WormBase-Caltech Weekly Calls

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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