Difference between revisions of "WormBase-Caltech Weekly Calls"
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Karen: I'd like to propose that the attendees combine our notes on the meeting and post them [http://wiki.wormbase.org/index.php/ISB2014_WormBase_notes#Speakers here]<br> | Karen: I'd like to propose that the attendees combine our notes on the meeting and post them [http://wiki.wormbase.org/index.php/ISB2014_WormBase_notes#Speakers here]<br> | ||
Perhaps we can go over the meeting next week when I'm in town? In the meantime people can check over the minutes of the meeting taken mainly by Abby (amazing job!), which I will copy onto our wiki. | Perhaps we can go over the meeting next week when I'm in town? In the meantime people can check over the minutes of the meeting taken mainly by Abby (amazing job!), which I will copy onto our wiki. | ||
− | + | === BioCurator Meeting === | |
− | === | + | * many text mining tools |
− | + | * many ontology systems, mapping ontologies | |
− | + | ** Aging ontologies | |
− | + | ** Anatomy ontology mapping (Uberon) | |
+ | ** Format convergence? OBO, OWL, RDF? Plugin for Protege to read OBO files | ||
+ | ** How extensive is OWL? How much has OWL been applied to biology? OWL is being used for reasoning | ||
+ | * Community Annotation | ||
+ | ** CANTO (Community ANotation TOol) workshop (Wen attended) | ||
+ | *** PombeBase use CANTO and works well | ||
+ | * Big data curation open discussion/workshop | ||
+ | ** Enormous datasets (e.g. genome sequencing of all cancer patients) | ||
+ | ** Data storage issue | ||
+ | ** Data stability issue | ||
+ | ** Clinical data, portal set up by Michael Cherry, ClinGene(?) | ||
+ | * Lincoln's talk | ||
+ | ** International Cancer Genome Consortium (ICGC) project (petabyte datasets) | ||
+ | ** 10,000 cancer patients already sequenced (18 PB by 2018) | ||
+ | ** Torent P2P data sharing | ||
+ | * BioCreative workshop | ||
+ | ** Text mining | ||
+ | *** Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566) | ||
+ | **** Curates sentences, marks up entities, only applied to abstract | ||
+ | ** GO annotation | ||
+ | *** GO Cat (http://eagl.unige.ch/GOCat/) | ||
+ | * Amazon "Mechanical Turk" community annotation | ||
+ | * EcoCyc, MetaCyc - pathway curation (will hear from Karen) | ||
+ | * Reactome | ||
+ | ** May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape) | ||
+ | ** Add a Reactome display to WormBase? | ||
+ | * SPELL - anything to replace SPELL? No. | ||
+ | ** Still lacking other tools for microarray and RNA-Seq data | ||
+ | === Heartbleed SSL security issue === | ||
+ | * Raymond updated all servers/machines | ||
+ | * All machines need to be rebooted | ||
+ | * Any user passwords should be changed | ||
+ | * Do we care about any non-root users? Best to change all passwords on machines that have been updated | ||
+ | === BioGrid C. elegans physical interactions === | ||
+ | * Kimberly has been using BioGrid's curation tool | ||
+ | * We have a table of C.elegans large scale genetic and physical interaction data | ||
+ | * We're still trying to get all data | ||
+ | === Timestamps === | ||
+ | * Curator evidence vs. history of curation | ||
+ | * Kevin and Juancarlos still looking for use-cases | ||
+ | * Need to consider for future database migration and potential use of a common central database | ||
+ | * Curators use timestamps for culling out bogus data objects/cleaning up data | ||
== April 17, 2014 == | == April 17, 2014 == | ||
===ISB2014 summary?=== | ===ISB2014 summary?=== |
Revision as of 16:04, 11 April 2014
Contents
Previous Years
2014 Meetings
April 3, 2014
WOBr
- Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser)
- As one-offs, Raymond can take newly generated GAFs from curators and process for testing.
Murray Expression datasets
- Still need to acquire primary expression data from Waterston lab
- Problems with handling inferred expression of genes in cells
- Thus inferred expression data will be removed
- Expression object will retain graphical representations supplied by Murray et al.
- A friendly reminder will be sent to Waterston requesting tabulated, processed primary expression data.
April 10, 2014
Apologies
- Karen: attending impromptu OICR group meeting, won't be on the Caltech call.
ISB2014
Karen: I'd like to propose that the attendees combine our notes on the meeting and post them here
Perhaps we can go over the meeting next week when I'm in town? In the meantime people can check over the minutes of the meeting taken mainly by Abby (amazing job!), which I will copy onto our wiki.
BioCurator Meeting
- many text mining tools
- many ontology systems, mapping ontologies
- Aging ontologies
- Anatomy ontology mapping (Uberon)
- Format convergence? OBO, OWL, RDF? Plugin for Protege to read OBO files
- How extensive is OWL? How much has OWL been applied to biology? OWL is being used for reasoning
- Community Annotation
- CANTO (Community ANotation TOol) workshop (Wen attended)
- PombeBase use CANTO and works well
- CANTO (Community ANotation TOol) workshop (Wen attended)
- Big data curation open discussion/workshop
- Enormous datasets (e.g. genome sequencing of all cancer patients)
- Data storage issue
- Data stability issue
- Clinical data, portal set up by Michael Cherry, ClinGene(?)
- Lincoln's talk
- International Cancer Genome Consortium (ICGC) project (petabyte datasets)
- 10,000 cancer patients already sequenced (18 PB by 2018)
- Torent P2P data sharing
- BioCreative workshop
- Text mining
- Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
- Curates sentences, marks up entities, only applied to abstract
- Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
- GO annotation
- GO Cat (http://eagl.unige.ch/GOCat/)
- Text mining
- Amazon "Mechanical Turk" community annotation
- EcoCyc, MetaCyc - pathway curation (will hear from Karen)
- Reactome
- May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape)
- Add a Reactome display to WormBase?
- SPELL - anything to replace SPELL? No.
- Still lacking other tools for microarray and RNA-Seq data
Heartbleed SSL security issue
- Raymond updated all servers/machines
- All machines need to be rebooted
- Any user passwords should be changed
- Do we care about any non-root users? Best to change all passwords on machines that have been updated
BioGrid C. elegans physical interactions
- Kimberly has been using BioGrid's curation tool
- We have a table of C.elegans large scale genetic and physical interaction data
- We're still trying to get all data
Timestamps
- Curator evidence vs. history of curation
- Kevin and Juancarlos still looking for use-cases
- Need to consider for future database migration and potential use of a common central database
- Curators use timestamps for culling out bogus data objects/cleaning up data