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| | [[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]] | | [[WormBase-Caltech_Weekly_Calls_2012|2012 Meetings]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_2013|2013 Meetings]] |
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| | [[WormBase-Caltech_Weekly_Calls_November_2013|November]] | | [[WormBase-Caltech_Weekly_Calls_November_2013|November]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_December_2013|December]] |
| − | == December 5, 2013 ==
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| − | | |
| − | === WBPapers sans ''C. elegans'' data ===
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| − | * There are papers in the WormBase collection that are used as paper evidence for some concise descriptions
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| − | * They don't refer to ''C. elegans'' experiments, but were used to write descriptions with characterizations in other organisms
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| − | * These papers are lumped in with all the other papers, come up as false positives in flagging pipelines
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| − | * They have a "functional annotation" tag
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| − | * Many of these were coming up in the disease paper pipeline
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| − | * Michael and Kimberly worked to pull out all papers with this problem
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| − | * Some are methods papers, some possibly mistakes, etc.
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| − | * Main question: do we want to take 'functional annotation' papers out of Textpresso/Curation pipelines?
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| − | * Are the 'functional annotation' tags unique or otherwise mutually exclusive? Yes, historically
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| − | * We will change the name of the tag to "non_nematode" and exclude the papers from flagging pipelines (SVM, Textpresso, etc.)
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| − | * Will need to change in Postgres (Paper Display "curation_flags", Paper Editor). Curators need to check their scripts to see if they use this and update it or talk to Juancarlos (search for 'functional_annotation')
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| − | | |
| − | === Topic Curation ===
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| − | | |
| − | ==== WS241 ====
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| − | * UPR (Unfolded Protein Response)
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| − | * Chris and Karen playing with pathways diagrams on WikiPathways, Google Slides, and Prezi (SVG presentation); will send around
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| − | * May be nice to have a video overview with narration from Prezi presentation, and details (with evidence) captured in WikiPathways
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| − | | |
| − | ==== WS242 ====
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| − | * Small/ncRNA pathways?
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| − | * We will stick to miRNA pathways, specifically biogenesis (transcription through to mature miRNA)
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| − | * Chris will send around WBPaper IDs for papers flagged by PubMed Mesh headers for "C. elegans" and "miRNAs"
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| − | * We will get a copy of [http://www.ncbi.nlm.nih.gov/pubmed/23890211 Alla Grishok's recent (2013) small RNA pathway review]
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| − | * We can identify core components of the miRNA biogenesis pathway and filter the WBPaper list based on references to those genes
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| − | * Alternatively (or in parallel), we can break up the ~300 miRNA ''C. elegans'' papers into groups and delegate the screening of relevance
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| − | | |
| − | ==== LEGO (Logical Extensions of Gene Ontology) ====
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| − | * Discussions with Paul Thomas on Thursday, January 23, 2014
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| − | | |
| − | ==== Topics and Subtopics ====
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| − | * We don't want to recreate Gene Ontology or a complicated hierarchy of topics
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| − | * We may need to create simple parent/child, topic/subtopic relationships
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| − | * We can show general pathway/topic overview on parent topic, specifics on subtopic pages
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| − | | |
| − | ==== Discussions with WikiPathways ====
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| − | * We may consider inviting Alex Pico to come talk to us about feature requests, discussion of future plans, current WikiPathway features
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| − | * Would be nice to link out to other pathways from inside a pathway (e.g. Link to "Innate Immunity" from "Unfolded Protein Response")
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| − | | |
| − | === AMIGO development ===
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| − | * Setting up backend:
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| − | ** Juancarlos is learning how to use Catalyst
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| − | ** Todd gave Juancarlos access to a development environment
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| − | ** Raymond and Juancarlos figuring out web code structure
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| − | * May be good to have Juancarlos visit/meet with web team to determine best integration practices
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| − | | |
| − | === Database changes to WormBase ===
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| − | * Discussion/meeting in March 2014
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| − | * Paul Sternberg, Juancarlos, and maybe one curator will join in
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| − | * Need to 'boil down' the candidates to a small number and test things like: data model changes, capturing biological data, scalability, web performance
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| − | | |
| − | | |
| − | | |
| − | == December 12, 2013 ==
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| − | | |
| − | === AGENDA ===
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| − | * Progress on collecting papers for miRNA biogenesis topic
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| − | | |
| − | === Topic Curation WS242: miRNA pathway ===
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| − | * Currently have Google Docs for tracking miRNA papers
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| − | * Collected all papers from PubMed with MeSH headers for "micro RNAs" and "Caenorhabditis elegans"
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| − | * Will upload all WBPapers for miRNAs into the Topic Curation OA, under "miRNA Pathway"
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| − | * Will break up remaining "unchecked" papers 5 ways to check for relevance
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| − | | |
| − | === ?Construct Model ===
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| − | * Need to discuss how the construct model should be structured
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| − | * Incorporation for expression pattern curation, sequence features, Crispr-Cas genome editing alleles, ...
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| − | * Hopefully we can sort out this model for the next upload
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| − | | |
| − | | |
| − | | |
| − | == December 19, 2013 ==
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| − | | |
| − | === AGENDA ===
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| − | * miRNA Pathway topic curation
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| − | ** Please continue to add pathway figures from papers [https://docs.google.com/a/wormbase.org/presentation/d/1Pt8uICOgsrHfHBamqe4jSBE4owlEfbLCzZ3G7mFGbkQ/edit#slide=id.p here]
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| − | ** Feel free to play around with ways to diagram the miRNA pathway in Google Slides [https://docs.google.com/a/wormbase.org/presentation/d/1CXhUO42v2cefh5ws_9u48K03nNJZ5-wxviSw834tKh8/edit#slide=id.g29979cf49_08 here]
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| − | * Curation of protein complexes?
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| − | * Updated Mitochondrial UPR WikiPathway [http://www.wikipathways.org/index.php/Pathway:WP525 here]
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| − | | |
| − | === Conference Calls in January 2014 ===
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| − | * January 9th and 23rd
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| − | * Should discuss ?Construct model on the 9th?
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| − | | |
| − | === WormBase Models meeting: March 9, 2014, Toronto, Canada ===
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| − | * Which curators should join?
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| − | * What are the important considerations?
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| − | * What system might enable ~real-time annotations or corrections to the database/site?
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| − | | |
| − | === Life Stages for Burgia malayi ===
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| − | * Defined by Mark Blaxter et al
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| − | * "Infective Juveniles", "IJs" included
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| − | | |
| − | === Topic Curation ===
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| − | * WikiPathways is good but clunky; easier to draw up ideas in other formats (e.g. Google Slides?)
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| − | * Would be good to discuss feature development of WikiPathways (and others?) with respective developers
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| − | * Reactome? LEGO?
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| − | * We can discuss with Alex Pico, for example, about WikiPathways features
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| − | ** May be best if we wait until the new WikiPathways layout is released, or maybe we can get access to a Beta version of the new interface
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