Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Might be best to have a separate ParaSite-specific curation status form | * Might be best to have a separate ParaSite-specific curation status form | ||
* We may be able to just add new columns to the curation status form, Caltech vs EBI | * We may be able to just add new columns to the curation status form, Caltech vs EBI | ||
+ | * Michael and Jane want to curate gene function, e.g. GO; not sure what else |
Revision as of 19:19, 10 March 2016
Contents
Previous Years
2016 Meetings
March 3, 2016
Sentence-level indexing
- Chris playing around with flagging sentences as positive/negative for phenotype and flagging keywords as true or false positives
- It may be helpful to objectify sentences and generate unambiguous, unique IDs for sentences
- There will likely be difficulty in unambiguously pulling out sentences from re-processed papers
- Best identifier would be the sentence itself
- Sentence 'objects' could be connected to annotations in WB
Proteomic datasets
- Wen wants to systematically collect proteomic datasets
- Many are scattered across different resources
- Would also help ParaSite to index similar datasets for parasites
- MESH terms may help identify proteomic papers
MOD-human disease collaboration
- FlyBase working on a shared template for curating human disease
- SGD, ZFIN, MGI, FlyBase, and WormBase meeting at Caltech to discuss
- One priority is minimizing redundancy of effort
- There is a common portal for human diseases in progress
- Should consider Monarch initiative approach
AddGene & WB constructs
- Karen working with AddGene to pull in worm reagents (plasmids/constructs)
- AddGene does want to have better linking to WormBase
Metabolomic data
- Can we show chemical structures for metabolites?
- User (M. Witting) says metabolism people will want monoisotopic masses - these masses aren't available through ChEBI at the moment and it will be a while for them to provide them. Will find a formula and sources files for Juancarlos to implement a calculator in the OA.
- We already use, sync and collaborate with ChEBI
March 10, 2016
Adding WormBase-Parasite Paper to the Curation Pipeline (Kimberly)
- Developing new paper editor for Jane and Michael P. to approve parasite papers
- Adding species information to ALL papers; can be one or more species per paper
- Would like to then incorporate parasite papers into downstream SVM flagging pipeline and curation status form
- Species information could be used to keep curation stats clear
- We should discuss the curation and tracking of non-elegans species on the next site-wide call
- Might be best to have a separate ParaSite-specific curation status form
- We may be able to just add new columns to the curation status form, Caltech vs EBI
- Michael and Jane want to curate gene function, e.g. GO; not sure what else