View source for WormBase-Caltech Weekly Calls March 2016

== 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; depends on use-case
* 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

=== Dynamo-DB backend for Datomic ===
* REST-API now switched to dynamodb backend.
* Juancarlos could set up a form to try Datomic queries

=== WB FAQ page ===
* Need to request write access from Todd
* We should find out whether this page is used much. It needs updating considerably.


== March 17, 2016 ==

=== Xiaodong taking year leave ===
* Will try working with company in China for a year
* Xiaodong will start April 15
* Daniela taking over antibody curation, Chris & Daniela taking over gene regulation and sequence feature
* Xiaodong will discuss antibodies for disease with Ranjana

=== Tissue enrichment tool (Raymond) ===
* Should development continue with integration into WormBase? Yes, no one else is doing it
* GO enrichment tool in Intermine?

=== Text mining: brainstorming ===
* We can likely explore many more options in terms of text mining
* All possibly recognizable entities could have data filled and displayed to curators and/or end users
* What about showing PDF markup from papers in PubMed Central? There is increasing interest in participation
* We're trying sentence-level SVM for phenotype; will see how that works
* We can quote papers verbatim in annotations, but should probably use double quotes from now on
* We'll try to generate putative annotations automatically that can be confirmed or rejected by a curator or author


== March 24, 2016 ==

=== Outsourcing compute time ===
* SPELL requires 30 hours with 16GB memory
* Amazon cloud could offer 244GB memory at $3 per hour
* We already have an Amazon account


== March 31, 2016 ==

=== Reagent data submission form (from Nobert Perrimon) ===
* Data table provided as an example submission of reagent information at point of publication
* Several reagent types included
* We may want more specific information, e.g. sequence(s), relevant gene(s)
* Would we need/want other follow-up tables to fill in more specific information?
* Genetic variations should be added, including sequence
* WB curators should draw up a table of minimal information for their data type
* Chris will clean up and send around table for RNAi data submission

=== Proteomic papers (Wen) ===
* Searching title for "proteome"
* ~230 papers total
* ~187 proteomic papers might be curatable
* Many may not have expression clusters, but Wen did find new datasets