WormBase-Caltech Weekly Calls
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Contents
Previous Years
2013 Meetings
December 5, 2013
WBPapers sans C. elegans data
- There are papers in the WormBase collection that are used as paper evidence for some concise descriptions
- They don't refer to C. elegans experiments, but were used to write descriptions with characterizations in other organisms
- These papers are lumped in with all the other papers, come up as false positives in flagging pipelines
- They have a "functional annotation" tag
- Many of these were coming up in the disease paper pipeline
- Michael and Kimberly worked to pull out all papers with this problem
- Some are methods papers, some possibly mistakes, etc.
- Main question: do we want to take 'functional annotation' papers out of Textpresso/Curation pipelines?
- Are the 'functional annotation' tags unique or otherwise mutually exclusive? Yes, historically
- We will change the name of the tag to "non_nematode" and exclude the papers from flagging pipelines (SVM, Textpresso, etc.)
- 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')
Topic Curation
WS241
- UPR (Unfolded Protein Response)
- Chris and Karen playing with pathways diagrams on WikiPathways, Google Slides, and Prezi (SVG presentation); will send around
- May be nice to have a video overview with narration from Prezi presentation, and details (with evidence) captured in WikiPathways
WS242
- Small/ncRNA pathways?
- We will stick to miRNA pathways, specifically biogenesis (transcription through to mature miRNA)
- Chris will send around WBPaper IDs for papers flagged by PubMed Mesh headers for "C. elegans" and "miRNAs"
- We will get a copy of Alla Grishok's recent (2013) small RNA pathway review
- We can identify core components of the miRNA biogenesis pathway and filter the WBPaper list based on references to those genes
- Alternatively (or in parallel), we can break up the ~300 miRNA C. elegans papers into groups and delegate the screening of relevance
LEGO (Logical Extensions of Gene Ontology)
- Discussions with Paul Thomas on Thursday, January 23, 2014
Topics and Subtopics
- We don't want to recreate Gene Ontology or a complicated hierarchy of topics
- We may need to create simple parent/child, topic/subtopic relationships
- We can show general pathway/topic overview on parent topic, specifics on subtopic pages
Discussions with WikiPathways
- We may consider inviting Alex Pico to come talk to us about feature requests, discussion of future plans, current WikiPathway features
- Would be nice to link out to other pathways from inside a pathway (e.g. Link to "Innate Immunity" from "Unfolded Protein Response")
AMIGO development
- Setting up backend:
- Juancarlos is learning how to use Catalyst
- Todd gave Juancarlos access to a development environment
- Raymond and Juancarlos figuring out web code structure
- May be good to have Juancarlos visit/meet with web team to determine best integration practices
Database changes to WormBase
- Discussion/meeting in March 2014
- Paul Sternberg, Juancarlos, and maybe one curator will join in
- Need to 'boil down' the candidates to a small number and test things like: data model changes, capturing biological data, scalability, web performance
December 12, 2013
AGENDA
- Progress on collecting papers for miRNA biogenesis topic
Topic Curation WS242: miRNA pathway
- Currently have Google Docs for tracking miRNA papers
- Collected all papers from PubMed with MeSH headers for "micro RNAs" and "Caenorhabditis elegans"
- Will upload all WBPapers for miRNAs into the Topic Curation OA, under "miRNA Pathway"
- Will break up remaining "unchecked" papers 5 ways to check for relevance
?Construct Model
- Need to discuss how the construct model should be structured
- Incorporation for expression pattern curation, sequence features, Crispr-Cas genome editing alleles, ...
- Hopefully we can sort out this model for the next upload
December 19, 2013
AGENDA
- miRNA Pathway topic curation
- Curation of protein complexes?
- Updated Mitochondrial UPR WikiPathway here
Conference Calls in January 2014
- January 9th and 23rd
WormBase Models meeting March 9 2014, Toronto, Canada
- Which curators should join?
- What are the important considerations?