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| | [[WormBase-Caltech_Weekly_Calls_August_2012|August]] | | [[WormBase-Caltech_Weekly_Calls_August_2012|August]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_September_2012|September]] |
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| − | == September 6, 2012 ==
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| − | Canopus
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| − | *Will become a server (heavy outside access)
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| − | *Raymond will take precautions to restore properly; should take a week or less
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| − | *Used for:
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| − | **Picture curation
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| − | **Virtual worm web page & FTP
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| − | Grant Writing
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| − | *Approach & future plans - do we need to discuss and add more to proposal?
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| − | *Virtual worm access to data
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| − | *Browsing data
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| − | **Browse genes/proteins by class/GO annotation
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| − | *Intermine queries
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| − | **Queries can be saved and used again later (available to other users)
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| − | **Results can be stored and displayed on web pages
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| − | *Displaying large scale expression (microarray) data (from SPELL)
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| − | **SPELL data currently stored in relational (MySQL?) form
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| − | **We could extend the WormBase web app to interact with SPELL data
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| − | **RESTful-compliant data serving would be best
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| − | Migration away from ACEDB?
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| − | *Scalability - ACEDB does not scale to genome-scale studies
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| − | *We (EBI & OICR) spend a lot of time building ACEDB database
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| − | *ACEDB not actually used so much
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| − | *Makes more sense to adopt a more central database
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| − | *Migration would take place over entire grant cycle
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| − | *We should continue extending models as we see fit, in the meantime
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| − | Massmails
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| − | *Discuss again with Paul about Worm Breeder's Gazette and WormBook.
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| − | == September 13, 2012 ==
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| − | Grant
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| − | *Two things to work on:
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| − | **1) Metrics and quality control
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| − | ***Metrics: Transparent about our coverage (e.g. "We estimate XXX many RNAi experiments/papers and we have ~62% coverage")
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| − | ****SVM form (in development) vs Curation Status form (needs work/update); can generate numbers for coverage to display on the web?
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| − | ****What is the vision of a new Curation Status form? (Daniela will write something)
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| − | ****Stats with new SVM results on pre-2000 papers: state them in grant as pre-2000 corpus
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| − | ***Quality Control: How do we demonstrate that our curation is correct/accurate?
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| − | ****Sampling First-pass curation (false negative estimates)
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| − | ****WormBase person would check on case-by-case basis the accuracy of data (e.g. expression pattern, RNAi experiment, etc.); what percent do you need to check to ensure good quality control? Blind/independent re-curation? Collection of facts to use for metrics
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| − | ****Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pass
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| − | ****Data-type specific issues
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| − | ****Internal consistency checks
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| − | ****Ontology based curation checks (granularity; branch-consistency)
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| − | **2) Training and user interaction
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| − | ***Screencasts and FAQs list (Chris will write some sentences)
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| − | ***User guide status? Currently needs major revamp and new information (old Wiki User Guide is now obsolete)
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| − | ***Online chat: has been broken for months; should it only be allowed for logged-in users?
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| − | *Daily updates with low-connectivity data (not relying on sequence mapping) from PostgreSQL database?
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| − | **Have different CGI forms to populate the data on the website?
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| − | *Are we committed to migrating away from ACEDB? Who then is responsible for managing data models?
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| − | **Migrate to Chado? Do we need detailed plan for this?
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| − | **FlyBase has migrated; they like Chado, but the migration was painful
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| − | Worm Breeder's Gazette & WormBook outreach
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| − | *Mass mailings should be an Opt-in system, as opposed to blanket mass mailings
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| − | *One mass mail for each to ask about Opting-in to e-mail alerts?
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| − | *Regional & International worm meetings; don't hand all e-mails over to meeting organizers.
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| − | Itai Yanai expression datasets
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| − | *Including images from microarray expression data directly from paper for now
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| − | *Plan is to generate time-course expression data 'on-the-fly' later on so that other data sources can be compared and included in the same graph, given that they are the same type of data
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| − | *Eventually, the paper images will be superceded by the new, calculated 'on-the-fly' images
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| − | Phenotype Images
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| − | *We were asked if we wanted to join a consortium that is collecting images portraying different phenotypes
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| − | *We may in the future, but not right now; we would need to develop a method for collecting and curating such images
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| − | == September 20, 2012 ==
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| − | Canopus back online
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| − | *Cron job for pulling pictures; need to make sure it still works
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| − | *Raymond lifted Todd's directories over to new hard drive
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| − | */usr/local gone; Raymond did not restore
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| − | *Todd was pulling from somewhere in /usr/local (/usr/local/wormbase/image ?)
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| − | *Pictures in OICR directory
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| − | *Raymond will send directory to Todd
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| − | Molecule curation
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| − | *"Drug" vs. "Molecule"
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| − | *Synthetic vs Non-Synthetic?
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| − | *Endogenous vs. Exogenous?
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| − | *Focus of study
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| − | *Textpresso categories including some molecules (e.g. 'glucose') throw off predictions for papers having 'drugs'
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| − | | |
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| − | Remote backup storage
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| − | *Juancarlos suggesting storing some data/files remotely
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| − | *Amazon will back up 1 GB data 12.5 cents/month; Essentially free to upload; Pay for download (12 cents/GB)
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| − | *Data to store: Postgres data (for example)
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| − | *Data could be encrypted, if we are concerned
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| − | | |
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| − | Curation Prioritization
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| − | *Curating papers by process or topic
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| − | **Reinstate some Textpresso categorization of papers by topic/process
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| − | **Tied to pathway curation (LEGO and WikiPathways)
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| − | *Prioritization of curation for genes that currently have no annotations
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| − | == September 27, 2012 ==
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| − | Microarrays from other species
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| − | *Storing data?
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| − | *Will keep in a separate database (separate from C. elegans)
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| − | *Curating Itai Yanai's paper (5 species)
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| − | *Only found 4 microarray data sets from C. briggsae (from GO search) including Yanai paper; very few from other species so far
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| − | *There may be more microarray data on non-Caenorhabditis species (parasites, etc.)
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| − | *No way, currently, to inter-compare data sets (across species)
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| − | Yanai data set
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| − | *Everything in sandbox (images and data)
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| − | Process Pages
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| − | *Marc Perry is working on generating the pages
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| − | *Newer data not available on website yet
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| − | *WikiPathway for male mating (Karen made); Marc made mock page and put it up
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| − | *Interactive pages; can click on entities
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| − | *Process search not up and running yet
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| − | *Can we get WormBase data into WikiPathways programatically? Not yet
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| − | *Can use GenMAPP files
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| − | *Wikipathways has node/edge hyperlinks
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| − | *Figure out a way to pull data (programatically) from WormBase process
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| − | **Create and place GPML objects spaced evenly on a page
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| − | *Process pages have lists of: genes, cells, molecules, microarray expression clusters
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| − | *Process pages are a good home for expression clusters
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| − | *Process page: Summary, WikiPathways widget, lists
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| − | *Phenotype to Process mapping of objects
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| − | *Big-picture mapping of pathways (top down approach)
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| − | *LEGO will become the bottom up approah
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| − | *Would be good to capture pathway connections/structure in the ACEDB data model
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| − | | |
| − | GO Meeting @ Caltech
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| − | *[http://wiki.geneontology.org/index.php/Consortium_Meetings GO Wiki] has details
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| − | *October 7-9
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| − | PWM data
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| − | *Gary Stormo paper coming out with lots of new PWM data (5000 binding sites)
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| − | *Genome wide conserved elements (some experimentally verified)
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| − | Transcription Factor -to- Target Gene Associations
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| − | *We need better data display methods/tools
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| − | *ModENCODE ChIP-seq data really would benefit from conversion to digital/discrete objects/associations
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| − | Curating with respect to topic
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| − | *Karen already doing this to some extent for processes
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| − | *Clustering (papers) based on GO Biological Process terms
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