WormBase-Caltech Weekly Calls
Contents
Previous Years
2015 Meetings
August 20, 2015
retracted papers
Is there a systematic way to find these papers?
Is there a systematic way to deal with the data curated from papers that are then retracted?
These papers were retracted, they both have curated data in WB attached to them
WBPaper00042572 Leung, C. K., Wang, Y., Deonarine, A., Tang, L., Prasse, S., & Choe, K. P.(2013). A negative-feedback loop between the detoxification/antioxidant response factor SKN-1 and its repressor WDR-23 matches organism needs with environmental conditions. Mol Cell Biol, 33, 3524-37.doi:10.1128/MCB.00245-13
WBPaper00045362 Leung, C. K., Hasegawa, K., Wang, Y., Deonarine, A., Tang, L., Miwa, J., &Choe, K. P. (2014). Direct interaction between the WD40 repeat protein WDR-23 and SKN-1/Nrf inhibits binding to target DNA. Mol Cell Biol, 34, 3156-67.doi:10.1128/MCB.00114-14
August 6, 2015
WormMine
- prioritize new data types into WormMine
- RNAi phenotype, interactions, human disease...
- WormMine wiki page: http://wiki.wormbase.org/index.php/WormMine
WormMart machine
- Wen wants to use the machine when WormMart retires
UniProt/wormbase gene class
- need to talk to UniProt C.elegans curator
Raymond, Chris and Juancarlos are working on phenotype viewer
James: list of genes, enrich in what tissues
- python code
- biotype ontology, tissue expression from postgres as input
August 13, 2015
We are really sad about our friend Bill Gelbart
We will try to help FlyBase as much as possible
Phenotype term annotation summary graph
Goal: Provides an ontology-relationship-aware summary view of a gene's phenotype annotations. Prototype link aex-3 (fewer phenotypes) existing phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000086#-b-3> summary graph <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000086>
daf-2 (lots of phenotypes) phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000898#-b-3> summary <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898>
Proposed development procedure:
- standalone prototyping, commenting and improvements within the group.
- implementation as a widget on dev site (juancarlos.wormbase.org), more testing and soliciting comments from selected end users.
- committing to main site for general use.
Outline of graph processing:
To gather information:
- WOBr query to collect all phenotypes annotated to the gene of interest.
- WOBr query to collect all transitive relationships of the phenotypes from (1) towards the ontology root.
To simplify and to control graph size:
- Remove all nodes (phenotype terms) that are not directly annotated with or at branching points where two branches of annotations merge (LCA lowest common ancestor, if you will).
- Scale node size according to annotation count (includes inferred annotations). width of node is (scale multiplier of 1.5 * log(max count in graph)/log(current node) ) + minimum size value (.1)
- Limit appearance of label to nodes above a given size (roughly big enough to hold term name).
- Show annotation counts in mouse-over bubble, add hyperlink to term pages to each node
Group comments:
- key of red vs blue nodes
International Biocuration Conference
Propose to submit paper on Community Curation
- Mary Ann happy to lead.
- Daniela on board.
- push out the emails (Ranjana and Chris are thinking about it) Sept.1 so we can get some submissions in the Sept.
- We should visit labs to publicize Annotation. target labs with data
- target senior graduate students.
ModSeek and SPELL updates
- Wen is working with Seek developer to install a ModSeek mirror, still debugging the software.
- Wen will try to install a WormSPELL mirror on the Textpresso server because the machine still runs RedHat 5, which is compatible with the requirement of SPELL.
August 20, 2015
Phenotype annotation display
- New graph view available that emphasizes number of annotations
- Raymond and Juancarlos working on alternate displays to allow for rapid visual review of all annotations
WormSeek mirror running on Athena
- Do we still need another machine (Caprica)? Cannot run on Athena long term
- modSeek vs. SPELL: modSeek is easy to install but uses a lot of disk space and memory
- Probably need ~2 Terabytes, ~16 Gigabytes of memory for WormSeek