View source for WormBase-Caltech Weekly Calls April 2015

= April 2015 =

== April 2, 2015 ==

=== Adding Species information to nightly geneace dumps ===
** Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file
** Does anyone want Species information for any of the other files
** For list of files, see: ftp://ftp.sanger.ac.uk/pub/consortia/wormbase/STAFF/mh6/nightly_geneace/
** Data in postgres in table gin_species

=== WormBase Ontology Browser WS248 online on Dev ===
* Caveat: the rest of the WormBase data on the Dev site is WS247 (one release behind)
** Would explain some discrepancies

=== Micropublication form ===
* Daniela waiting for feedback from Paul's lab
* Will send to Alison Frand and Elissa Hallem at UCLA to get input

=== Mary Ann's IWM abstract for community annotation ===
* People can send comment over next day or two
* Will make revisions and send around next week


== April 9, 2015 ==

=== Tazendra ===
* Had some glitches with secondary hard drive this week, not sure what the problem is
* /home2 directory is not intended as a primary storage; curators need to back data up
* Paper PDFs stored on /home2 as the primary storage location
* Papers are backed up on Athena (Wen's computer)
* TIF files are stored on CDs
* Main Tazendra hard drive backed up (RAIDed/mirrored), backed up nightly up to ~1 month (or 0.5 month), monthly for a year, but no older versions

=== Citace data upload ===
* April 28th, 10am

=== Community Annotation Forms ===
* Mary Ann's IWM (poster) abstract includes community annotation forms
* Community annotation form list:
** Micropublication
** Gene Expression form (made 15 years ago); mostly not used; micropublication form could be co-opted
** Gene description form (primarily for the community to edit the automated concise descriptions)
** "Submit Data" list on WormBase (http://www.wormbase.org/about/userguide/submit_data#0--10)
* Would be good to have a community annotation portal/landing page
* Mary Ann will send around a summary of discussions about community annotation, along with prioritization of forms for curators and Juancarlos
* Relevant curators should consider reviewing existing forms for updates

=== modSeek ===
* http://seek.princeton.edu/modSeek/
* Princeton 6th year grad student developed it (leaving within 6 months)
* "Seek" developed for human on microarray and RNAseq data
* 5 model organisms in "modSeek": yeast, worm, fly, mouse, zebrafish
* Pulls in data from Gene Expression Omnibus (GEO)
* Analysis computed from raw data
* Data from SPELL should be reasonably transferred to modSeek
* We need to determine if WormBase data can be updated per release
* Has text mining
* Cross-species comparisons available


== April 16, 2015 ==

=== Topic Images ===
* Daniela importing Lipid Metabolism topic images
* Daniela may also try to create gene-image connections
* Picture OA could capture relevant genes
* For now, Daniela will only import images for which we have permissions

=== WormBook Chapters ===
* Would be good to make sure relevant FTP files are mentioned and pointed to
* We can add a section on concise description and automated description
** Not sure yet where to put it; maybe in introduction chapter


== April 23, 2015 ==

=== WormBook Chapters ===
* Importing figures or screenshots can result in lost resolution
* We may need to play with image manipulation/editing to fix
* Gene function chapter has intermine section; maybe should be an appendix or separate chapter
** Will make separate chapter; will reference Intermine with a single screenshot in gene function chapter
* We will make sure the gene function chapter properly links to GO chapter

=== Wikipathway ===
* Karen created Lipid metabolism pathway
* Dennis Kim and Jonathan Ewbank are updating their WormBook chapter on innate immunity; working with Karen on WikiPathway

=== LEGO ===
* Kimberly participating in conference calls
* Progress being made on back-end to handle evidence properly
* Curators have been going through specific use cases
* Talking about generally how to best model different biological scenarios
* Estimate for getting back end finished on the order of weeks
* Front-end still being developed; getting close
* Karen asks: How will LEGO integrate with Process&Pathway curation at WormBase?
** Kimberly: LEGO is very molecular-function-centric; may be more granular than WB Topics/Process&Pathway
** We should see soon how these two will interface

=== Controlled vocabulary for institutions ===
* How to handle synonyms of institution names
* We will accept entries of synonyms, but will only actually store/track the (English) official name


== April 30, 2015 ==

=== modSeek ===
* http://seek.princeton.edu/modSeek/
* Wen has established an account
* Wen is running scripts to generate worm data for modSeek
* Data in modSeek is G.E.O. (Gene Expression Omnibus) based
* Links at modSeek go to G.E.O. data, not WormBase
* Wen is considering a WB-specific search with links back to WB data
* modSeek only has (and supports) C. elegans data, not other nematodes for which we have data
* Maybe we could have a "WormBaseSeek"/"WB-Seek"?
* We can run a mirror at WB
* Wen is modifying SPELL scripts for modSeek
* Would we be able to perform cross-species comparisons with a WB-Seek?
* Textpresso-Dev is currently running our modSeek instance
** Textpresso-Dev probably would not be able to handle mouse, human, fly data for species comparisons etc.
* We would like to be able to perform cross-species comparisons for all nematode species as well as the other MODs/human
* WB data is paper-centric, unlike data in modSeek
* WB data is processed data (author processed), modSeek data is raw data
** We want to be able to keep/maintain the processed data in addition to the raw data


=== BioCurator Meeting 2015 (China) ===
* ~300 people in attendance, about 1/3 from outside China
* Mouse (MGI), yeast (SGD), EBI, NCBI, and WB represented at meeting
* Xiaodong's training session
** Q&A about literature curation
** Many small bio-databases in China, focused mainly on genome annotation analysis; no literature curation
** Xiaodong demonstrated the Ontology Annotator (OA) tool
* Currently there is no bio-data center in China; Biocuration society would like to establish one
* Web Apollo, JBrowse, phylogenetic G.O. annotation info presented
* Yeast database (SGD?) use IntAct (in collaboration with BioGrid) to curate protein complexes
* There was considerable discussion about the use of Uberon as a cross-species anatomy ontology
** Would be good for WB to establish connections to Uberon with C. elegans anatomy ontology
** This will require specification of relationships; non-trivial
* Yuling presented work on SVM analysis
** People had questions about whether SVM could be used for hierarchical flagging (data types and then subtypes)
*** This requires training sets; could consider moving forward
*** (Karen) We already run SVM for allele data followed by Textpresso entity recognition
*** We would likely run the entire corpus through the SVM for a whole new datatype with proper training sets
** Can SVM be applied at the paragraph or sentence level?
*** Possible, and we have some curated sentences saved, for example with cell component curation (CCC)
* UniProt developing UniRule system for large scale protein annotation
** Manually establish (text mining?) rules for future recognition and annotation
* Reactome is beginning to use ORCID person IDs to give attribution for Reactome pathways


=== FTE estimates for WB staff ===
* Paul S. sent around an e-mail with a spreadsheet for filling out FTE estimates
* Paul asks that people fill it out today and send it back to him
* Two e-mails; first with complete form, second with simpler form
* Please fill out complete form, or simpler form if necessary