross-references. <br />
** EC<br />
** KEGG reaction <br />
** MetaCyc reaction<br />
** TCDB (for transporters)<br />
<br />
* '''Cross references specific for Biological Process terms'''<br />
** MetaCyc pathway<br />
** KEGG pathway<br />
<br />
<br />
<br />
* EC: GO editors can use provisional ECs. Preliminary ECs have a letter in the last section of the EC number, for e.g., 3.5.1.n3. Preliminary EC numbers can be sued as cross references and definition cross references, since they are unique like the complete ones. When they are turned into real EC numbers they are "transferred", so the new ID is traceable.<br />
* KEGG<br />
* MetaCyc<br />
* Reactome<br />
* RHEA: GO editors can use new (not yet public) RHEA IDs as database cross-references. These are filtered out from the public version of the ontology until they are available. Note that they cannot be used as definition xrefs.<br />
* TCDB for transporters (abbreviated as 'TC')<br />
<br />
=How to=<br />
==Adding a database cross-reference==<br />
* To add a cross-reference: <br />
*# In Protege, navigate to the term to which you wish to add to a database cross references'.<br />
*# In the Annotation window on the right, click on the <code>+</code> to the right of <code>Annotations</code> at the very top of the window.<br />
*# In the pop-up window that appears, select 'database_cross_reference' in the left hand window, and 'Literal' tab on the right side.<br />
*# Add cross reference ID and select 'xsd:string' as Datatype.<br />
*# Click on OK to save your edits.<br />
*# See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
==Adding database cross-reference types==<br />
Database cross-references may have a <code>type</code> (optional). Note that these do not apply to definition cross-references. <br />
* The db xref types are derived from the [https://www.w3.org/TR/skos-reference/#mapping W3.org standards]. The types of <code>skos:mappingRelation</code> used by GO are: exactMatch, broadMatch, narrowMatch and relatedMatch.<br />
* To edit a cross-reference type:<br />
** Click on the <code>@</code> sign next to the cross-reference. <br />
** Click on the <code>+</code> sign on the right to add an annotation.<br />
** Select <code>source</code> in the left-hand menu, and <code>Literal</code> in the right-hand menu. Add the cross-reference type:<br />
*** <code>skos:exactMatch</code>: GO term meaning is exactly the same as the cross-referenced term; single EXACT or RELATED match allowed per term for any xref type<br />
*** <code>skos:broadMatch</code>: GO term meaning is narrower than that of the cross-referenced term. More than one BROAD xref is allowed per term, and BROAD xref can be mapped to multiple terms; need to add this to have multiple RHEA cross refs<br />
*** <code>skos:narrowMatch</code>: GO term meaning is more general than that of the cross-referenced term. More than one NARROW xref is allowed per term, but a given NARROW xref can only be mapped to a single term<br />
*** <code>skos:relatedMatch</code>: GO term meaning is not exactly the same as the cross-referenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type<br />
<br />
* Most Rhea cross-references are <code>skos:exactMatch</code>; but exceptions are allowed<br />
* Most EC and MetaCyc cross-references are <code>skos:narrowMatch</code> by default but can be upgraded to <code>skos:exactMatch</code> if there is a 1:1 correspondence. <br />
* Only one <code>skos:exactMatch</code> for each cross-reference source is allowed.<br />
* See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
== Review Status ==<br />
Last reviewed: August 4, 2021<br />
<br />
[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]<br />
<br />
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Guidelines_for_database_cross_references&diff=85714Guidelines for database cross references2023-07-21T17:20:10Z<p>Edith: /* Adding database cross-reference types */</p>
<hr />
<div>We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General database cross-references. <br />
<br />
==Database cross-references==<br />
General database cross-references are links to external resources. Main resources GO links to are: <br />
<br />
* '''Cross references relevant for any term'''<br />
** Wikipedia<br />
<br />
* '''Cross references specific for Molecular Function terms'''<br />
** RHEA for enzymes (preferred). Note that RHEAs IDs that are not yet public cannot be used in definition cross-references. <br />
** EC<br />
** KEGG reaction <br />
** MetaCyc reaction<br />
** TCDB (for transporters)<br />
<br />
* '''Cross references specific for Biological Process terms'''<br />
** MetaCyc pathway<br />
** KEGG pathway<br />
<br />
<br />
<br />
* EC: GO editors can use provisional ECs. Preliminary ECs have a letter in the last section of the EC number, for e.g., 3.5.1.n3. Preliminary EC numbers can be sued as cross references and definition cross references, since they are unique like the complete ones. When they are turned into real EC numbers they are "transferred", so the new ID is traceable.<br />
* KEGG<br />
* MetaCyc<br />
* Reactome<br />
* RHEA: GO editors can use new (not yet public) RHEA IDs as database cross-references. These are filtered out from the public version of the ontology until they are available. Note that they cannot be used as definition xrefs.<br />
* TCDB for transporters (abbreviated as 'TC')<br />
<br />
=How to=<br />
==Adding a database cross-reference==<br />
* To add a cross-reference: <br />
*# In Protege, navigate to the term to which you wish to add to a database cross references'.<br />
*# In the Annotation window on the right, click on the <code>+</code> to the right of <code>Annotations</code> at the very top of the window.<br />
*# In the pop-up window that appears, click on the synonym type you wish to add: EXACT, NARROW, BROAD or RELATED.<br />
*# In the right-hand panel enter the synonym label as a <code>Literal</code> value.<br />
*# Click on OK to save your edits.<br />
*# See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
==Adding database cross-reference types==<br />
Database cross-references may have a <code>type</code> (optional). Note that these do not apply to definition cross-references. <br />
* The db xref types are derived from the [https://www.w3.org/TR/skos-reference/#mapping W3.org standards]. The types of <code>skos:mappingRelation</code> used by GO are: exactMatch, broadMatch, narrowMatch and relatedMatch.<br />
* To edit a cross-reference type:<br />
** Click on the <code>@</code> sign next to the cross-reference. <br />
** Click on the <code>+</code> sign on the right to add an annotation.<br />
** Select <code>source</code> in the left-hand menu, and <code>Literal</code> in the right-hand menu. Add the cross-reference type:<br />
*** <code>skos:exactMatch</code>: GO term meaning is exactly the same as the cross-referenced term; single EXACT or RELATED match allowed per term for any xref type<br />
*** <code>skos:broadMatch</code>: GO term meaning is narrower than that of the cross-referenced term. More than one BROAD xref is allowed per term, and BROAD xref can be mapped to multiple terms; need to add this to have multiple RHEA cross refs<br />
*** <code>skos:narrowMatch</code>: GO term meaning is more general than that of the cross-referenced term. More than one NARROW xref is allowed per term, but a given NARROW xref can only be mapped to a single term<br />
*** <code>skos:relatedMatch</code>: GO term meaning is not exactly the same as the cross-referenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type<br />
<br />
* Most Rhea cross-references are <code>skos:exactMatch</code>; but exceptions are allowed<br />
* Most EC and MetaCyc cross-references are <code>skos:narrowMatch</code> by default but can be upgraded to <code>skos:exactMatch</code> if there is a 1:1 correspondence. <br />
* Only one <code>skos:exactMatch</code> for each cross-reference source is allowed.<br />
* See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.<br />
<br />
== Review Status ==<br />
Last reviewed: August 4, 2021<br />
<br />
[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]<br />
<br />
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2021-07-06&diff=80520Annotation Conf. Call 2021-07-062021-07-06T15:15:12Z<p>Edith: /* Attendance */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== October Consortium Meeting ===<br />
* Wednesday, October 13th - Friday, October 15th<br />
* Hosted by:<br />
** University of Maryland Medical School, Baltimore MD<br />
** Michelle Gwinn-Giglio<br />
* [https://docs.google.com/document/d/15_TIWfnu2X_3CVzdcou14PyV4Ff8F9Hz8WSASi1bsaE Agenda]<br />
<br />
=== Noctua Outages ===<br />
* Thursday, July 8th, for ontology/software updates (will now update Noctua every two weeks)<br />
* CHANGE: Friday, July 16th, (2PM - 8PM EDT) for LBL maintenance<br />
* These outages are on the GO's Google calendar<br />
* Will send notification, but please save your work!<br />
<br />
=== No GO Calls Week ===<br />
* July 11th - July 17th: no regularly scheduled GO calls<br />
<br />
== Annotation Review ==<br />
*[https://github.com/geneontology/go-annotation/issues/3817 Review annotations to GO:0070615 nucleosome-dependent ATPase]<br />
** For today's annotation call: all proteins annotated to 'GO:0070615 nucleosome-dependent ATPase' can be re-annotated to 'GO:0140658 ATP-dependent chromatin remodeler activity'. Thanks, Pascale<br />
*** FlyBase<br />
*** MGI<br />
*** RGD<br />
*** SGD<br />
*** PomBase<br />
*** UniProt<br />
*[https://github.com/geneontology/go-annotation/issues/3819 Review annotations to regulation of motor activity & children]<br />
*** AspGD<br />
*** ARUK-UCL<br />
*** UniProt (SWIS)<br />
*[https://github.com/geneontology/go-annotation/issues/3833 Review annotations to GO:0043044 ATP-dependent chromatin remodeling] <br />
*[https://github.com/geneontology/go-annotation/issues/3834 Review annotations to regulation of histone exchange and children]<br />
*[https://github.com/geneontology/go-ontology/issues/20712 Review annotations to regulation of cAMP signaling]<br />
*Others...[https://drive.google.com/drive/u/0/folders/1FDfp4yXlLZjrcB0NIbsAgUukDWDwhJe_ Annotation Review Folder on Google Drive]<br />
<br />
= Attendance =<br />
* On call: Antonia, Birgit, Cailey, Colin, David, Debby, Dmitry, Edith, Harold, Karen, Kimberly, Li, Mary, Pascale, Peter, Raymond, Seth<br />
<br />
[[Category:Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2020-06-09&diff=78290Annotation Conf. Call 2020-06-092020-06-09T15:04:43Z<p>Edith: </p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Zoom Meeting Passwords ==<br />
* Meetings now have passwords<br />
<br />
== GAF 2.2 and GPAD/GPI 2.0 ==<br />
* Check in to see if there is any additional feedback from groups<br />
<br />
== Post-meeting action items ==<br />
* Transcription annotation review<br />
* Use of 'contributes to'<br />
<br />
== MOD imports into Noctua ==<br />
* Working on GPAD 2.0 files<br />
* Working on modeling annotation metadata, comments<br />
<br />
= Attendance =<br />
* On call: Colin, David, Dmitry, Edith, Giulia, Helen, Judy, Karen, Kimberly, Laurent-Philippe, Li, Mary, Midori, Pascale, Petra, Rob, Ruth, Seth, Stacia, Stan, Tanya<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2020_Paris_GOC_Meeting_Logistics&diff=781722020 Paris GOC Meeting Logistics2020-05-07T20:43:15Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Paris , May 12th - 14th, 2020=<br />
<br />
==Location==<br />
* Virtual: Zoom, URL TBA<br />
<br />
Please register to ensure you receive the meeting URL.<br />
<br />
==GO Main Meeting Registration==<br />
* [https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 Register here]<br />
* Add your name to the list of attendees: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics#Attendees . If you can't edit the wiki, alternatively you can fill [https://forms.gle/5jJKaXj2XNLGykVH9 that form]<br />
'''Deadline:''' April 10th, or until full (max 50 people)<br />
<br />
==Optional: GO User Meeting Registration==<br />
* There will be a GO User Meeting on Monday May 11. The aim of the meeting is to present GO and discuss with local groups.<br />
* If you wish to attend the GO User Meeting, you have to [https://www.eventbrite.com/e/gene-ontology-user-meeting-registration-92720269823 register here]<br />
'''Deadline''': April 15th, or until full (max 50 people)<br />
<br />
==Attendees==<br />
Please add yourself to the table if you plan to attend! (If you don't have permission to add your name here, [https://forms.gle/5jJKaXj2XNLGykVH9 use that form])<br />
Don't forget to register and pay via [https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 Eventbrite]<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization?<br />
! GOC meeting (May 12-14)<br />
! GOC dinner (May 13)<br />
! Users Meeting (May 11)<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
|<br />
|<br />
| <br />
|<br />
|<br />
|-<br />
|Judith Blake<br />
|JAX<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Ben Good<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Deepak Unni<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| yes<br />
| yes<br />
| yes<br />
| N/A<br />
| N/A<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| yes<br />
| yes<br />
| possibly<br />
|<br />
|<br />
|-<br />
| Alan Bridge<br />
| SIB/Swiss-Prot/UniProt<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|yes<br />
|yes<br />
| no<br />
|Hôtel Aberotel Montparnasse<br />
|-<br />
|Suzi Aleksander<br />
|SGD<br />
|yes<br />
|yes<br />
|likely<br />
| <br />
| <br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Penelope Garmiri<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Alex Ignatchenko<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Maria Martin<br />
|EMBL-EBI, UniProt<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Rizwan Ishtiaq<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|David Hill<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Harold Drabkin<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Anne Morgat<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Marc Feuermann<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Patrick Masson<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Helen Attrill<br />
|FlyBase<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome NYULMC<br />
| yes<br />
| yes<br />
| yes<br />
| Eiffel Blomet<br />
| <br />
|-<br />
|Debby Siegele<br />
|OMP Texas A&M Univ.<br />
|yes, (may have to leave on May 14)<br />
|yes<br />
|yes<br />
|Hôtel Aberotel Montparnasse<br />
|<br />
|-<br />
|Rob Nash<br />
|SGD<br />
|yes<br />
|yes<br />
|no<br />
|N/A<br />
| <br />
|-<br />
|Edith Wong<br />
|SGD<br />
|yes<br />
|no<br />
|no<br />
|N/A<br />
| <br />
|-<br />
|Barbara Dunn<br />
|SGD<br />
|yes<br />
|no<br />
|no<br />
|N/A<br />
| <br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Sabrina Toro (ZFIN) will attend remotely<br />
<br>Mary Dolan (MGI) will attend remotely<br />
<br>Stacia Engel SGD will attend remotely<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2020_Paris_GOC_Meeting_Logistics&diff=781692020 Paris GOC Meeting Logistics2020-05-07T18:13:26Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Paris , May 12th - 14th, 2020=<br />
<br />
==Location==<br />
* [https://research.pasteur.fr/en/network/institut-pasteur-paris-france/#location Pasteur Institute], [https://goo.gl/maps/x5M9YR7Z3urQ8rLM9 28 Rue du Dr Roux] - Lwoff Building - Retrovirus Room.<br />
* Entrance / Security checkin and access to Retrovirus Room: [https://drive.google.com/open?id=1rinBeOdfCaQhChDNfrJOzPWSEYTsXUuS 2D view] [https://drive.google.com/open?id=1XsqfBYeZjVUUHi-zp8HomPk15pGtvREO 3D view]<br />
'''Be sure to have your current valid ID (eg passport) as it will be required to enter the institute''' !<br />
<br />
==GO Main Meeting Registration==<br />
* [https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 Register here]<br />
* Add your name to the list of attendees: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics#Attendees . If you can't edit the wiki, alternatively you can fill [https://forms.gle/5jJKaXj2XNLGykVH9 that form]<br />
'''Deadline:''' April 10th, or until full (max 50 people)<br />
<br />
==Optional: GO User Meeting Registration==<br />
* There will be a GO User Meeting on Monday May 11. The aim of the meeting is to present GO and discuss with local groups.<br />
* If you wish to attend the GO User Meeting, you have to [https://www.eventbrite.com/e/gene-ontology-user-meeting-registration-92720269823 register here]<br />
'''Deadline''': April 15th, or until full (max 50 people)<br />
<br />
==Consortium dinner May 13 at 8 PM==<br />
* We'll have a diner cruise hosted on [https://www.bateauxparisiens.com/en/practical-info.html bateaux parisiens], close to the Eiffel Tower. From Pasteur, you can take the line 6 up to the station [https://goo.gl/maps/QCQTuHsoXZc48TzQ7 Bir-Hakeim]<br />
* Full address: Bateaux Parisiens, Port de la Bourdonnais, 75007 Paris, France<br />
<br />
==Hotels==<br />
<br />
<br />
===Hotel Aberotel (recommended by Pasteur, 8mn walk) ===<br />
24 rue Blomet, 75015 Paris<br />
<br />
Email: aberotel@wanadoo.fr<br />
<br />
Phone: +33 1 40 61 70 50<br />
<br />
[https://www.aberotelparishotel.com website]<br />
<br />
<br />
===Hotel Eiffel Blomet (more modern, 12mn walk)===<br />
78 Rue Blomet, 75015 Paris, France<br />
<br />
Email: info@hoteleiffelblomet.com<br />
<br />
Phone: +33 1 53 68 70 00<br />
<br />
[https://www.hoteleiffelblomet.com website]<br />
<br />
<br />
===Hotel Concorde Montparnasse (13mn walk)===<br />
40 rue du Commandant René Mouchotte, 75014 Paris<br />
<br />
Email: reception@hotel-montparnasse.com<br />
<br />
Phone: +33 1 56 54 84 00<br />
<br />
[http://www.hotel-montparnasse.com/ website]<br />
<br />
<br />
===Hotel Louison (13mn walk)===<br />
105 rue de Vaugirard, 75006 Paris<br />
<br />
Phone: +33 1 53 63 25 50<br />
<br />
Email: welcome@louisonhotel.com<br />
<br />
[https://www.louison-hotel.com/fr website]<br />
<br />
<br />
===Hotel L'aiglon (24mn walk) ===<br />
232 bd Raspail, 75014 Paris<br />
<br />
Email: aiglon@espritdefrance.com<br />
<br />
Phone: +33 1 43 20 82 42<br />
<br />
[http://www.paris-hotel-aiglon.com/ website]<br />
<br />
<br />
==Notes on Hotels==<br />
There are a number of pretty nice apartments in Paris, so if you have time, checking [https://www.airbnb.com/s/Paris--Île-de-France--France/homes?adults=1&children=0&checkin=2020-05-12&checkout=2020-05-14&source=mc_search_bar&place_id=ChIJD7fiBh9u5kcRYJSMaMOCCwQ&click_referer=t%3ASEE_ALL%7Csid%3A9d4e0e3d-0997-4655-808c-570feaaaf297%7Cst%3ALANDING_PAGE_MARQUEE&title_type=NONE&refinement_paths%5B%5D=%2Fhomes AirBnb] could find you a gem for the same price.<br />
<br />
If you don't mind taking the metro (2 stations on line 6 from Edgard Quinet to Pasteur), [https://www.hotelsaintebeuve.com Hotel Sainte-Beuve] is also very nice and closer to the center of Paris and [https://en.wikipedia.org/wiki/Jardin_du_Luxembourg Jardin du Luxembourg]<br />
<br />
==Getting around==<br />
<br />
===Airports===<br />
From Charles de Gaulles Airport, you can go to Paris through:<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/public-transport public transport] and the "RER B" line or "le bus direct"<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/taxi/paris-cdg-taxi Taxi] for 50 / 55 euros<br />
<br />
===Public transport===<br />
Public transport (RATP) is usually very good in Paris and can get you pretty much everywhere: [https://www.ratp.fr/sites/default/files/plans-lignes/Plans-essentiels/Plan-Metro.1571994565.pdf Downloadable Map]. Metro are mostly to travel within Paris and RER, faster trains can get you to the suburban, including [https://parisbytrain.com/paris-to-chateau-versailles-by-train/ Versailles] (~ 1h).<br />
<br />
The station to get to the meeting is "Pasteur" (south west) and is deserved by both line 6 and 12. <br />
<br />
If you want more precise / up-to-date itineraries than google map, you can use the [RATP site https://www.ratp.fr/en/itineraires].<br />
<br />
===Taxi===<br />
Official Paris Taxi are easily recognizable thanks to their [https://media.timeout.com/images/100013459/1372/772/image.jpg sign], a green light indicating they are available and will stop if you call them. <br />
<br />
===Shared ride===<br />
Uber is available in Paris but not Lyft.<br />
<br />
===Bicycle===<br />
Paris also has a number of biking stations called [https://www.velib-metropole.fr/en/map#/ velib'].<br />
<br />
==Local activities==<br />
The Institut Pasteur is very close to the "Quartier Latin", a very lively part of Paris which concentrate most universities and engineering schools. The [https://en.wikipedia.org/wiki/Rue_Mouffetard rue Mouffetard] and the [https://www.google.com/maps/@48.8444538,2.3492678,3a,75y,77.02h,91.34t/data=!3m7!1e1!3m5!1sevihytHn5fwm5b4jKwbj-A!2e0!6s%2F%2Fgeo3.ggpht.com%2Fcbk%3Fpanoid%3DevihytHn5fwm5b4jKwbj-A%26output%3Dthumbnail%26cb_client%3Dsearch.revgeo_and_fetch.gps%26thumb%3D2%26w%3D96%26h%3D64%26yaw%3D24.475828%26pitch%3D0%26thumbfov%3D100!7i16384!8i8192 Place de la Contrescarpe] are typical of a Paris student life and hold many restaurants. <br />
<br />
This [https://www.discoverwalks.com/blog/10-things-to-see-in-the-latin-quarter/ article] gives some ideas of what can be seen in the area. In 25mn walk you can get to the Gardens of Luxembourg, 35mn will get you to the medieval museum of Cluny, 45mn to the island of the city with Notre Dame cathedral and the Sainte Chapelle (many classical concerts are usually available). If you prefer to use public transportation, taking the line 12 from Pasteur and line 4 from Montparnasse will get you to Saint Michel Notre Dame in 20mn. <br />
<br />
Walking along the Seine river around that area and by a sunny day is always enjoyable. Along the way, it's easy to find the Louvres, the City town hall (Hotel de Ville), the Orsay museum and the [https://www.cometoparis.com/paris-guide/paris-monuments/pont-des-arts-s959 Pont des arts] which leads to the [https://en.wikipedia.org/wiki/Institut_de_France Institut de France] where the French Academy of Science is.<br />
<br />
A one hour tour of Paris by boat is also possible on the [https://www.bateaux-mouches.fr/en/reservation/tickets bateaux mouches] for 14 euros and can be boarded at [https://goo.gl/maps/GkZn4SfyZPjmgLws9 Pont de l'Alma].<br />
<br />
<br />
==Attendees==<br />
Please add yourself to the table if you plan to attend! (If you don't have permission to add your name here, [https://forms.gle/5jJKaXj2XNLGykVH9 use that form])<br />
Don't forget to register and pay via [https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 Eventbrite]<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization?<br />
! GOC meeting (May 12-14)<br />
! GOC dinner (May 13)<br />
! Users Meeting (May 11)<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
|<br />
|<br />
| <br />
|<br />
|<br />
|-<br />
|Judith Blake<br />
|JAX<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Ben Good<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Deepak Unni<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| yes<br />
| yes<br />
| yes<br />
| N/A<br />
| N/A<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| yes<br />
| yes<br />
| possibly<br />
|<br />
|<br />
|-<br />
| Alan Bridge<br />
| SIB/Swiss-Prot/UniProt<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|yes<br />
|yes<br />
| no<br />
|Hôtel Aberotel Montparnasse<br />
|-<br />
|Suzi Aleksander<br />
|SGD<br />
|yes<br />
|yes<br />
|likely<br />
| <br />
| <br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Penelope Garmiri<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Alex Ignatchenko<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Maria Martin<br />
|EMBL-EBI, UniProt<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Rizwan Ishtiaq<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|David Hill<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Harold Drabkin<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Anne Morgat<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Marc Feuermann<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Patrick Masson<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Helen Attrill<br />
|FlyBase<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome NYULMC<br />
| yes<br />
| yes<br />
| yes<br />
| Eiffel Blomet<br />
| <br />
|-<br />
|Debby Siegele<br />
|OMP Texas A&M Univ.<br />
|yes, (may have to leave on May 14)<br />
|yes<br />
|yes<br />
|Hôtel Aberotel Montparnasse<br />
|<br />
|-<br />
|Rob Nash<br />
|SGD<br />
|yes<br />
|yes<br />
|no<br />
|N/A<br />
| <br />
|-<br />
|Edith Wong<br />
|SGD<br />
|no<br />
|no<br />
|no<br />
|N/A<br />
| <br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Sabrina Toro (ZFIN) will attend remotely<br />
<br>Mary Dolan (MGI) will attend remotely<br />
<br>Stacia Engel SGD will attend remotely<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2020_Paris_GOC_Meeting_Logistics&diff=781682020 Paris GOC Meeting Logistics2020-05-07T18:12:51Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Paris , May 12th - 14th, 2020=<br />
<br />
==Location==<br />
* [https://research.pasteur.fr/en/network/institut-pasteur-paris-france/#location Pasteur Institute], [https://goo.gl/maps/x5M9YR7Z3urQ8rLM9 28 Rue du Dr Roux] - Lwoff Building - Retrovirus Room.<br />
* Entrance / Security checkin and access to Retrovirus Room: [https://drive.google.com/open?id=1rinBeOdfCaQhChDNfrJOzPWSEYTsXUuS 2D view] [https://drive.google.com/open?id=1XsqfBYeZjVUUHi-zp8HomPk15pGtvREO 3D view]<br />
'''Be sure to have your current valid ID (eg passport) as it will be required to enter the institute''' !<br />
<br />
==GO Main Meeting Registration==<br />
* [https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 Register here]<br />
* Add your name to the list of attendees: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics#Attendees . If you can't edit the wiki, alternatively you can fill [https://forms.gle/5jJKaXj2XNLGykVH9 that form]<br />
'''Deadline:''' April 10th, or until full (max 50 people)<br />
<br />
==Optional: GO User Meeting Registration==<br />
* There will be a GO User Meeting on Monday May 11. The aim of the meeting is to present GO and discuss with local groups.<br />
* If you wish to attend the GO User Meeting, you have to [https://www.eventbrite.com/e/gene-ontology-user-meeting-registration-92720269823 register here]<br />
'''Deadline''': April 15th, or until full (max 50 people)<br />
<br />
==Consortium dinner May 13 at 8 PM==<br />
* We'll have a diner cruise hosted on [https://www.bateauxparisiens.com/en/practical-info.html bateaux parisiens], close to the Eiffel Tower. From Pasteur, you can take the line 6 up to the station [https://goo.gl/maps/QCQTuHsoXZc48TzQ7 Bir-Hakeim]<br />
* Full address: Bateaux Parisiens, Port de la Bourdonnais, 75007 Paris, France<br />
<br />
==Hotels==<br />
<br />
<br />
===Hotel Aberotel (recommended by Pasteur, 8mn walk) ===<br />
24 rue Blomet, 75015 Paris<br />
<br />
Email: aberotel@wanadoo.fr<br />
<br />
Phone: +33 1 40 61 70 50<br />
<br />
[https://www.aberotelparishotel.com website]<br />
<br />
<br />
===Hotel Eiffel Blomet (more modern, 12mn walk)===<br />
78 Rue Blomet, 75015 Paris, France<br />
<br />
Email: info@hoteleiffelblomet.com<br />
<br />
Phone: +33 1 53 68 70 00<br />
<br />
[https://www.hoteleiffelblomet.com website]<br />
<br />
<br />
===Hotel Concorde Montparnasse (13mn walk)===<br />
40 rue du Commandant René Mouchotte, 75014 Paris<br />
<br />
Email: reception@hotel-montparnasse.com<br />
<br />
Phone: +33 1 56 54 84 00<br />
<br />
[http://www.hotel-montparnasse.com/ website]<br />
<br />
<br />
===Hotel Louison (13mn walk)===<br />
105 rue de Vaugirard, 75006 Paris<br />
<br />
Phone: +33 1 53 63 25 50<br />
<br />
Email: welcome@louisonhotel.com<br />
<br />
[https://www.louison-hotel.com/fr website]<br />
<br />
<br />
===Hotel L'aiglon (24mn walk) ===<br />
232 bd Raspail, 75014 Paris<br />
<br />
Email: aiglon@espritdefrance.com<br />
<br />
Phone: +33 1 43 20 82 42<br />
<br />
[http://www.paris-hotel-aiglon.com/ website]<br />
<br />
<br />
==Notes on Hotels==<br />
There are a number of pretty nice apartments in Paris, so if you have time, checking [https://www.airbnb.com/s/Paris--Île-de-France--France/homes?adults=1&children=0&checkin=2020-05-12&checkout=2020-05-14&source=mc_search_bar&place_id=ChIJD7fiBh9u5kcRYJSMaMOCCwQ&click_referer=t%3ASEE_ALL%7Csid%3A9d4e0e3d-0997-4655-808c-570feaaaf297%7Cst%3ALANDING_PAGE_MARQUEE&title_type=NONE&refinement_paths%5B%5D=%2Fhomes AirBnb] could find you a gem for the same price.<br />
<br />
If you don't mind taking the metro (2 stations on line 6 from Edgard Quinet to Pasteur), [https://www.hotelsaintebeuve.com Hotel Sainte-Beuve] is also very nice and closer to the center of Paris and [https://en.wikipedia.org/wiki/Jardin_du_Luxembourg Jardin du Luxembourg]<br />
<br />
==Getting around==<br />
<br />
===Airports===<br />
From Charles de Gaulles Airport, you can go to Paris through:<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/public-transport public transport] and the "RER B" line or "le bus direct"<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/taxi/paris-cdg-taxi Taxi] for 50 / 55 euros<br />
<br />
===Public transport===<br />
Public transport (RATP) is usually very good in Paris and can get you pretty much everywhere: [https://www.ratp.fr/sites/default/files/plans-lignes/Plans-essentiels/Plan-Metro.1571994565.pdf Downloadable Map]. Metro are mostly to travel within Paris and RER, faster trains can get you to the suburban, including [https://parisbytrain.com/paris-to-chateau-versailles-by-train/ Versailles] (~ 1h).<br />
<br />
The station to get to the meeting is "Pasteur" (south west) and is deserved by both line 6 and 12. <br />
<br />
If you want more precise / up-to-date itineraries than google map, you can use the [RATP site https://www.ratp.fr/en/itineraires].<br />
<br />
===Taxi===<br />
Official Paris Taxi are easily recognizable thanks to their [https://media.timeout.com/images/100013459/1372/772/image.jpg sign], a green light indicating they are available and will stop if you call them. <br />
<br />
===Shared ride===<br />
Uber is available in Paris but not Lyft.<br />
<br />
===Bicycle===<br />
Paris also has a number of biking stations called [https://www.velib-metropole.fr/en/map#/ velib'].<br />
<br />
==Local activities==<br />
The Institut Pasteur is very close to the "Quartier Latin", a very lively part of Paris which concentrate most universities and engineering schools. The [https://en.wikipedia.org/wiki/Rue_Mouffetard rue Mouffetard] and the [https://www.google.com/maps/@48.8444538,2.3492678,3a,75y,77.02h,91.34t/data=!3m7!1e1!3m5!1sevihytHn5fwm5b4jKwbj-A!2e0!6s%2F%2Fgeo3.ggpht.com%2Fcbk%3Fpanoid%3DevihytHn5fwm5b4jKwbj-A%26output%3Dthumbnail%26cb_client%3Dsearch.revgeo_and_fetch.gps%26thumb%3D2%26w%3D96%26h%3D64%26yaw%3D24.475828%26pitch%3D0%26thumbfov%3D100!7i16384!8i8192 Place de la Contrescarpe] are typical of a Paris student life and hold many restaurants. <br />
<br />
This [https://www.discoverwalks.com/blog/10-things-to-see-in-the-latin-quarter/ article] gives some ideas of what can be seen in the area. In 25mn walk you can get to the Gardens of Luxembourg, 35mn will get you to the medieval museum of Cluny, 45mn to the island of the city with Notre Dame cathedral and the Sainte Chapelle (many classical concerts are usually available). If you prefer to use public transportation, taking the line 12 from Pasteur and line 4 from Montparnasse will get you to Saint Michel Notre Dame in 20mn. <br />
<br />
Walking along the Seine river around that area and by a sunny day is always enjoyable. Along the way, it's easy to find the Louvres, the City town hall (Hotel de Ville), the Orsay museum and the [https://www.cometoparis.com/paris-guide/paris-monuments/pont-des-arts-s959 Pont des arts] which leads to the [https://en.wikipedia.org/wiki/Institut_de_France Institut de France] where the French Academy of Science is.<br />
<br />
A one hour tour of Paris by boat is also possible on the [https://www.bateaux-mouches.fr/en/reservation/tickets bateaux mouches] for 14 euros and can be boarded at [https://goo.gl/maps/GkZn4SfyZPjmgLws9 Pont de l'Alma].<br />
<br />
<br />
==Attendees==<br />
Please add yourself to the table if you plan to attend! (If you don't have permission to add your name here, [https://forms.gle/5jJKaXj2XNLGykVH9 use that form])<br />
Don't forget to register and pay via [https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 Eventbrite]<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization?<br />
! GOC meeting (May 12-14)<br />
! GOC dinner (May 13)<br />
! Users Meeting (May 11)<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
|<br />
|<br />
| <br />
|<br />
|<br />
|-<br />
|Judith Blake<br />
|JAX<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Ben Good<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Deepak Unni<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| yes<br />
| yes<br />
| yes<br />
| N/A<br />
| N/A<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| yes<br />
| yes<br />
| possibly<br />
|<br />
|<br />
|-<br />
| Alan Bridge<br />
| SIB/Swiss-Prot/UniProt<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|yes<br />
|yes<br />
| no<br />
|Hôtel Aberotel Montparnasse<br />
|-<br />
|Suzi Aleksander<br />
|SGD<br />
|yes<br />
|yes<br />
|likely<br />
| <br />
| <br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Penelope Garmiri<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Alex Ignatchenko<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Maria Martin<br />
|EMBL-EBI, UniProt<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Rizwan Ishtiaq<br />
|EMBL-EBI, GOA<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|David Hill<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Harold Drabkin<br />
|MGI/GOC<br />
|yes<br />
|yes<br />
|yes<br />
|<br />
|<br />
|-<br />
|Anne Morgat<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Marc Feuermann<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Patrick Masson<br />
|SIB<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
|Helen Attrill<br />
|FlyBase<br />
|yes<br />
|yes<br />
|<br />
|<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome NYULMC<br />
| yes<br />
| yes<br />
| yes<br />
| Eiffel Blomet<br />
| <br />
|-<br />
|Debby Siegele<br />
|OMP Texas A&M Univ.<br />
|yes, (may have to leave on May 14)<br />
|yes<br />
|yes<br />
|Hôtel Aberotel Montparnasse<br />
|<br />
|-<br />
|Rob Nash<br />
|SGD<br />
|yes<br />
|yes<br />
|no<br />
|N/A<br />
| <br />
|-<br />
|Edith Wong<br />
|SGD<br />
|yes<br />
|yes<br />
|no<br />
|N/A<br />
| <br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Sabrina Toro (ZFIN) will attend remotely<br />
<br>Mary Dolan (MGI) will attend remotely<br />
<br>Stacia Engel SGD will attend remotely<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2020-05-05&diff=78144Annotation Conf. Call 2020-05-052020-05-05T15:03:25Z<p>Edith: </p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== GOC Meeting - May 2020 ==<br />
* Paris consortium meeting scheduled for May 12th - 14th will be held virtually<br />
* We are planning for four hours each day to accommodate the different time zones<br />
* [https://docs.google.com/document/d/1DTBCxib8aRwyw5IWLbYRHtPLCnmcbjUNAV1gwj_2hlo Agenda]<br />
* Users meeting - May 11th<br />
** [http://wiki.geneontology.org/index.php/2020_Remote_GO_Users_Meeting_Logistics Register for users meeting]<br />
<br />
= Attendance =<br />
* On call: Benedict, Birgit, Bob, Colin, David, Edith, Giulia, Harold, Helen, Kimberly, Laurent-Philippe, Li, Midori, Pascale, Patrick, Petra, Sabrina, Seth, Stacia, Tanya<br />
<br />
[[Category:Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=762332019 Berkeley GOC Meeting Logistics2019-09-23T17:36:50Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
** $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages). It does NOT cover any expenses for the User Meeting or the SAB meeting.<br />
* Please also fill in the fields in the [[#Attendees | Attendees list]] at the bottom of this page.<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley).<br />
* Note that food and beverages at the User Meeting are not covered by the GOC meeting registration fee--you are responsible for paying for your own food and beverages during the User Meeting.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in [https://goo.gl/maps/kFG8EPBBjWJnuy6EA Stanley Hall] on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the Potter Street meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/event-reservations/reservation-link.mi?id=1563407776453&key=GRP&app=resvlink| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the Potter Street meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the Potter Street meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the Potter Street meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details and fill out the [http://bit.ly/2019GOCBerkeleyTransportation form] so we can submit for site access in the week before the meeting.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi and fill out the [http://bit.ly/2019GOCBerkeleyTransportation form] so we can submit for site access in the week before the meeting. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==== Official and unofficial GOC dinners ====<br />
<br />
Tuesday, October 8, 5:30pm: [http://www.rottencitypizza.com/#board Rotten City Pizza], located walking distance between Potter Street and Emeryville. Beer, wine, cider, pizza, pool & darts. Pay your own way.<br />
<br />
Wednesday, October 9, 6pm: GOC meeting dinner, Stella Nonna Restaurant. Covered by registration fee.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 9, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 10, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! (If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].)<br />
Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
|<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Berkeley Inn<br />
| Yes<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Berkeley Inn <br />
| Yes<br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hotel Shattuck Plaza<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hotel Shattuck Plaza<br />
| not yet<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jeff De Pons<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| Cambridge<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airb&b<br />
| Yes<br />
|-<br />
| Felix Gondwe<br />
| SGD, Stanford<br />
| Yes<br />
| Yes <br />
| No<br />
| N/A<br />
| <br />
|-<br />
| Patrick Masson<br />
| SIB<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
| ?<br />
| ?<br />
| ?<br />
| ?<br />
| not yet<br />
|-<br />
| <br />
| <br />
| <br />
| <br />
|<br />
| <br />
| <br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Li Ni (MGI) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Stacia Engel (SGD) not attending - son on Fall Break so we're doing family stuff<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=759412019 Berkeley GOC Meeting Logistics2019-08-13T17:58:22Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
* $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages)<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): SAB Meeting, UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in Stanley Hall on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== LBL shuttle ====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. As well, the shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
If you are planning to use this shuttle, you will need to make sure that you have the appropriate LBL guest pass.<br />
<br />
==== AC Transit ====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=726952019 Cambridge GOC Meeting Logistics2019-01-18T00:32:39Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th). <br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 1 min from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.<br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=GO-CAM_Conference_Call_-_2019-01-15&diff=72672GO-CAM Conference Call - 2019-01-152019-01-15T16:28:40Z<p>Edith: /* Minutes */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda =<br />
*From 2019-01-07 annotation conference call:<br />
**Import of whole genomes<br />
***Working meeting at Berkeley the end of this month<br />
***WormBase and MGI will be the first genome annotation sets to be imported<br />
****gp2term relations<br />
****evidence and annotation extensions<br />
****search, display, editing<br />
****gpad output<br />
****overall data flow<br />
****documentation<br />
**Continued discussion of modeling questions<br />
***Annotation of protein complexes and their respective members<br />
****When to annotate to a complex vs making each individual MF just 'part of' the same process?<br />
****[https://docs.google.com/document/d/1MssCGE45H3IFHvVq9y7BUo9Brw5bIwXnOSl7efPf1fI/edit Nuclear Pores Regulate Muscle Development and Maintenance by Assembling a Localized Mef2C Complex]<br />
***Instance-level representation<br />
****When to annotate to the same 'instance' of a biological process vs different 'instances'?<br />
****Implications for curator workflow<br />
***Modeling from multiple species<br />
****Creating a model for one species when the evidence derives from experiments in multiple species<br />
****Creating models for processes that involve more than one species<br />
**Import of Reactome pathways<br />
***Glycolysis<br />
***MAPK<br />
***BMP<br />
***Wnt<br />
***ER-UPR<br />
***GPI synthesis<br />
***Size limitations and delineation of 'models'<br />
****How to 'stitch' or connect large models in a consistent manner that allows us to represent dependencies (upstream, downstream) in a biologically meaningful way that is also computationally amenable<br />
**Model manipulation<br />
***Generation and use of templates<br />
***Merging models<br />
***Copying and/or re-using annotations<br />
<br />
= Minutes =<br />
*On call: Barbara, Chris, David, Dustin, Edith, Elena, Giulia, Harold, Helen, Kimberly, Laurent-Philippe, Marie-Claire, Petra, Rob, Ruth, Sabrina, Seth, Stacia, Suzi A<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category: Annotation]] [[Category:Working Groups]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2018-10-09&diff=71710Annotation Conf. Call 2018-10-092018-10-09T15:16:04Z<p>Edith: /* Minutes */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
== GO Conference Calls ==<br />
*Tuesdays at 8am PDT<br />
**1st Tuesday: Alliance Biological Function<br />
**2nd Tuesday: GO Consortium<br />
**3rd Tuesday: Alliance Biological Function/GO-CAM Working Group<br />
**4th Tuesday: GO-CAM Working Group<br />
**5th Tuesday: ad hoc, as needed<br />
*One Zoom URL for all - https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda = <br />
<br />
== Molecular Function Refactor ==<br />
=== Distal/Proximal Promoter Binding Terms ===<br />
*Proposal: use parent term and capture binding as contextual information using SO terms<br />
<br />
== Pipeline ==<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
=== Annotation QC/QC Reports ===<br />
*New reports page: http://snapshot.geneontology.org/reports/gorule-report.html<br />
<br />
=== Reminder - Update datasets.yaml file ===<br />
*For groups that haven't already, please update your corresponding datasets.yaml file (e.g. mgi.yaml) on github to update the source URL for your annotation files<br />
*https://github.com/geneontology/go-site/tree/master/metadata/datasets<br />
**FB, Reactome, RGD, TAIR (others)<br />
*Question about UniProt ftp source for MODs<br />
<br />
===Annotation File Formats===<br />
====GPAD/GPI for Internal Consortium Annotation Exchange====<br />
*At NYC meeting in May, proposal was made that we would eventually switch to using GPAD/GPI file format for data exchange within the consortium<br />
*Reasons to switch to GPAD/GPI:<br />
**Less redundacy<br />
**Ability to use expanded set of annotation relations (gp2term)<br />
**Ability to use unique ECO identifiers instead of 3-letter GO codes<br />
**Annotation properties field - allows for capturing annotation metadata <br />
*Many groups consume GPAD (any external group using Protein2GO; groups consuming derived GPAD from GO-CAM models)<br />
*Not all groups produce a GPAD<br />
*Any barriers to moving to GPAD/GPI?<br />
*Timeline - by start of new year (2019)?<br />
<br />
== Montreal Meeting, October Wednesday, 17th - Friday, 19th ==<br />
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Logistics Logistics]<br />
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda Agenda]<br />
<br />
= Minutes =<br />
*On call: David, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Li, Liz, Marie-Claire, Midori, Pascale, Penelope, Petra, Rachael, Rob, Ruth, Sabrina, Seth, Shur-Jen, Suzi<br />
<br />
[[Category:Annotation Working Group]]<br />
Ruth</div>Edithhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Logistics&diff=712172018 Montreal GOC Meeting Logistics2018-09-05T18:52:11Z<p>Edith: /* Attendees */</p>
<hr />
<div><br />
=Start and end of meeting=<br />
* Main meeting starts on: Wednesday October 17, 8h30 AM<br />
* Meeting ends on Friday October 19th, 4 PM <br />
<br />
=Registration fee=<br />
To be announced <br />
<br />
=Meeting site=<br />
'''Université du Québec à Montreal (UQAM), Pavillon Président-Kennedy'''<br />
* 201 Avenue du Président-Kennedy, Montréal, QC H2X 3Y7<br />
* Location: https://goo.gl/V1ZrsJ<br />
<br />
=Call-in information=<br />
To be announced<br />
<br />
=Travel=<br />
<br />
remember to get a Canadian [https://www.canada.ca/en/immigration-refugees-citizenship/services/visit-canada/eta.html?utm_source=slash-eta_ave&utm_medium=short-url-en&utm_campaign=eta eTA] $7<br />
<br />
=Accommodations=<br />
<br />
Two options: Delta Hotel and Hotel Zero1<br />
<br />
==1) Delta Hotel Montreal==<br />
* https://www.marriott.com/hotels/travel/yuldb-delta-hotels-montreal/<br />
* '''Address:''' 475 President-Kennedy Avenue, Montreal, QC H3A 1J7<br />
* '''Directions to meeting venue:''' https://goo.gl/ha8fay<br />
* '''Phone:''' 1 (514) 286-1986<br />
* '''Reservation:''' Call Marriott Reservations at 1 (844) 860-3753 or use this link: <br />
https://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=UQAM%20GO%20Meeting%202018^yuldb`q78q78z`188.00`CAD`false`4`10/15/18`10/21/18`9/18/18&app=resvlink&stop_mobi=yes<br />
<br />
** Book under: UQAM GO Meeting 2018<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until Tuesday, September 18, 2018'''. <br />
* '''Cancellation policy''': Individual reservations may be cancelled up until 48 hours local time prior to arrival with no penalty. Cancellations received after this time will be subject to one night’s room & tax, applied to the credit card used to guarantee the reservation.<br />
* '''Rates for October 16th-19th (rates are valid from Oct 15th to the 20th (checkout on the 21st))'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| Single/Double<br />
| CAN $188<br />
| CAN $222<br />
|-<br />
| Triple<br />
| CAN $208 <br />
| CAN $246<br />
|-<br />
| Quad<br />
| CAN $228<br />
| CAN $270<br />
|-<br />
|}<br />
<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room (+ wires) and WiFi in all public areas<br />
* Breakfast not included<br />
* Gym<br />
* Parking available: On-site parking: CAN $ 26.50 daily; Valet parking: CAN $32 daily<br />
<br />
==2) Hotel Zero1 Montreal== <br />
* http://www.zero1-mtl.com/en/default.html<br />
* '''Address:''' 1 RenéLévesque Est Montréal QC H2X 3Z5<br />
* '''Directions to meeting venue:''' https://goo.gl/1BkxYh<br />
* '''Phone:''' 1 (514) 871-9696 / 1 (855) 301-0001<br />
* '''Reservation:''' Call the hotel at 1 (514) 871-9696 / 1 (855) 301-0001<br />
** Book under: GO meeting at UQAM<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until September 8st, 2018'''. <br />
* '''Cancellation policy''': Inform the hotel in writing 48 hours prior to arrival date. If no notice is received, a penalty of one night (including all taxes) will be charged on the credit card on file (no show). <br />
* Upon arrival of the participant at the hotel, a deposit corresponding to the total accommodation fees (including taxes) + a security deposit will be due. <br />
* '''Rates for October 16th-19th (rates are valid from Oct 13th to the 24th)'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| "Pop room" - 1 queen bed <br />
| CAN $169<br />
| CAN $200<br />
|-<br />
|}<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room and all public areas<br />
* Free local calls<br />
* Shower only<br />
* Gym (seems small)<br />
* American buffet breakfast included at the Z Tapas Lounge<br />
* Valet service available for CAN $28.00/day + applicable taxes.<br />
<br />
=Food=<br />
* World-famous Montreal bagels: [http://www.stviateurbagel.com/ St. Viateur] and [https://fairmountbagel.com/ Fairmount Bagel] (both opened 24 hours, in case you need a 3 am warm snack)<br />
* World-famous Montreal smoked meat: [http://www.schwartzsdeli.com/ Schwartzs Deli]<br />
* Poutine: [http://labanquise.com/ La Banquise] (opened 24h) and [https://www.yelp.ca/biz/chez-claudette-montr%C3%A9al Chez Claudette] (opened 24h Thu-Sat)<br />
* Croissants and Kouign-Amann: [https://www.yelp.ca/biz/au-kouign-amann-montr%C3%A9al-2 Au Kouign-Amann]<br />
* [http://dieuduciel.com/en/ Dieu du Ciel] microbrewery <br />
* [http://saintbock.com/ Saint Bock] microbrewery<br />
* [http://www.brasseriebenelux.com/ Benelux] artisanal brewery<br />
<br />
=Bicycling and walking / running=<br />
* The venue is less than 1 km away from [https://goo.gl/v5fyYq Parc Mont Royal], great for walking and running (and biking if you like small hills)<br />
* [https://goo.gl/maps/6kscfTfshhw Parc La Fontaine]<br />
* [https://www.yelp.ca/search?cflt=bikerentals&find_loc=Montreal%2C+QC Bike rental] places<br />
* If you have an afternoon, rent a bike or roller blades in the Old port and bike the Canal Lachine<br />
<br />
=To do and see=<br />
* [https://www.quartierdesspectacles.com/en/ Quartier des spectacles] (the venue is right in that neighborhood)<br />
* Rue [http://www.ruesaintdenis.ca/en/ Saint-Denis]<br />
* Boulevard [http://boulevardsaintlaurent.com/en/ Saint-Laurent] ("La Main")<br />
* [https://localfoodtours.com/montreal/10-things-to-do-in-the-mile-end-montreal/ Mile End neighbourhood] (a couple of km North/East of the venue; very trendy right now)<br />
* [http://www.oldportofmontreal.com/ Old port]<br />
* [https://www.mtl.org/en/explore/neighbourhoods/old-montreal Old Montreal]<br />
* [https://www.marchespublics-mtl.com/en/marches/jean-talon-market/ Jean Talon Market]<br />
* [https://www.marchespublics-mtl.com/en/marches/atwater-market/ Atwater Market]<br />
* [https://www.saint-joseph.org/en/ Saint Joseph's Oratory] of Mount Royal<br />
* [https://www.basiliquenotredame.ca/en Notre-Dame Basilica]<br />
* [http://espacepourlavie.ca/en/botanical-garden Botanical Garden]<br />
* [https://www.mbam.qc.ca/en/ Montreal Museum of Fine Arts]<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC dinner (Thursday 18th)? <br />
! Food restrictions<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GO Central<br />
| Yes<br />
| <br />
|-<br />
| Val Wood<br />
| PomBase<br />
| Yes<br />
| <br />
|-<br />
| Suzanna Lewis<br />
| BBOP/LBNL<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP/LBNL<br />
| Yes<br />
| Fish and vegetarian<br />
|-<br />
| Seth Carbon<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
| Deepak Unni<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
| David Hill (leaving early 10/19)<br />
| GOC/MGI<br />
| Yes? Yes :)<br />
|<br />
|-<br />
| Harold Drabkin<br />
| MGI/GO/PRO<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| MGI/GO<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Yes<br />
| Vegetarian preferred<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
|<br />
|--<br />
| Tony Sawford<br />
| EBI<br />
| Yes<br />
| <br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
|<br />
|-<br />
| Alex Ignachenko<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Sandra Orchard<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Maria Martin<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Laurent-Philippe Albou<br />
| USC / LBNL<br />
| Yes<br />
| <br />
|--<br />
| Debby Siegele<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Sandy LaBonte<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Jim Hu<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Tanya Berardini<br />
| TAIR/Phoenix<br />
| Yes<br />
|<br />
|--<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Fish and Vegetarian<br />
|--<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
|<br />
|--<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Fish and Vegetarian<br />
|--<br />
| Liz Bolton<br />
| RGD<br />
| Yes<br />
| Fish and Vegetarian<br />
|--<br />
| Paul Thomas<br />
| GOC-USC<br />
| Yes<br />
| <br />
|--<br />
| Michelle Giglio<br />
| IGS/UMB<br />
| Yes<br />
|<br />
|--<br />
| Benjamin Good<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|--<br />
| Nomi Harris<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|--<br />
| Giulia Antonazzo<br />
| FB<br />
| Yes<br />
| <br />
|--<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Yes<br />
| <br />
|--<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
|<br />
|--<br />
|}<br />
<br />
=Remote attendees=<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
|-<br />
|}<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2017-08-22&diff=64904Annotation Conf. Call 2017-08-222017-08-22T16:25:17Z<p>Edith: /* Signaling pathway reports */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda = <br />
<br />
== Cambridge Meeting, October 2-4, 2017 ==<br />
* [[2017 Cambridge GOC Meeting Logistics]]<br />
**Registration - confirm pay in cash<br />
* [[2017 Cambridge GOC Meeting Agenda]]<br />
**Poster session Monday night<br />
**Wednesday afternoon hands-on/workshop session. Suggestions:<br />
***Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.<br />
****Presentations from Val (PomBase), Mary Dolan (MGI)<br />
***Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.<br />
****Conventional annotation display as well as GO-CAM model display<br />
***Good annotation practice: phenotype vs process<br />
***Representing biologists’ view of biology<br />
****Author intent & protein domains; IDA v IC v New evidence code<br />
<br />
== 2017 Cambridge GOC Signalling Workshop, October 1, 2017 ==<br />
*[[2017 Cambridge GOC Signalling Workshop]]<br />
*Start thinking about agenda<br />
*We have four different pathways being worked on<br />
**Four presentations, and time for a wrap-up?<br />
***Summary of analysis work, followed by specific proposals?<br />
**Some of the same annotations issues are surfacing for different pathways<br />
<br />
== Signaling Project ==<br />
*Update on progress to date, github tickets<br />
**Wnt - Giulia, Helen, Kimberly<br />
***[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis]<br />
***[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets]<br />
***Annotation and Ontology Issues:<br />
****Wnts<br />
*****Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but note that this is generally an underused term<br />
******Definition:Interacts with receptors such that the proportion of receptors in the active form is increased.<br />
******For the experiments that we are annotating, it is unlikely that the assay will directly measure the “proportion of receptors in the active form”. Rather, the assay will examine an endpoint of signaling, such as activation of a TCF/LEF transcriptional reporter. Is this sufficient evidence to annotate to a 'receptor agonist activity' term? <br />
******If so, do we want more specific child terms? <br />
******Possible proposal: Add terms like 'Wnt receptor agonist activity' and 'Wnt receptor antagonist activity'<br />
******Note that we have terms like 'Wnt-activated receptor activity' to describe receptors<br />
******Is this a generally reasonable and sustainable approach for describing the molecular functions of signaling ligands and their receptors?<br />
******Related issues: look at parent terms of 'signal transducer activity' and 'receptor activator activity'. Some inconsistencies with our current annotation guidelines.<br />
*****Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common<br />
******Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology; this would be in agreement with synonyms for 'Wnt-activated receptor activity'<br />
*******Multiple frizzleds exist, but we only have a separate term for frizzled-2; 11 mouse and human frizzleds, 4 Drosophila frizzleds, 4 C. elegans frizzleds<br />
*******Only 8 experimental annotations to Frizzled-2 binding<br />
******Related proposal: Move 'smoothened binding' to be a sibling, rather than child, of 'frizzled binding' . [http://www.sciencedirect.com/science/article/pii/S0888754306001054 See: Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse] and [http://dev.biologists.org/content/130/22/5297.long Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface]<br />
*****Some annotation with terms like 'cytokine activity'<br />
******Should we have terms in the ontology like 'cytokine receptor agonist activity' as a child of 'receptor agonist activity' and 'cytokine receptor antagonist activity' as a child of 'receptor antagonist activity'<br />
******The 'cytokine' term definition in GO is very broad ("Functions to control the survival, growth, differentiation and effector function of tissues and cells.”), so annotations to Wnts fit the definition. But, do researchers really think of Wnts as cytokines?<br />
*******Some preliminary Textpresso searchers (Wnt AND cytokine) suggest that they are thought of as distinct activities.<br />
****Receptors<br />
*****Frizzleds are 7-transmembrane proteins that are class F members of the GPCR family of receptors<br />
*****Most frizzleds, however, do not appear to signal via G-proteins<br />
******Proposal: Create a specific term for Wnt-activated GPCR activity<br />
**MAPK - David H. and Sabrina<br />
***Examining gene products annotated to the process with no experimental support for known MFs<br />
***Thinking about how to define the beginning and parts of the pathway<br />
**Ca2+ Signaling<br />
***Fertilization - Penelope<br />
**GPCR - Pascale, Petra<br />
***Some ontology tickets have been addressed<br />
***Needs global annotation review<br />
***Needs GO-CAM model<br />
**Reminder - discussion on specific github tickets, not on project page<br />
<br />
= Minutes =<br />
*On call: Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Liz, Midori, Penelope, Rob, Sabrina, Shur-Jen, Stacia, Stan, Suzi, Terry<br />
<br />
== Cambridge meeting discussion ==<br />
* Oct 2-4 (M-W)<br />
* sign up now if you are going and haven't signed up yet. Final numbers are needed soon.<br />
* Registration will be paid in cash; final fee will be determined soon<br />
* Add ideas/suggestions for agenda items to the agenda page and they'll be sorted/organized later<br />
* Might be better to have small working groups/break out sessions earlier in the meeting and reports at the end of the meeting<br />
* Discussion of one of the suggested working group topics - 'Representing biologists' view of biology - discussed about what evidence shows and what biologists expect.<br />
** '''ACTION ITEM:''' Form a working group to discuss this before the Cambridge meeting. Paul, Suzi, Judy, and Karen are interested/volunteered. Before Cambridge, group should examine/discuss specific cases where curators don’t feel comfortable making an IDA annotation just based on a particular experiment; cases where people need to take more than 1 piece of evidence to make an assertion. Haven’t been consistent, try to come up with guidelines.<br />
* Meeting will be streamed; Please add name to agenda to get an estimate of who to expect remotely<br />
== Signaling pathway workshop on Oct 1==<br />
* Four pathways are being worked on; suggestion for presentations from all pathway working groups, plus a wrap up<br />
* Suggested content in presentations - analysis, summary, what led to specific proposals<br />
* Groups are experiencing similar annotation issues<br />
<br />
== Signaling pathway reports ==<br />
* Wnt pathway (Helen, Kimberly)<br />
** focusing on canonical pathway<br />
** Google docs should be accessible; please e-mail Kimberly if you can't access and want to.<br />
** Wnts - looking at MF annotations; seeing inconsistencies about how we are annotating MF<br />
*** inconsistency being defined as: given a certain assay, curators are choosing different terms<br />
*** would like to come up with guidelines for choosing terms<br />
*** cytokine - may want to work on definition or usage notes<br />
<br />
* MAPK (Sabrina)<br />
** spreadsheet with all annotations to MAPK pathway; looking at gene product annotations to process terms, but no expt evidence for MF annotations<br />
** Found some problematic annotations <br />
*** most experiments that authors report - look at phosphorylation of a member of the pathway or target; some annotations are made to MF of kinase activity<br />
** looking into examples of good papers with evidence to make annotations to the pathways, specifically to MF terms<br />
*** many have been based on sequence similarities to genes a different species; difficult to find an original paper where there is enough evidence to make MF annotation<br />
** coming up with guidelines for making MF annotations<br />
** looking at scaffold proteins - how these should be annotated, where they should be in the GO-CAM model; if they are regulating the pathway or part of the pathway<br />
** MAP kinase import into nucleus term - haven't found evidence that there is active transport into the nucleus; looking to see if we should have this term or be obsoleted<br />
** Paul has a GO-CAM example with scaffolding protein in it; will dig it up.<br />
<br />
* Sept 12 call will start with Ca2+ Signaling and GPCR<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2017-08-22&diff=64903Annotation Conf. Call 2017-08-222017-08-22T16:24:54Z<p>Edith: /* Signaling pathway workshop on Oct 1 */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda = <br />
<br />
== Cambridge Meeting, October 2-4, 2017 ==<br />
* [[2017 Cambridge GOC Meeting Logistics]]<br />
**Registration - confirm pay in cash<br />
* [[2017 Cambridge GOC Meeting Agenda]]<br />
**Poster session Monday night<br />
**Wednesday afternoon hands-on/workshop session. Suggestions:<br />
***Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.<br />
****Presentations from Val (PomBase), Mary Dolan (MGI)<br />
***Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.<br />
****Conventional annotation display as well as GO-CAM model display<br />
***Good annotation practice: phenotype vs process<br />
***Representing biologists’ view of biology<br />
****Author intent & protein domains; IDA v IC v New evidence code<br />
<br />
== 2017 Cambridge GOC Signalling Workshop, October 1, 2017 ==<br />
*[[2017 Cambridge GOC Signalling Workshop]]<br />
*Start thinking about agenda<br />
*We have four different pathways being worked on<br />
**Four presentations, and time for a wrap-up?<br />
***Summary of analysis work, followed by specific proposals?<br />
**Some of the same annotations issues are surfacing for different pathways<br />
<br />
== Signaling Project ==<br />
*Update on progress to date, github tickets<br />
**Wnt - Giulia, Helen, Kimberly<br />
***[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis]<br />
***[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets]<br />
***Annotation and Ontology Issues:<br />
****Wnts<br />
*****Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but note that this is generally an underused term<br />
******Definition:Interacts with receptors such that the proportion of receptors in the active form is increased.<br />
******For the experiments that we are annotating, it is unlikely that the assay will directly measure the “proportion of receptors in the active form”. Rather, the assay will examine an endpoint of signaling, such as activation of a TCF/LEF transcriptional reporter. Is this sufficient evidence to annotate to a 'receptor agonist activity' term? <br />
******If so, do we want more specific child terms? <br />
******Possible proposal: Add terms like 'Wnt receptor agonist activity' and 'Wnt receptor antagonist activity'<br />
******Note that we have terms like 'Wnt-activated receptor activity' to describe receptors<br />
******Is this a generally reasonable and sustainable approach for describing the molecular functions of signaling ligands and their receptors?<br />
******Related issues: look at parent terms of 'signal transducer activity' and 'receptor activator activity'. Some inconsistencies with our current annotation guidelines.<br />
*****Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common<br />
******Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology; this would be in agreement with synonyms for 'Wnt-activated receptor activity'<br />
*******Multiple frizzleds exist, but we only have a separate term for frizzled-2; 11 mouse and human frizzleds, 4 Drosophila frizzleds, 4 C. elegans frizzleds<br />
*******Only 8 experimental annotations to Frizzled-2 binding<br />
******Related proposal: Move 'smoothened binding' to be a sibling, rather than child, of 'frizzled binding' . [http://www.sciencedirect.com/science/article/pii/S0888754306001054 See: Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse] and [http://dev.biologists.org/content/130/22/5297.long Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface]<br />
*****Some annotation with terms like 'cytokine activity'<br />
******Should we have terms in the ontology like 'cytokine receptor agonist activity' as a child of 'receptor agonist activity' and 'cytokine receptor antagonist activity' as a child of 'receptor antagonist activity'<br />
******The 'cytokine' term definition in GO is very broad ("Functions to control the survival, growth, differentiation and effector function of tissues and cells.”), so annotations to Wnts fit the definition. But, do researchers really think of Wnts as cytokines?<br />
*******Some preliminary Textpresso searchers (Wnt AND cytokine) suggest that they are thought of as distinct activities.<br />
****Receptors<br />
*****Frizzleds are 7-transmembrane proteins that are class F members of the GPCR family of receptors<br />
*****Most frizzleds, however, do not appear to signal via G-proteins<br />
******Proposal: Create a specific term for Wnt-activated GPCR activity<br />
**MAPK - David H. and Sabrina<br />
***Examining gene products annotated to the process with no experimental support for known MFs<br />
***Thinking about how to define the beginning and parts of the pathway<br />
**Ca2+ Signaling<br />
***Fertilization - Penelope<br />
**GPCR - Pascale, Petra<br />
***Some ontology tickets have been addressed<br />
***Needs global annotation review<br />
***Needs GO-CAM model<br />
**Reminder - discussion on specific github tickets, not on project page<br />
<br />
= Minutes =<br />
*On call: Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Liz, Midori, Penelope, Rob, Sabrina, Shur-Jen, Stacia, Stan, Suzi, Terry<br />
<br />
== Cambridge meeting discussion ==<br />
* Oct 2-4 (M-W)<br />
* sign up now if you are going and haven't signed up yet. Final numbers are needed soon.<br />
* Registration will be paid in cash; final fee will be determined soon<br />
* Add ideas/suggestions for agenda items to the agenda page and they'll be sorted/organized later<br />
* Might be better to have small working groups/break out sessions earlier in the meeting and reports at the end of the meeting<br />
* Discussion of one of the suggested working group topics - 'Representing biologists' view of biology - discussed about what evidence shows and what biologists expect.<br />
** '''ACTION ITEM:''' Form a working group to discuss this before the Cambridge meeting. Paul, Suzi, Judy, and Karen are interested/volunteered. Before Cambridge, group should examine/discuss specific cases where curators don’t feel comfortable making an IDA annotation just based on a particular experiment; cases where people need to take more than 1 piece of evidence to make an assertion. Haven’t been consistent, try to come up with guidelines.<br />
* Meeting will be streamed; Please add name to agenda to get an estimate of who to expect remotely<br />
== Signaling pathway workshop on Oct 1==<br />
* Four pathways are being worked on; suggestion for presentations from all pathway working groups, plus a wrap up<br />
* Suggested content in presentations - analysis, summary, what led to specific proposals<br />
* Groups are experiencing similar annotation issues<br />
<br />
== Signaling pathway reports ==<br />
* Wnt pathway (Helen, Kimberly)<br />
** focusing on canonical pathway<br />
** Google docs should be accessible; please e-mail Kimberly if you can't access and want to.<br />
** Wnts - looking at MF annotations; seeing inconsistencies about how we are annotating MF<br />
*** inconsistency being defined as: given a certain assay, curators are choosing different terms<br />
*** would like to come up with guidelines for choosing terms<br />
*** cytokine - may want to work on definition or usage notes<br />
<br />
* MAPK (Sabrina)<br />
** spreadsheet with all annotations to MAPK pathway; looking at gene product annotations to process terms, but no expt evidence for MF annotations<br />
** Found some problematic annotations <br />
*** most experiments that authors report - look at phosphorylation of a member of the pathway or target; some annotations are made to MF of kinase activity<br />
** looking into examples of good papers with evidence to make annotations to the pathways, specifically to MF terms<br />
*** many have been based on sequence similarities to genes a different species; difficult to find an original paper where there is enough evidence to make MF annotation<br />
** coming up with guidelines for making MF annotations<br />
** looking at scaffold proteins - how these should be annotated, where they should be in the GO-CAM model; if they are regulating the pathway or part of the pathway<br />
** MAP kinase import into nucleus term - haven't found evidence that there is active transport into the nucleus; looking to see if we should have this term or be obsoleted<br />
** Paul has a GO-CAM example with scaffolding protein in it; will dig it up.<br />
<br />
Sept 12 call will start with Ca2+ Signaling and GPCR<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2017-08-22&diff=64902Annotation Conf. Call 2017-08-222017-08-22T16:24:44Z<p>Edith: /* Cambridge meeting discussion */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda = <br />
<br />
== Cambridge Meeting, October 2-4, 2017 ==<br />
* [[2017 Cambridge GOC Meeting Logistics]]<br />
**Registration - confirm pay in cash<br />
* [[2017 Cambridge GOC Meeting Agenda]]<br />
**Poster session Monday night<br />
**Wednesday afternoon hands-on/workshop session. Suggestions:<br />
***Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.<br />
****Presentations from Val (PomBase), Mary Dolan (MGI)<br />
***Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.<br />
****Conventional annotation display as well as GO-CAM model display<br />
***Good annotation practice: phenotype vs process<br />
***Representing biologists’ view of biology<br />
****Author intent & protein domains; IDA v IC v New evidence code<br />
<br />
== 2017 Cambridge GOC Signalling Workshop, October 1, 2017 ==<br />
*[[2017 Cambridge GOC Signalling Workshop]]<br />
*Start thinking about agenda<br />
*We have four different pathways being worked on<br />
**Four presentations, and time for a wrap-up?<br />
***Summary of analysis work, followed by specific proposals?<br />
**Some of the same annotations issues are surfacing for different pathways<br />
<br />
== Signaling Project ==<br />
*Update on progress to date, github tickets<br />
**Wnt - Giulia, Helen, Kimberly<br />
***[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis]<br />
***[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets]<br />
***Annotation and Ontology Issues:<br />
****Wnts<br />
*****Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but note that this is generally an underused term<br />
******Definition:Interacts with receptors such that the proportion of receptors in the active form is increased.<br />
******For the experiments that we are annotating, it is unlikely that the assay will directly measure the “proportion of receptors in the active form”. Rather, the assay will examine an endpoint of signaling, such as activation of a TCF/LEF transcriptional reporter. Is this sufficient evidence to annotate to a 'receptor agonist activity' term? <br />
******If so, do we want more specific child terms? <br />
******Possible proposal: Add terms like 'Wnt receptor agonist activity' and 'Wnt receptor antagonist activity'<br />
******Note that we have terms like 'Wnt-activated receptor activity' to describe receptors<br />
******Is this a generally reasonable and sustainable approach for describing the molecular functions of signaling ligands and their receptors?<br />
******Related issues: look at parent terms of 'signal transducer activity' and 'receptor activator activity'. Some inconsistencies with our current annotation guidelines.<br />
*****Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common<br />
******Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology; this would be in agreement with synonyms for 'Wnt-activated receptor activity'<br />
*******Multiple frizzleds exist, but we only have a separate term for frizzled-2; 11 mouse and human frizzleds, 4 Drosophila frizzleds, 4 C. elegans frizzleds<br />
*******Only 8 experimental annotations to Frizzled-2 binding<br />
******Related proposal: Move 'smoothened binding' to be a sibling, rather than child, of 'frizzled binding' . [http://www.sciencedirect.com/science/article/pii/S0888754306001054 See: Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse] and [http://dev.biologists.org/content/130/22/5297.long Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface]<br />
*****Some annotation with terms like 'cytokine activity'<br />
******Should we have terms in the ontology like 'cytokine receptor agonist activity' as a child of 'receptor agonist activity' and 'cytokine receptor antagonist activity' as a child of 'receptor antagonist activity'<br />
******The 'cytokine' term definition in GO is very broad ("Functions to control the survival, growth, differentiation and effector function of tissues and cells.”), so annotations to Wnts fit the definition. But, do researchers really think of Wnts as cytokines?<br />
*******Some preliminary Textpresso searchers (Wnt AND cytokine) suggest that they are thought of as distinct activities.<br />
****Receptors<br />
*****Frizzleds are 7-transmembrane proteins that are class F members of the GPCR family of receptors<br />
*****Most frizzleds, however, do not appear to signal via G-proteins<br />
******Proposal: Create a specific term for Wnt-activated GPCR activity<br />
**MAPK - David H. and Sabrina<br />
***Examining gene products annotated to the process with no experimental support for known MFs<br />
***Thinking about how to define the beginning and parts of the pathway<br />
**Ca2+ Signaling<br />
***Fertilization - Penelope<br />
**GPCR - Pascale, Petra<br />
***Some ontology tickets have been addressed<br />
***Needs global annotation review<br />
***Needs GO-CAM model<br />
**Reminder - discussion on specific github tickets, not on project page<br />
<br />
= Minutes =<br />
*On call: Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Liz, Midori, Penelope, Rob, Sabrina, Shur-Jen, Stacia, Stan, Suzi, Terry<br />
<br />
== Cambridge meeting discussion ==<br />
* Oct 2-4 (M-W)<br />
* sign up now if you are going and haven't signed up yet. Final numbers are needed soon.<br />
* Registration will be paid in cash; final fee will be determined soon<br />
* Add ideas/suggestions for agenda items to the agenda page and they'll be sorted/organized later<br />
* Might be better to have small working groups/break out sessions earlier in the meeting and reports at the end of the meeting<br />
* Discussion of one of the suggested working group topics - 'Representing biologists' view of biology - discussed about what evidence shows and what biologists expect.<br />
** '''ACTION ITEM:''' Form a working group to discuss this before the Cambridge meeting. Paul, Suzi, Judy, and Karen are interested/volunteered. Before Cambridge, group should examine/discuss specific cases where curators don’t feel comfortable making an IDA annotation just based on a particular experiment; cases where people need to take more than 1 piece of evidence to make an assertion. Haven’t been consistent, try to come up with guidelines.<br />
* Meeting will be streamed; Please add name to agenda to get an estimate of who to expect remotely<br />
== Signaling pathway workshop on Oct 1==<br />
** Four pathways are being worked on; suggestion for presentations from all pathway working groups, plus a wrap up<br />
** Suggested content in presentations - analysis, summary, what led to specific proposals<br />
** Groups are experiencing similar annotation issues<br />
<br />
== Signaling pathway reports ==<br />
* Wnt pathway (Helen, Kimberly)<br />
** focusing on canonical pathway<br />
** Google docs should be accessible; please e-mail Kimberly if you can't access and want to.<br />
** Wnts - looking at MF annotations; seeing inconsistencies about how we are annotating MF<br />
*** inconsistency being defined as: given a certain assay, curators are choosing different terms<br />
*** would like to come up with guidelines for choosing terms<br />
*** cytokine - may want to work on definition or usage notes<br />
<br />
* MAPK (Sabrina)<br />
** spreadsheet with all annotations to MAPK pathway; looking at gene product annotations to process terms, but no expt evidence for MF annotations<br />
** Found some problematic annotations <br />
*** most experiments that authors report - look at phosphorylation of a member of the pathway or target; some annotations are made to MF of kinase activity<br />
** looking into examples of good papers with evidence to make annotations to the pathways, specifically to MF terms<br />
*** many have been based on sequence similarities to genes a different species; difficult to find an original paper where there is enough evidence to make MF annotation<br />
** coming up with guidelines for making MF annotations<br />
** looking at scaffold proteins - how these should be annotated, where they should be in the GO-CAM model; if they are regulating the pathway or part of the pathway<br />
** MAP kinase import into nucleus term - haven't found evidence that there is active transport into the nucleus; looking to see if we should have this term or be obsoleted<br />
** Paul has a GO-CAM example with scaffolding protein in it; will dig it up.<br />
<br />
Sept 12 call will start with Ca2+ Signaling and GPCR<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2017-08-22&diff=64901Annotation Conf. Call 2017-08-222017-08-22T16:24:07Z<p>Edith: /* Minutes */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda = <br />
<br />
== Cambridge Meeting, October 2-4, 2017 ==<br />
* [[2017 Cambridge GOC Meeting Logistics]]<br />
**Registration - confirm pay in cash<br />
* [[2017 Cambridge GOC Meeting Agenda]]<br />
**Poster session Monday night<br />
**Wednesday afternoon hands-on/workshop session. Suggestions:<br />
***Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.<br />
****Presentations from Val (PomBase), Mary Dolan (MGI)<br />
***Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.<br />
****Conventional annotation display as well as GO-CAM model display<br />
***Good annotation practice: phenotype vs process<br />
***Representing biologists’ view of biology<br />
****Author intent & protein domains; IDA v IC v New evidence code<br />
<br />
== 2017 Cambridge GOC Signalling Workshop, October 1, 2017 ==<br />
*[[2017 Cambridge GOC Signalling Workshop]]<br />
*Start thinking about agenda<br />
*We have four different pathways being worked on<br />
**Four presentations, and time for a wrap-up?<br />
***Summary of analysis work, followed by specific proposals?<br />
**Some of the same annotations issues are surfacing for different pathways<br />
<br />
== Signaling Project ==<br />
*Update on progress to date, github tickets<br />
**Wnt - Giulia, Helen, Kimberly<br />
***[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis]<br />
***[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets]<br />
***Annotation and Ontology Issues:<br />
****Wnts<br />
*****Some annotation of activating Wnts to 'receptor agonist activity' (synonym: receptor ligand activity), but note that this is generally an underused term<br />
******Definition:Interacts with receptors such that the proportion of receptors in the active form is increased.<br />
******For the experiments that we are annotating, it is unlikely that the assay will directly measure the “proportion of receptors in the active form”. Rather, the assay will examine an endpoint of signaling, such as activation of a TCF/LEF transcriptional reporter. Is this sufficient evidence to annotate to a 'receptor agonist activity' term? <br />
******If so, do we want more specific child terms? <br />
******Possible proposal: Add terms like 'Wnt receptor agonist activity' and 'Wnt receptor antagonist activity'<br />
******Note that we have terms like 'Wnt-activated receptor activity' to describe receptors<br />
******Is this a generally reasonable and sustainable approach for describing the molecular functions of signaling ligands and their receptors?<br />
******Related issues: look at parent terms of 'signal transducer activity' and 'receptor activator activity'. Some inconsistencies with our current annotation guidelines.<br />
*****Some annotation with 'frizzled binding' or 'frizzled-2 binding'; annotation to a frizzled binding term is more common<br />
******Proposal: Merge frizzled-2 binding into frizzled binding to reduce a gene product-specific term in the ontology; this would be in agreement with synonyms for 'Wnt-activated receptor activity'<br />
*******Multiple frizzleds exist, but we only have a separate term for frizzled-2; 11 mouse and human frizzleds, 4 Drosophila frizzleds, 4 C. elegans frizzleds<br />
*******Only 8 experimental annotations to Frizzled-2 binding<br />
******Related proposal: Move 'smoothened binding' to be a sibling, rather than child, of 'frizzled binding' . [http://www.sciencedirect.com/science/article/pii/S0888754306001054 See: Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse] and [http://dev.biologists.org/content/130/22/5297.long Wnts and Hedgehogs: lipid-modified proteins and similarities in signaling mechanisms at the cell surface]<br />
*****Some annotation with terms like 'cytokine activity'<br />
******Should we have terms in the ontology like 'cytokine receptor agonist activity' as a child of 'receptor agonist activity' and 'cytokine receptor antagonist activity' as a child of 'receptor antagonist activity'<br />
******The 'cytokine' term definition in GO is very broad ("Functions to control the survival, growth, differentiation and effector function of tissues and cells.”), so annotations to Wnts fit the definition. But, do researchers really think of Wnts as cytokines?<br />
*******Some preliminary Textpresso searchers (Wnt AND cytokine) suggest that they are thought of as distinct activities.<br />
****Receptors<br />
*****Frizzleds are 7-transmembrane proteins that are class F members of the GPCR family of receptors<br />
*****Most frizzleds, however, do not appear to signal via G-proteins<br />
******Proposal: Create a specific term for Wnt-activated GPCR activity<br />
**MAPK - David H. and Sabrina<br />
***Examining gene products annotated to the process with no experimental support for known MFs<br />
***Thinking about how to define the beginning and parts of the pathway<br />
**Ca2+ Signaling<br />
***Fertilization - Penelope<br />
**GPCR - Pascale, Petra<br />
***Some ontology tickets have been addressed<br />
***Needs global annotation review<br />
***Needs GO-CAM model<br />
**Reminder - discussion on specific github tickets, not on project page<br />
<br />
= Minutes =<br />
*On call: Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Liz, Midori, Penelope, Rob, Sabrina, Shur-Jen, Stacia, Stan, Suzi, Terry<br />
<br />
== Cambridge meeting discussion ==<br />
* Oct 2-4 (M-W)<br />
* sign up now if you are going and haven't signed up yet. Final numbers are needed soon.<br />
* Registration will be paid in cash; final fee will be determined soon<br />
* Add ideas/suggestions for agenda items to the agenda page and they'll be sorted/organized later<br />
* Might be better to have small working groups/break out sessions earlier in the meeting and reports at the end of the meeting<br />
* Discussion of one of the suggested working group topics - 'Representing biologists' view of biology - discussed about what evidence shows and what biologists expect.<br />
** '''ACTION ITEM:''' Form a working group to discuss this before the Cambridge meeting. Paul, Suzi, Judy, and Karen are interested/volunteered. Before Cambridge, group should examine/discuss specific cases where curators don’t feel comfortable making an IDA annotation just based on a particular experiment; cases where people need to take more than 1 piece of evidence to make an assertion. Haven’t been consistent, try to come up with guidelines.<br />
* Meeting will be streamed; Please add name to agenda to get an estimate of who to expect remotely<br />
* Signaling pathway workshop on Oct 1<br />
** Four pathways are being worked on; suggestion for presentations from all pathway working groups, plus a wrap up<br />
** Suggested content in presentations - analysis, summary, what led to specific proposals<br />
** Groups are experiencing similar annotation issues<br />
<br />
== Signaling pathway reports ==<br />
* Wnt pathway (Helen, Kimberly)<br />
** focusing on canonical pathway<br />
** Google docs should be accessible; please e-mail Kimberly if you can't access and want to.<br />
** Wnts - looking at MF annotations; seeing inconsistencies about how we are annotating MF<br />
*** inconsistency being defined as: given a certain assay, curators are choosing different terms<br />
*** would like to come up with guidelines for choosing terms<br />
*** cytokine - may want to work on definition or usage notes<br />
<br />
* MAPK (Sabrina)<br />
** spreadsheet with all annotations to MAPK pathway; looking at gene product annotations to process terms, but no expt evidence for MF annotations<br />
** Found some problematic annotations <br />
*** most experiments that authors report - look at phosphorylation of a member of the pathway or target; some annotations are made to MF of kinase activity<br />
** looking into examples of good papers with evidence to make annotations to the pathways, specifically to MF terms<br />
*** many have been based on sequence similarities to genes a different species; difficult to find an original paper where there is enough evidence to make MF annotation<br />
** coming up with guidelines for making MF annotations<br />
** looking at scaffold proteins - how these should be annotated, where they should be in the GO-CAM model; if they are regulating the pathway or part of the pathway<br />
** MAP kinase import into nucleus term - haven't found evidence that there is active transport into the nucleus; looking to see if we should have this term or be obsoleted<br />
** Paul has a GO-CAM example with scaffolding protein in it; will dig it up.<br />
<br />
Sept 12 call will start with Ca2+ Signaling and GPCR<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=645042017 Cambridge GOC Meeting Logistics2017-07-18T18:17:08Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
===Arriving===<br />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
<br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk <br />
** To book phone +44 (0)1223 351631. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=645032017 Cambridge GOC Meeting Logistics2017-07-18T18:16:43Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
===Arriving===<br />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
<br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk <br />
** To book phone +44 (0)1223 351631. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=645022017 Cambridge GOC Meeting Logistics2017-07-18T18:16:06Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
===Arriving===<br />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|_<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
<br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk <br />
** To book phone +44 (0)1223 351631. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=645012017 Cambridge GOC Meeting Logistics2017-07-18T18:15:40Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
===Arriving===<br />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|_<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
<br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk <br />
** To book phone +44 (0)1223 351631. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=636832017 Corvallis GOC Meeting Agenda2017-05-01T15:51:04Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this? <br />
<br />
==Update on Ontology Editing==<br />
<br />
David + Chris 20min<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations? <br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=636582017 Corvallis GOC Meeting Agenda2017-04-27T15:50:31Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this? <br />
<br />
==Introduction to Ontology Editing (David, Chris)==<br />
*How are new terms added?<br />
<br />
==MF refactoring (Paul, David) ==<br />
<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Pascale & Sylvain<br />
See notes /list of papers: <br />
<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
<br />
<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations? <br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| <br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=636572017 Corvallis GOC Meeting Agenda2017-04-27T15:50:10Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this? <br />
<br />
==Introduction to Ontology Editing (David, Chris)==<br />
*How are new terms added?<br />
<br />
==MF refactoring (Paul, David) ==<br />
<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Pascale & Sylvain<br />
See notes /list of papers: <br />
<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
<br />
<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations? <br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=636562017 Corvallis GOC Meeting Agenda2017-04-27T15:49:48Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this? <br />
<br />
==Introduction to Ontology Editing (David, Chris)==<br />
*How are new terms added?<br />
<br />
==MF refactoring (Paul, David) ==<br />
<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Pascale & Sylvain<br />
See notes /list of papers: <br />
<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
<br />
<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations? <br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Logistics&diff=618752016 Los Angeles GOC Meeting Logistics2016-09-27T16:36:06Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Los Angeles, November 4-6, 2016=<br />
<br />
* Location: <br />
** University of Southern California<br />
<br />
==Registration==<br />
Registration site not available yet.<br />
<br />
==Consortium dinner Friday November 4==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday November 4''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday November 5''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Sunday November 6''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
*'''Monday November 7''': <br />
:* Noctua training workshop will run from 9 am to 3 pm<br />
<br />
==Meeting Venue and Directions==<br />
* University of Southern California, Ray I. Irani Hall, room 101.<br />
<br />
===Arriving===<br />
<br />
<br />
===Meeting Dinner===<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you planning to attend the Noctua/LEGO workshop the day after the meeting, Monday, November 7th?<br />
|-<br />
| Shur-Jen Wang<br />
| Rat Genome Database<br />
| Yes<br />
|<br />
| Yes<br />
<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
|<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|Yes<br />
|<br />
|Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|Yes<br />
|Yes<br />
|Yes<br />
|-<br />
| Mike Cherry<br />
| Stanford<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
|Yes<br />
|<br />
|Yes<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
| Yes<br />
|<br />
| No (previously organized meeting)<br />
|-<br />
| Seth Carbon<br />
| LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WB, Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes (note food: vegetarian or fish only)<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR<br />
| No<br />
|<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|<br />
|<br />
|Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
|Yes<br />
|Yes<br />
|No<br />
|-<br />
| David Hill<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Not sure<br />
|-<br />
| Karen Christie<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Mary Dolan<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
| Li Ni<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Fiona McCarthy<br />
| AgBase<br />
| No<br />
|<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| No<br />
|Yes (note: vegetarian or fish only)<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Olivia Lang<br />
| SGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
|<br />
| No<br />
|-<br />
|-<br />
| Helen Parkinson<br />
| EBI<br />
| No<br />
|<br />
| No<br />
|-<br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| Yes<br />
|<br />
| No (It's my daughter's birthday!)<br />
|-<br />
|-<br />
| Val Wood<br />
| PomBase<br />
| No<br />
|<br />
| No<br />
|-<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
|<br />
| Yes<br />
|-<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| <br />
|<br />
| No<br />
|-<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| <br />
|<br />
| No<br />
|-<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| <br />
|<br />
| Yes<br />
|-<br />
|-<br />
| Jim Hu<br />
| TAMU<br />
|<br />
|<br />
|<br />
|-<br />
|-<br />
| Debby Siegele<br />
| TAMU<br />
|<br />
| <br />
| No<br />
|-<br />
| Jim Balhoff<br />
| RTI<br />
| Yes<br />
|<br />
| Yes<br />
|- <br />
|Xiaosong Huang<br />
| USC<br />
| Yes<br />
|<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB <br />
|Yes<br />
|<br />
|Yes<br />
|-<br />
| Chris Grove<br />
| WB<br />
| No<br />
| No<br />
| Yes<br />
|-<br />
| Raymond Lee<br />
| WB<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
|}<br />
<br />
NOT attending:<br />
<br />
Moni Munoz-Torres - Previous commitment to attend http://www.icg-11.org/<br />
<br />
Melanie Courtot<br />
<br />
Paola Roncaglia<br />
<br />
==Accommodations==<br />
* PLEASE BOOK USING CODE "GOCON" BY OCTOBER 13 TO ENSURE RATE<br />
* Make hotel reservations with your personal access code “GOCON” either <br />
** online https://www.radisson.com/los-angeles-hotel-ca-90007/cafiguer<br />
** by phone +1.800.333.3333<br />
* We have arranged for a group rate at the Radisson Hotel across the street from the USC campus.<br />
* Make sure to book by October 13, as there may be no availability after that date<br />
** the weekend of November 5-6 there will be two big football games at the Coliseum<br />
* Individuals will pay on own for all charges<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Logistics&diff=614282016 Los Angeles GOC Meeting Logistics2016-08-12T17:27:36Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Los Angeles, November 4-6, 2016=<br />
<br />
* Location: <br />
** University of Southern California<br />
<br />
==Registration==<br />
Registration site not available yet.<br />
<br />
==Consortium dinner Friday November 4==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday November 4''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday November 5''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Sunday November 6''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* University of Southern California, Ray I. Irani Hall, room 101.<br />
<br />
===Arriving===<br />
<br />
<br />
===Meeting Dinner===<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Would you be able to attend an adjoining Noctua/LEGO workshop the day before the meeting?<br />
! The day after?<br />
|-<br />
| Shur-Jen Wang<br />
| Rat Genome Database<br />
| Yes<br />
|<br />
<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|No<br />
|Yes<br />
|-<br />
| Mike Cherry<br />
| Stanford<br />
|<br />
|<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
|<br />
|<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
|<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
| Yes<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WB, Caltech<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
|<br />
|<br />
|-<br />
| Leonore Reiser<br />
| TAIR<br />
|<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| The Jackson Laboratory<br />
| No<br />
| Yes<br />
|-<br />
| Fiona McCarthy<br />
| AgBase<br />
| No<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| No<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Yes<br />
| No<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|-<br />
|}<br />
<br />
NOT attending:<br />
<br />
Moni Munoz-Torres - Previous commitment to attend http://www.icg-11.org/<br />
<br />
Melanie Courtot<br />
<br />
Paola Roncaglia<br />
<br />
==Accommodations==<br />
* We will arrange for a group rate at the Radisson Hotel across the street from the campus. Stay tuned for details.<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Logistics&diff=614272016 Los Angeles GOC Meeting Logistics2016-08-12T17:26:34Z<p>Edith: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Los Angeles, November 4-6, 2016=<br />
<br />
* Location: <br />
** University of Southern California<br />
<br />
==Registration==<br />
Registration site not available yet.<br />
<br />
==Consortium dinner Friday November 4==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday November 4''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday November 5''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Sunday November 6''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* University of Southern California, Ray I. Irani Hall, room 101.<br />
<br />
===Arriving===<br />
<br />
<br />
===Meeting Dinner===<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Would you be able to attend an adjoining Noctua/LEGO workshop the day before the meeting?<br />
! The day after?<br />
|-<br />
| Shur-Jen Wang<br />
| Rat Genome Database<br />
| Yes<br />
|<br />
<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|No<br />
|Yes<br />
|-<br />
| Mike Cherry<br />
| Stanford<br />
|<br />
|<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
|<br />
|<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
|<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
| Yes<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WB, Caltech<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
|<br />
|<br />
|-<br />
| Leonore Reiser<br />
| TAIR<br />
|<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| The Jackson Laboratory<br />
| No<br />
| Yes<br />
|<br />
|-<br />
| Fiona McCarthy<br />
| AgBase<br />
| No<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| No<br />
| Yes<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Yes<br />
| No<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|-<br />
<br />
|}<br />
<br />
NOT attending:<br />
<br />
Moni Munoz-Torres - Previous commitment to attend http://www.icg-11.org/<br />
<br />
Melanie Courtot<br />
<br />
Paola Roncaglia<br />
<br />
==Accommodations==<br />
* We will arrange for a group rate at the Radisson Hotel across the street from the campus. Stay tuned for details.<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_February_10,_2015&diff=56008Annotation Conf. Call, February 10, 20152015-02-10T17:35:49Z<p>Edith: /* Demo of CalTech annotation tool */</p>
<hr />
<div><br />
<br />
=Agenda=<br />
<br />
==Jenkins reports==<br />
http://build.berkeleybop.org/view/GAF/<br />
<br />
==RNA Central==<br />
Please send the identifiers for RNA gene products that is being used internally by your MOD for GO annotation. This will provide the initial mappings so that we can then switch over to using the RNACentral IDs. Contact RNA Central using this form - http://rnacentral.org/contact<br />
<br />
==Demo of CalTech annotation tool==<br />
We will use CalTech's annotation tool for our curation consistency exercises. This tool allows us to highlight a sentence and enter specific GO terms/evidence etc. Kimberly will give a demo of how it works. If you want an account in this tool, please put your name down here on this wiki page so Kimberly can send one email to her programmer requesting for accounts.<br />
* Petra<br />
* Val<br />
* Bob<br />
* Aleks (EBI)<br />
* Penelope (EBI)<br />
* Dmitry (MGI)<br />
* David H (MGI)<br />
* Stacia (SGD)<br />
* Tanya (TAIR)<br />
* Donghui (TAIR)<br />
* Leonore (TAIR)<br />
* Doug (ZFIN)<br />
* Sabrina (ZFIN)<br />
* Edith (SGD)<br />
<br />
==Annotation Consistency Exercise - February 24, 2015==<br />
Here is a link to the paper that I've chosen for the first annotation consistency exercise/discussion:<br />
<br />
http://www.ncbi.nlm.nih.gov/pubmed/25569233<br />
<br />
It describes studies on C. elegans bcl-7 (http://www.wormbase.org/species/c_elegans/gene/WBGene00016192) and human BCL7B (http://www.uniprot.org/uniprot/Q9BQE9).<br />
<br />
The main thing I'd like to focus on for the annotation exercise is what Biological Process annotations curators make, noting that, at the moment, the all-encompassing Biological Process terms might not yet exist for what is described in the paper. In particular, I'd like to discuss annotating to a process vs. regulation of a process, and the use of annotation extensions to provide more context for the BP terms. <br />
<br />
I don't want people to get too hung up on the C. elegans biology, but I've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:<br />
*Seam cells<br />
**http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm<br />
**http://www.wormatlas.org/hermaphrodite/seam%20cells/Images/Seamfig3leg.htm<br />
*Egl phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000006<br />
*Pvl phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000697<br />
*Burst phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000038<br />
*Alae morphology phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0001412<br />
<br />
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype. This is fairly typical.<br />
<br />
--Kimberly<br />
<br />
<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>Edithhttps://wiki.geneontology.org/index.php?title=2013_Bar_Harbor_Logistics&diff=461682013 Bar Harbor Logistics2013-09-18T02:54:50Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Dates=<br />
<br />
The Fall 2013 GO Consortium meeting will be held October 4-6, in Bar Harbor, ME. On the 3rd, we are considering scheduling a few small working-group sessions. Communication about this meeting will be done via the GO-list. If you are not registered for the GO-list please do so. [https://mailman.stanford.edu/mailman/listinfo/go-consortium GO mailing list subscription]<br />
<br />
=Agenda=<br />
<br />
* [[2013 Bar Harbor GOC Meeting Agenda]]<br />
<br />
=Meeting information=<br />
<br />
==Venue==<br />
<br />
The meeting will be held in the [http://www.barharborclub.com/ Bar Harbor Club]. The primary meeting hotel, Harborside Hotel, is next door to the Bar Harbor Club; both located in downtown Bar Harbor.<br />
<br />
==Lodging Information==<br />
<br />
[http://www.theharborsidehotel.com/ Harborside Hotel] (downtown BHB, next to meeting venue) for rooms (set aside for 3 nights, Thu, Fri Sat)<br />
<br />
* Two double bed $239.<br />
* Premium King $209.<br />
* Deluxe King $229.<br />
* Premium King $229.<br />
<br />
'''Booking'''<br />
<br />
Online registration code: GOC13; otherwise call 1-800-288-5033<br />
<br />
<br />
<br />
[http://www.barharborregency.com/ Bar Harbor Regency]<br />
<br />
* $149 / night<br />
<br />
'''Booking'''<br />
Online registration code: JLG; or call 1-800-234-6835<br />
<br />
Please book your rooms when you register so we know we have enough rooms.<br />
<br />
==Airports==<br />
<br />
[http://www.flybangor.com/ Bangor International Airport] - This is the nearest airport that is served by USAirways and Delta airlines. See shuttle service below. We hope to co-ordinate shuttle service. <br />
<br />
[http://www.bhbairport.com/ Hancock County - Bar Harbor Airport] - This is the closest airport. However, only small planes from Boston fly to it (Cape Air, Penn Air).<br />
These flights come in from Terminal C (Jet Blue, United).<br />
<br />
==Ground transportation== <br />
<br />
[http://www.barharborbangorshuttle.com/ Bar Harbor Shuttle LLC] - Bar Harbor Shuttle LLC is located in Bar Harbor and makes at least 4 round-trip runs to Bangor on a daily basis between June and October. They are not usually able to provide a departure from Bangor any earlier than 11:30 (but call to be sure). Bangor to Bar Harbor costs $40 one say and they offer discounted rates for round-trip tickets and Group Rates for 3 or more on the same reservation. Phone: 207-479-5911<br />
<br />
[http://atyourservicetaxi.com/ At Your Service Taxi] - operates 24 hours a day, seven days a week, year-round and accepts most major credit cards and reservations. Great for local transit around Bar Harbor. Will also pick up/drop off at Bangor Airport; cost one way is $95. Phone: 207-288-9222<br />
<br />
[http://www.barharborcoastalcab.com/fare-details.html Bar Harbor Coastal Cab] - charges a flat rate for rides. When you call, they tell you exactly how much it is from where you are to where you want to go. Does local transit around Bar Harbor, and also does taxi tours of the island or Acadia NP. Will also pick up/drop off at Bangor Airport; cost one way is between $90-100, depending on time of year. Phone: 207-288-1222<br />
<br />
==Registration==<br />
<br />
<br />
Please fill in the [[#Attendees|Attendees table]] below.<br />
<br />
* Registration fee: $150.00 US<br />
includes conference dinner<br />
<br />
<br />
Please be prepared to pay in US dollars at the meeting.<br />
For other arrangements, please contact <br />
Annie McDonnell, 1-207-288-6885<br />
annie.mcdonnell at jax.org<br />
<br />
Remote attendees please register on the table.<br />
<br />
==Remote Attendees==<br />
<br />
For audio and visual we will be using GoToMeeting. An invite will be sent to the GO list and you will need to download the software to join the meeting.<br />
<br />
==Conference Dinner==<br />
<br />
Conference Dinner will be held at 5:30 pm on Friday night Oct 4 at Cafe This Way. <br><br />
Cafe This Way is within walking distance of the meeting venue.<br />
<br />
* [http://www.cafethisway.com/menus.html Cafe This Way]<br />
<br />
==Contacts==<br />
<br />
Judy Blake (judith.blake at jax.org)<br><br />
Harold Drabkin (harold.drabkin at jax.org)<br><br />
Annie McDonnell (annie.mcdonnell at jax.org)<br />
<br />
= Local Information =<br />
<br />
==Restaurants==<br />
<br />
* [http://www.2catsbarharbor.com/menu.html Two Cats] (breakfast & lunch)<br />
* [http://www.cafethisway.com/menus.html Cafe This Way] (breakfast & dinner)<br />
* [http://www.geddys.com/ Geddys] [http://www.geddys.com/geddycams/videocam/ Check out downtown Bar Harbor on the Geddy Cam!]<br />
* [http://www.sidestreetbarharbor.com/menu.html Side Street Cafe]<br />
* [http://www.mckayspublichouse.com/index.php Macay's Public House]<br />
* [http://www.thirstywhaletavern.com/menu.html Thirsty Whale Tavern]<br />
* [http://www.galynsbarharbor.com/menus.html Galyn's Restaurant]<br />
* [http://chartroombarharbor.com/ Chart Room Restaurant]<br />
* [http://www.reelpizza.net/ Reel Pizza] (dinner while you watch a movie)<br />
* [http://www.barharborlobsterbakes.com/ Bar Harbor Lobster Bakes] (traditional Maine lobster bakes, a mile out of town)<br />
* [https://www.facebook.com/pages/Jack-Russells-Steakhouse-Brewery/50265656155 Jack Russells Steakhouse]<br />
<br />
==Weather==<br />
<br />
Averages for October: 59°F high, 42°F Low<br />
<br />
[http://weatherspark.com/averages/29745/10/Bar-Harbor-Maine-United-States see weather graphic]<br />
<br />
==Maps==<br />
<br />
* [http://www.barharborinfo.com/getting_here/maps/ downtown Bar Harbor]<br />
* [http://www.nps.gov/acad/planyourvisit/maps.htm for Acadia National Park]<br />
<br />
==Local activities==<br />
Some suggestions:<br />
* [http://www.barharborwhales.com/default.php Whale Watching tours]<br />
* [http://www.olistrolley.com/ Oli's Trolley island tour]<br />
* [http://downeastwindjammer.com/cruises/margaret-todd-windjammer-cruises/ Mary Todd windjammer cruises]<br />
* [http://www.theoceanarium.com/ Mt Desert Oceanarium]<br />
* [http://www.nps.gov/acad/index.htm Acadia National Park]<br />
* [http://www.acadiafun.com/ Coastal Kayaking Tour]<br />
* Bike rental/tours<br />
** [http://www.barharborbike.com/index.html Bar Harbor Bike Shop]<br />
** [http://acadiabike.com/grouptour.html Acadia Bike]<br />
* Brewery tour/tasting<br />
** [http://www.barharborbrewing.com/tasting.html Bar Harbor Brewing Company] (in town)<br />
** [http://www.atlanticbrewing.com/home Atlantic Brewing Company] (near the north end of the island)<br />
* [http://www.reelpizza.net/ Movie theatre with pizzaria] (eat while you watch)<br />
* [http://www.barharborinfo.com/things_to_do/ more ideas]<br />
<br />
=Attendees=<br />
<br />
<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Nights required for accommodation (Oct 3,4,5)<br />
! Airport (BGR or BHB) and ETA (for coordinating shuttles)<br />
! Remote attendee? (Y/N)<br />
! Attending conference dinner?<br />
! Dietary requirements<br />
|-<br />
|Hans-Michael Muller<br />
|Caltech (WormBase/Textpresso)<br />
|Oct 2-5<br />
|TBD<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Ruth Lovering<br />
|BHF-UCL<br />
|Oct 2-5 (Booked in Regency)<br />
|BHB arrive Wed 02-Oct-13 16:00; leave Sun 06-Oct-13 16:30. would be happy to share a shuttle from/to BHB<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Paul Sternberg<br />
|Caltech, WormBase<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|1 lobster/week<br />
|-<br />
|Kimberly Van Auken<br />
|Caltech, WormBase<br />
|Oct 2-5 (Harborside)<br />
|Arrive BGR 10/2 3pm; Depart BGR 10/6 1:25pm would be happy to share a shuttle from/to BGR<br />
|N<br />
|Y<br />
|Ovo-lacto veg (Paul can have my lobster)<br />
|-<br />
|Jane Lomax<br />
|EBI<br />
|Oct 2-4 (Booked in Regency)<br />
|BHB 4pm<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Paola Roncaglia<br />
|EBI<br />
|Oct 2-5 (Booked in Regency)<br />
|10/2 BHB @8:05 PM<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Helen Parkinson<br />
|EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|No shellfish<br />
|-<br />
|Rolf Apweiler<br />
|EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Susan Tweedie<br />
|FlyBase/EBI<br />
|Oct 2-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Rebecca Foulger<br />
|GO-EBI<br />
|Oct 3-5 (Booked in Regency)<br />
|10/3 BHB @8:05 PM<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Judy Blake<br />
|JAX, MGI<br />
|local<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Harold Drabkin<br />
|JAX, MGI<br />
|local<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|David Hill<br />
|JAX, MGI<br />
|local<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Karen Christie<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y - lobster<br />
|None<br />
|-<br />
|Li Ni<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Mary Dolan<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Dmitry Sitnikov<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Joao Ascensao<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Seth Carbon<br />
|LBL, Berkeley<br />
|@Cromwell<br />
|10/2 BHB @8:05 PM<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Heiko Dietze<br />
|LBL, Berkeley<br />
|Oct 2-6 @Cromwell<br />
|Oct 2nd BHB 6:45pm<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Chris Mungall<br />
|LBL, Berkeley<br />
|Oct 2-5 regency<br />
|<br />
|N<br />
|Y<br />
|Veggie (but will eat lobster)<br />
|-<br />
|Suzi Lewis<br />
|LBL, Berkeley<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Shur-Jen Wang<br />
|Medical College of WI (RGD)<br />
|Oct 3-5 (Harborside)<br />
|Oct 3rd<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Peter D'Eustachio<br />
|Reactome, NYUMC<br />
|@Anchorage<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Pascale Gaudet<br />
|SIB<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Alan Bridge<br />
|SIB<br />
|remote<br />
|remote<br />
|Y<br />
|na<br />
|na<br />
|-<br />
|Mike Cherry<br />
|Stanford University (SGD)<br />
|Oct 2-5 (Harborside)<br />
|10/2 BHB @6:45 PM<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Edith Wong<br />
|Stanford University (SGD)<br />
|Oct 2-5 (Booked in Regency)<br />
|Oct 2nd BHB @ 6:45pm<br />
|N<br />
|Y -lobster<br />
|None<br />
|-<br />
|Rama Balakrishnan<br />
|Stanford University (SGD)<br />
|Oct 2-5 (Booked in Regency)<br />
|Oct 2nd<br />
|N<br />
|Y<br />
|Vegetarian, Vegan if possible<br />
|-<br />
|Paul Lloyd<br />
|Stanford University (SGD)<br />
|Oct 2-5 (Booked in Regency)<br />
|Oct 2nd<br />
|N<br />
|Y<br />
|no shellfish<br />
|-<br />
|Tanya Berardini<br />
|TAIR<br />
|local<br />
|<br />
|N<br />
|Y (lobstah)<br />
|None<br />
|-<br />
|Eva Huala<br />
|TAIR<br />
|Oct 3-6 (Harborside)<br />
|10/2 BHB @8:05 PM<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Jim Hu<br />
|TAMU PortEco<br />
|Oct 3-5 (Harborside)<br />
|Oct 3rd 10:38 pm BGR<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Doug Howe<br />
|U. Oregon, ZFIN<br />
|Oct 4-5 (Harborside)<br />
|Oct 3rd 10:38 pm BGR <br />
|N<br />
|Y - Lobster<br />
|None<br />
|-<br />
|Rachael Huntley<br />
|UniProt, EBI<br />
|Oct 2-6 (Harborside)<br />
|Arrive Oct 2nd 6.45pm BHB; Depart Oct 6th 3.35pm BHB<br />
|N<br />
|Y<br />
|Ovo-Lacto vegetarian<br />
|-<br />
|Claire O'Donovan<br />
|UniProt, EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|Gluten Free<br />
|-<br />
|Maria Martin<br />
|UniProt, EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Tony Sawford<br />
|UniProt, EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Huaiyu Mi<br />
|USC<br />
|Oct 2-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Paul Thomas<br />
|USC<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Moni Munoz-Torres<br />
|LBNL<br />
|Oct 2-6 (Cromwell)<br />
|10/2 BHB @8:05 PM <br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Val Wood<br />
|PomBase<br />
|Oct 2-5 regency<br />
|BHB 4pm 2nd<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|Oct 3-5<br />
|Oct 3. BHB 4 pm<br />
|N<br />
|Y<br />
|No red meat<br />
|-<br />
|Midori Harris<br />
|PomBase<br />
|N/A<br />
|N/A<br />
|Y<br />
|N<br />
|N/A<br />
|}</div>Edithhttps://wiki.geneontology.org/index.php?title=2013_Bar_Harbor_Logistics&diff=458482013 Bar Harbor Logistics2013-08-02T16:02:09Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Dates=<br />
<br />
The Fall 2013 GO Consortium meeting will be held October 4-6, in Bar Harbor, ME. On the 3rd, we are considering scheduling a few small working-group sessions. Communication about this meeting will be done via the GO-list. If you are not registered for the GO-list please do so. [https://mailman.stanford.edu/mailman/listinfo/go-consortium GO mailing list subscription]<br />
<br />
=Agenda=<br />
<br />
* [[2013 Bar Harbor GOC Meeting Agenda]]<br />
<br />
=Meeting information=<br />
<br />
==Venue==<br />
<br />
The meeting will be held in the [http://www.barharborclub.com/ Bar Harbor Club]. The primary meeting hotel, Harborside Hotel, is next door to the Bar Harbor Club; both located in downtown Bar Harbor.<br />
<br />
==Lodging Information==<br />
<br />
[http://www.theharborsidehotel.com/ Harborside Hotel] (downtown BHB, next to meeting venue) for rooms (set aside for 3 nights, Thu, Fri Sat)<br />
<br />
* Two double bed $239.<br />
* Premium King $209.<br />
* Deluxe King $229.<br />
* Premium King $229.<br />
<br />
'''Booking'''<br />
<br />
Online registration code: GOC13; otherwise call 1-800-288-5033<br />
<br />
<br />
<br />
[http://www.barharborregency.com/ Bar Harbor Regency]<br />
<br />
* $149 / night<br />
<br />
'''Booking'''<br />
Online registration code: JLG; or call 1-800-234-6835<br />
<br />
Please book your rooms when you register so we know we have enough rooms.<br />
<br />
==Airports==<br />
<br />
[http://www.flybangor.com/ Bangor International Airport] - This is the nearest airport that is served by USAirways and Delta airlines. See shuttle service below. We hope to co-ordinate shuttle service. <br />
<br />
[http://www.bhbairport.com/ Hancock County - Bar Harbor Airport] - This is the closest airport. However, only small planes from Boston fly to it (Cape Air, Penn Air).<br />
These flights come in from Terminal C (Jet Blue, United).<br />
<br />
==Ground transportation== <br />
<br />
[http://www.barharborbangorshuttle.com/ Bar Harbor Shuttle LLC] - Bar Harbor Shuttle LLC is located in Bar Harbor and makes at least 4 round-trip runs to Bangor on a daily basis between June and October. They are not usually able to provide a departure from Bangor any earlier than 11:30 (but call to be sure). Bangor to Bar Harbor costs $40 one say and they offer discounted rates for round-trip tickets and Group Rates for 3 or more on the same reservation. Phone: 207-479-5911<br />
<br />
[http://atyourservicetaxi.com/ At Your Service Taxi] - operates 24 hours a day, seven days a week, year-round and accepts most major credit cards and reservations. Great for local transit around Bar Harbor. Will also pick up/drop off at Bangor Airport; cost one way is $95. Phone: 207-288-9222<br />
<br />
[http://www.barharborcoastalcab.com/fare-details.html Bar Harbor Coastal Cab] - charges a flat rate for rides. When you call, they tell you exactly how much it is from where you are to where you want to go. Does local transit around Bar Harbor, and also does taxi tours of the island or Acadia NP. Will also pick up/drop off at Bangor Airport; cost one way is between $90-100, depending on time of year. Phone: 207-288-1222<br />
<br />
==Registration==<br />
<br />
<br />
Please fill in the [[#Attendees|Attendees table]] below.<br />
<br />
* Registration fee TBD<br />
<br />
Remote attendees please register on the table.<br />
<br />
==Remote Attendees==<br />
<br />
For audio and visual we will be using GoToMeeting. An invite will be sent to the GO list and you will need to download the software to join the meeting.<br />
<br />
==Contacts==<br />
<br />
Judy Blake (Judith.Blake at jax.org); Harold Drabkin (harold.drabkin@jax.org)<br />
<br />
= Local Information =<br />
<br />
==Restaurants==<br />
<br />
* [http://www.2catsbarharbor.com/menu.html Two Cats] (breakfast & lunch)<br />
* [http://www.cafethisway.com/menus.html Cafe This Way] (breakfast & dinner)<br />
* [http://www.geddys.com/ Geddys] [http://www.geddys.com/geddycams/videocam/ Check out downtown Bar Harbor on the Geddy Cam!]<br />
* [http://www.sidestreetbarharbor.com/menu.html Side Street Cafe]<br />
* [http://www.mckayspublichouse.com/index.php Macay's Public House]<br />
* [http://www.thirstywhaletavern.com/menu.html Thirsty Whale Tavern]<br />
* [http://www.galynsbarharbor.com/menus.html Galyn's Restaurant]<br />
* [http://chartroombarharbor.com/ Chart Room Restaurant]<br />
* [http://www.reelpizza.net/ Reel Pizza] (dinner while you watch a movie)<br />
* [http://www.barharborlobsterbakes.com/ Bar Harbor Lobster Bakes] (traditional Maine lobster bakes, a mile out of town)<br />
* [https://www.facebook.com/pages/Jack-Russells-Steakhouse-Brewery/50265656155 Jack Russells Steakhouse]<br />
<br />
==Weather==<br />
<br />
Averages for October: 59°F high, 42°F Low<br />
<br />
[http://weatherspark.com/averages/29745/10/Bar-Harbor-Maine-United-States see weather graphic]<br />
<br />
==Maps==<br />
<br />
* [http://www.barharborinfo.com/getting_here/maps/ downtown Bar Harbor]<br />
* [http://www.nps.gov/acad/planyourvisit/maps.htm for Acadia National Park]<br />
<br />
==Local activities==<br />
Some suggestions:<br />
* [http://www.barharborwhales.com/default.php Whale Watching tours]<br />
* [http://www.olistrolley.com/ Oli's Trolley island tour]<br />
* [http://downeastwindjammer.com/cruises/margaret-todd-windjammer-cruises/ Mary Todd windjammer cruises]<br />
* [http://www.theoceanarium.com/ Mt Desert Oceanarium]<br />
* [http://www.nps.gov/acad/index.htm Acadia National Park]<br />
* [http://www.acadiafun.com/ Coastal Kayaking Tour]<br />
* Bike rental/tours<br />
** [http://www.barharborbike.com/index.html Bar Harbor Bike Shop]<br />
** [http://acadiabike.com/grouptour.html Acadia Bike]<br />
* Brewery tour/tasting<br />
** [http://www.barharborbrewing.com/tasting.html Bar Harbor Brewing Company] (in town)<br />
** [http://www.atlanticbrewing.com/home Atlantic Brewing Company] (near the north end of the island)<br />
* [http://www.reelpizza.net/ Movie theatre with pizzaria] (eat while you watch)<br />
* [http://www.barharborinfo.com/things_to_do/ more ideas]<br />
<br />
=Attendees=<br />
<br />
<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Nights required for accommodation (Oct 3,4,5)<br />
! Airport (BGR or BHB) and ETA (for coordinating shuttles)<br />
! Remote attendee? (Y/N)<br />
! Attending conference dinner?<br />
! Dietary requirements<br />
|-<br />
|Suzi Lewis<br />
|LBL, Berkeley<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Paul Thomas<br />
|USC<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Seth Carbon<br />
|BBOP<br />
|@Cromwell<br />
|10/2 BHB @8:05 PM<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Judy Blake<br />
|JAX, MGI<br />
|local<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Harold Drabkin<br />
|JAX, MGI<br />
|local<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|David Hill<br />
|JAX, MGI<br />
|local<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Tanya Berardini<br />
|TAIR<br />
|local<br />
|<br />
|N<br />
|Y<br />
|No Restrictions<br />
|-<br />
|Karen Christie<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Li Ni<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Mary Dolan<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Heiko Dietze<br />
|BBOP<br />
|Oct (2?,) 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Dmitry Sitnikov<br />
|JAX, MGI<br />
|NA<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Rachael Huntley<br />
|UniProt, EBI<br />
|Oct (2?) 3-5<br />
|<br />
|N<br />
|Y<br />
|Ovo-Lacto vegetarian<br />
|-<br />
|Claire O'Donovan<br />
|UniProt, EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|Gluten Free<br />
|-<br />
|Maria Martin<br />
|UniProt, EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
-<br />
|Paul Sternberg<br />
|Caltech, WormBase<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|1 lobster/week<br />
|-<br />
-<br />
|Doug Howe<br />
|U. Oregon, ZFIN<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Tony Sawford<br />
|UniProt, EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Rolf Apweiler<br />
|EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Helen Parkinson<br />
|EBI<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|No shellfish<br />
|-<br />
|Pascale Gaudet<br />
|SIB<br />
|Oct 3-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|October 2-5<br />
|<br />
|N<br />
|Y<br />
|Ovo-lacto veg (Paul can have my lobster)<br />
|-<br />
|Huaiyu Mi<br />
|USC<br />
|Oct 2-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|-<br />
|Jane Lomax<br />
|EBI<br />
|Oct 2-4 (Booked in Regency)<br />
|BHB 4pm<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|-<br />
|Paola Roncaglia<br />
|EBI<br />
|Oct 2-5 (Booked in Regency)<br />
|BHB 8:05pm (Oct. 2nd)<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Chris Mungall<br />
|LBL<br />
|Oct 2-5<br />
|<br />
|N<br />
|Y<br />
|Veggie (but will eat lobster)<br />
|-<br />
|Susan Tweedie<br />
|FlyBase/EBI<br />
|Oct 2-5<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Peter D'Eustachio<br />
|Reactome, NYUMC<br />
|@Anchorage<br />
|<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Alan Bridge<br />
|SIB<br />
|<br />
|<br />
|Y<br />
|<br />
|-<br />
|Ruth Lovering<br />
|BHF-UCL<br />
|Oct 2-5 (Booked in Regency)<br />
|BHB arrive Wed 02-Oct-13 14:45; leave Sun 06-Oct-13 16:30<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Rebecca Foulger<br />
|GO-EBI<br />
|Oct 3-5 (Booked in Regency)<br />
|BHB 20:05. Oct 3rd<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|Rama Balakrishnan<br />
|Stanford University (SGD)<br />
|Oct 2-5 (Booked in Regency)<br />
|Oct 2nd<br />
|N<br />
|Y<br />
|Vegetarian, Vegan if possible<br />
|-<br />
|Edith Wong<br />
|Stanford University (SGD)<br />
|Oct 2-5 (Booked in Regency)<br />
|Oct 2nd<br />
|N<br />
|Y<br />
|None<br />
|-<br />
|}</div>Edithhttps://wiki.geneontology.org/index.php?title=2013_Cambridge_Logistics&diff=438432013 Cambridge Logistics2013-02-02T20:15:28Z<p>Edith: /* Attendees */</p>
<hr />
<div>=Dates=<br />
<br />
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013].<br />
<br />
=Agendas=<br />
<br />
* [[2013 Cambridge GOC Meeting Agenda]]<br />
* [[2013 Cambridge GO SAB Meeting Agenda]]<br />
<br />
=Venue=<br />
<br />
The meeting will be held in the [http://www.mollercentre.co.uk/index.html Moller Centre], Churchill College, Cambridge.<br />
<br />
==Restaurants==<br />
<br />
There will be a group dinner on Thursday 11th April at the Moller Centre.<br />
<br />
Other evenings you will be on your own.<br />
<br />
Some suggestions of restaurants reasonably close to the Moller Centre:<br />
<br />
[http://www.cafenaz.co.uk/cambridge.php?id=7 Cafe Naz (Indian)]<br />
<br />
[http://www.restaurant-guide.com/maharajah.htm The Maharajah (Indian)]<br />
<br />
[http://www.cambscuisine.com/st-johns-chop-house/ St. John's Chop House (British)]<br />
<br />
[http://www.lamargheritacambridge.com/index.php La Margherita (Italian)]<br />
<br />
[http://www.prezzorestaurants.co.uk/restaurant/cambridge Prezzo (Italian)]<br />
<br />
[http://www.yippeenoodlebar.co.uk/ Yippee Noodle Bar (Asian)]<br />
<br />
[http://www.restaurant-guide.com/the-river-bar-steakhouse-and-grill.htm The River Bar (Steakhouse and Grill)]<br />
<br />
<br />
You will pass numerous pubs as you walk into Cambridge, some of which serve food, and plenty of other restaurants/cafes in the centre.<br />
<br />
Pubs:<br />
<br />
[http://thecastleinncambridge.com/ The Castle]<br />
<br />
[http://www.taylor-walker.co.uk/pub/pickerel-cambridge/c3602/ The Pickerel]<br />
<br />
[http://www.maypolefreehouse.co.uk/Welcome.html The Maypole]<br />
<br />
[http://gkpubs.co.uk/pubs-in-cambridge/eagle-pub/ The Eagle]<br />
<br />
The SAB dinner for PIs and SAB members will be on Friday 12th April<br />
<br />
==Weather==<br />
<br />
Cool, spring-like. <br />
<br />
==Maps==<br />
<br />
[http://map.cam.ac.uk/Churchill+College Interactive map of Cambridge]<br />
<br />
==Local activities==<br />
<br />
[http://cambridgesciencefestival.org/2013Festival/2013Festival.aspx Cambridge Science Festival] April 12-21st<br />
<br />
[http://www.kettlesyard.co.uk Kettles Yard Museum and House] - The gallery and house are well worth a visit and are just a short walk from the Moller Centre.<br />
<br />
[http://www.cam.ac.uk/museums/ Cambridge museums]<br />
<br />
Hopefully there will be some spring flowers along 'The Backs' down Queen's Road behind King's College.<br />
<br />
=Registration=<br />
<br />
Registration fees and a link to register for the meeting and book your accommodation will follow.<br />
<br />
Please indicate if you will be attending this meeting (on site or remotely) in the table below. <br />
We will provide toll free telephone & conferencing for remote attendees. <br />
<br />
==Remote Attendees==<br />
We will use the GO conference line. <br><br />
Toll-free USA number 1-866-953-9688 (US Toll number 1-212-548-2460 in case of problems with 866 number)<br><br />
Toll-free UK 0808 238 6001 (toll number: 646 834-9311)<br><br />
Toll-free Switzerland 0800 562 830 (toll number: 646 834-9311)<br><br />
<br />
Participant Pin: (801-561)<br><br />
<br />
=Lodging Information=<br />
<br />
Rooms have been reserved in [http://www.churchillconferences.co.uk/accommodation.php Churchill College] from 10-13th April.<br />
<br />
Breakfast is included.<br />
<br />
'''Booking'''<br />
<br />
Please indicate which nights you would like accommodation in the 'Attendees' table at the bottom of this page. You will be able to book your accommodation from the registration link as soon as it is available.<br />
<br />
N.B. If you are attending the Biocuration meeting before this meeting and would like to stay in the same room, please indicate 'Y' in the 'Extend room reservation from Biocuration meeting?' column.<br />
<br />
==Airports==<br />
<br />
[http://www.heathrowairport.com Heathrow Airport]<br />
<br />
[http://www.stanstedairport.com Stansted]<br />
<br />
[http://www.londoncityairport.com London City]<br />
<br />
==Ground transportation== <br />
<br />
[http://www.nationalrail.co.uk Train Information]<br />
<br />
[http://www.nationalexpress.com National Express coaches]<br />
<br />
[http://www.chu.cam.ac.uk/visitors/directions/ Driving directions] to the Moller Centre. For those driving, the Moller Centre has free parking.<br />
<br />
[http://www.theaa.com/route-planner/index.jsp AA Route planner]<br />
<br />
===Taxi Companies===<br />
<br />
Panther Taxis <br />
Website: www.panthertaxis.co.uk <br />
Tel: +44 (0)1223 715715<br />
<br />
Sawston Cab Co Ltd (Airport Specialist) <br />
Email: info@sawstoncabcoltd.co.uk <br />
Tel: +44 (0)1223 517008<br />
<br />
==Contacts==<br />
<br />
Rachael Huntley (huntley@ebi.ac.uk)<br />
<br />
Amy Cottage (cottage@ebi.ac.uk)<br />
<br />
=Attendees=<br />
<br />
'''Please note: if you are attending the Biocuration meeting before this meeting and would like to stay in the same room, please indicate 'Y' in the 'Extend room reservation from Biocuration meeting?' column.<br />
'''<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Nights required for accommodation (10,11,12,13 Apr?)<br />
! Extend room reservation from Biocuration meeting?<br />
! Remote attendee? (Y/N)<br />
! Attending Thursday dinner? (venue tbc)<br />
! Dietary requirements<br />
|-<br />
|Rachael Huntley<br />
|UniProt-GOA<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|Lacto-ovo vegetarian<br />
|-<br />
|Mike Cherry<br />
|Stanford University<br />
|N/A<br />
|N/A<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Ruth Lovering<br />
|BHF-UCL<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Stacia Engel<br />
|Stanford University<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|Edith Wong<br />
|Stanford University<br />
|Wed 10, Thur 11, Fri 12<br />
|yes<br />
|N<br />
|Y<br />
|none<br />
|-<br />
|}</div>Edithhttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15205October 2008 Meeting Logistics2008-09-03T21:38:34Z<p>Edith: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
| yummy<br />
| Oct 20, 5:09PM, UA8185, LGA-Montreal<br />
| Oct 23, 7:55PM, UA8400, Montreal-LGA<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
|<br />
| none<br />
|<br />
|<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|Mon, Oct 20, 4:50PM, Continental<br />
|Wed, Oct 22, 5:30PM departure<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Amina Abdulla<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| yes<br />
| no<br />
| none<br />
| 20 Oct, from SFO<br />
| 24 Oct, from Montreal<br />
|-<br />
| Candace Collmer<br />
| yes<br />
| no<br />
| none<br />
|20 Oct 17:15 US Airways<br />
|23 Oct 13:30 US Airways<br />
|-<br />
| Dmitry Sitnikov<br />
| yes<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15017October 2008 Meeting Logistics2008-08-25T17:48:00Z<p>Edith: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
|<br />
| none<br />
|<br />
|<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15016October 2008 Meeting Logistics2008-08-25T17:47:22Z<p>Edith: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
|<br />
| none<br />
|<br />
|<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|<br />
<br />
-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Edithhttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15015October 2008 Meeting Logistics2008-08-25T17:46:50Z<p>Edith: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
|<br />
| none<br />
|<br />
|<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Edith