WBConfCall 2014.09.03-Agenda and Minutes

Agenda and Minutes

WS246 release schedule (options)- Paul D

We haven't discussed plans for the remaining 2014 releases.

To get 2 more in for 2014 (not that we have to) we would need to start the schedule tomorrow with a schema being made available for use/testing. If we want to be a bit more flexible and avoid building while we are preparing for the SAB then we could push the schedule back by 2 weeks and have a more relaxed/extended schedule bridging December January for WS247 or start WS247 as nornal releasing the database at the end of December?

• Standard:

5th Sept models.wrm (tomorrow)    WS246
26th Sept upload data to hinxton  WS246
25th Oct data released to OICR    WS246
?? Staging site release           WS246
7th Nov models.wrm                WS247
28th Nov upload data to hinxton   WS247
26th Dec data released to OICR    WS247 (would have to release early probably)
?? Staging site release           WS247

• SAB:

19th Sept models.wrm              WS246
5th-7th Sept SAB
10th Oct upload data to hinxton   WS246
8th Nov data released to OICR     WS246
?? Staging site release           WS246
models and upload in December     WS247
build January                     WS247

Conclusion: We will take SAB schedule.

Adding worm disease models/data to the Monarch Initiative website

(From Ranjana)

• http://monarchinitiative.org/ : connects phenotypes, diseases, models, and genes for translational research across species (People involved: Melissa Haendel, Chris Mungall, Suzi Lewis, Nicole Washington and others)
• Last time I spoke to them, seems like they were still working on a lot of stuff; today, got a very enthusiastic response from Chris and Nicole about including worm disease model data
• Pointed them to our gene-disease association file, on the FTP site:ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/ONTOLOGY/disease_association.WS245.wb, however this is incomplete since it doesn't have the disease model descriptions, and the manually curated OMIM connections, so also sent them the WS245 caltech manual curations file
• Will wait to see whether they can work with the above files or would they need something else
• Link to monarchinitiative.org from WormBase? Possibly from the DO term page? there is documentation at http://monarchinitiative.org/page/services and http://monarchinitiative.org/docs/files/api-js.html?
• A page example for Parkinson's Disease: http://monarchinitiative.org/disease/DOID_14330, from here one can go to the different tabs for Models, Genes, Compare, etc.

Paul Sternberg: Monarch is stable and worth to work on. Sibyl: will take a look at the Monarch website

Model change requests for WS246

• Wen and Daniela: model changes to #Qualifier so that we can combine life stage with anatomy term in expression pattern annotation. We hope these changes can be included in WS246 models.wrm. We just need to add Life_stage and Anatomy_term fields to #Qualifier.

#Qualifier    Certain Text
              Uncertain Text   
              Partial Text  
              Anatomy_term ?Anatomy_term //Added by Wen and Daniela                
              Life_stage  ?Life_stage //Added by Wen and Daniela

Paul Davis: Approved for WS246.

• Ranjana: Addition of a new tag, 'Automated_description' to 'Structured_description' under ?Gene.

--James and I are working on a project here at Caltech, which will generate completely automated descriptions for genes based on data already curated in WormBase. Currently these data are: Orthology/Homology and the GO annotations for Process, Function and Cell component. Since this is a significant departure from the way the human written ones were generated, I'd like to request a new tag 'Automated_description' under 'Structured_description' in the Gene class for WS246.

?Gene
Structured_description	 Provisional_description  ?Text   #Evidence
                        Concise_description      ?Text   #Evidence            
                        Automated_description    ?Text   #Evidence     <--New tag

Paul Davis: Aprroved for WS246.

• Mary Ann: ?Transgene model and ?Multi_counts model WS245 data loss

Roll back to WS244 schema

1. Proposed change/roll-back:

?Multi_counts UNIQUE Gene UNIQUE ?Gene XREF Multi_point UNIQUE Int #Multi_counts
    Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
    Allele UNIQUE ?Variation XREF Multi_point UNIQUE Int #Multi_counts
    Rearrangement UNIQUE ?Rearrangement XREF Multi_point UNIQUE Int
#Multi_counts
    Transgene UNIQUE ?Transgene XREF Multi_point UNIQUE Int #Multi_counts

2. Proposed change/roll-back:

?Transgene
 Genetic_information  Extrachromosomal
 Integrated
 Map ?Map  #Map_position
 Map_evidence #Evidence
 Mapping_data  Multi_point ?Multi_pt_data
 Phenotype ?Phenotype XREF Transgene #Phenotype_info
 Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info

I think this is a straight forward change so shouldn't need much discussion.

Paul Davis: Aprroved for WS246.

SAB

Kevin already got the travel information of most of attendees. Free discussion time will be available on Sunday afternoon. Tuesday early morning and Tuesday afternoon.

JBrowse

Scott:

 JBrowse is in good shape. 
 Reguar expression search and sequence download are built-in feature. 
 Current plan is to add more data (exclude modENCODE data). It takes time to create configurations for all data types. Once C. elegans is done, other species will be easy. Nothing is difficult. It just takes time.