Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Juancarlos making progress on integrating into the WB site | * Juancarlos making progress on integrating into the WB site | ||
* There are difficulties getting SObA into it's own widget on the gene page | * There are difficulties getting SObA into it's own widget on the gene page | ||
− | ** Conflicts with other settings ( | + | ** Conflicts with other settings (javascript / cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer) |
− | ** Updated | + | ** Updated cytoscape.min.js version on Interactions viewer |
=== Corresponding author curation === | === Corresponding author curation === |
Revision as of 19:11, 19 November 2015
Contents
- 1 Previous Years
- 2 2015 Meetings
- 2.1 November 5, 2015
- 2.1.1 IEA GO Annotations informating descriptions for non-elegans
- 2.1.2 Wen using Textpresso machine to build SPELL
- 2.1.3 Community Curation Tracker CGI
- 2.1.4 SObA Graphs for phenotype
- 2.1.5 Micropublications
- 2.1.6 Status of WormBase User Survey?
- 2.1.7 Sending author updates
- 2.1.8 Objectifying/Itemizing annotations from Postgres
- 2.2 November 12, 2015
- 2.2.1 Citace upload Dec 1st
- 2.2.2 SAB set for Feb 4-5, 2016
- 2.2.3 Concise description form
- 2.2.4 Community curation CGI
- 2.2.5 Scripts for community description form
- 2.2.6 FlyBase text mining
- 2.2.7 Phenotype SObA graph
- 2.2.8 Data Visualization program opportunity
- 2.2.9 WormBook
- 2.2.10 Biocuration meeting
- 2.2.11 HT115 vs HT115(DE3) E.coli strains
- 2.2.12 Visualization plans
- 2.3 November 19, 2015
- 2.1 November 5, 2015
Previous Years
2015 Meetings
November 5, 2015
IEA GO Annotations informating descriptions for non-elegans
- Some non-elegans genes have confident-sounding descriptions, about localization for example; likely not manual
- Will make sure automated descriptions handle IEA's appropriately
Wen using Textpresso machine to build SPELL
- Athena was taking 48 hours to build SPELL (4GB max memory allotted)
- Textpresso machine took 24 hours (8GB memory allotted)
- Maybe we can use Textpresso machine for future builds
- SPELL java program running on Athena (alloted 4GB out of 6GB)
- Can monitor Athena memory usage; check for any memory leaks
Community Curation Tracker CGI
- Purpose: To automate many steps of the e-mailing process to authors requesting community curation and to track those papers for which we've sent e-mails
- There is a "Ready" form and a "Tracker" form; "Ready" for generating list of papers to e-mail about, "Tracker" to track the status of papers that have already been e-mailed about
- Wiki documentation at: http://wiki.wormbase.org/index.php/Contacting_the_Community#Community_Contact_.26_Curation_Tracker_CGI
- Sandbox CGI located at: http://mangolassi.caltech.edu/~postgres/cgi-bin/community_curation_tracker.cgi
- EMAIL FUNCTIONALITY IS LIVE: please note!
- Allele-phentoype("New mutant" datatype) CGI is live on Tazendra
- Concise description version will be cloned from the New Mutant CGI and modified as needed
SObA Graphs for phenotype
- Juancarlos will transfer code tomorrow, if there are no change requests before then
- Existing feature requests will be added to future releases of SObA
Micropublications
- Daniela spoke with Daniel about having web pages in WormBook style to house micropublications
Status of WormBase User Survey?
- Paul sent around paper this morning: http://www.nature.com/nature/journal/v527/n7576_supp/full/527S16a.html
- What aspects of databases really get used by users?
- How can we be more efficient with existing curation pipelines?
- Question of the month on WormBase?
- We could get user feedback when visiting labs
Sending author updates
- Would be nice to have a mechanism to update authors on what has been curated for their paper
- Could give paper data summaries as well as recent updates to curation for a paper
Objectifying/Itemizing annotations from Postgres
- What if we objectified itemized Postgres entries for easier display of all annotations per paper, for example?
- May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper
- This would be in lieu of actually objectifying all annotations
November 12, 2015
Citace upload Dec 1st
SAB set for Feb 4-5, 2016
Concise description form
- URL for listing genes mentioned in a paper
- Ranjana will send to Kimberly
Community curation CGI
- Almost ready for prime time
- ~155 e-mails sent out for allele-phenotype; ~25-30 responses
Scripts for community description form
- James wrote scripts that will need to inform community CGI
- Ranjana will work with Juancarlos
FlyBase text mining
- Text mining for Fly corpus, entity recognition and extraction, esp. for transgenes
- Need to improve SVM on transgene and allele recognition
- Textpresso working on tools for FlyBase
Phenotype SObA graph
- Making progress towards making the graph a widget on the gene page
- Still issues to iron out; working with Sibyl
- Some conflicts with Cytoscape for interactions vs. SObA
Data Visualization program opportunity
- Will have to write a grant
- Would pay for one person, get two with grant
- Anyone with ideas should consider a proposal
- Dec 15th deadline
WormBook
- Daniel prepared mockup for new web page
Biocuration meeting
- Mary Ann working out plans for community curation workshop
- Does PomBase track their community curation?
HT115 vs HT115(DE3) E.coli strains
- Redundant, should probably merge HT115 into HT115(DE3), as the RNAi-host E.coli strain
Visualization plans
- Karen e-mailed around older proposal for work with Santiago Lombeyda
- Original project was to upgrade visualization of pathways and virtual worm in WB page
November 19, 2015
Community curation
- Community e-mailing for allele-phenotype: 315 e-mails sent, 49 papers curated, 260 community annotations in the Phenotype OA
- Chris gave Paul list of all sy* alleles and phenotypes
- Paul going through table to add phenotypes not already in WB
- Paul using Textpresso and an allele-phenotype worksheet
- Do we want to create more elaborate forms or parallel forms? Probably parallel forms (in future)
- How can we assess completeness of curation? Very difficult to automate, currently
- Check figures and tables
- Ask authors about completeness
- Publication templates/worksheets? Streamline data submission concurrent with publication
- Can discuss at SAB in Feb
- We can send PI's/authors lists of alleles and what phenotypes WB has
Working with NCBI
- Interested in Textpresso text-mining and SVM categorizing
- How might we work with NCBI & PubMed Central to curate? They are willing to run SVM on PMC corpus
Minimum information requirements
- RNAi MI seemed bulky and not complete
- Asks authors for genes targeted, not dsRNA sequence
- We could write up a paragraph outlining the complaints about the proposed RNAi MI
- Maybe micropublish the paragraph
Micropublications
- Should go into PubMed Central
Allele descriptions
- Karen wants to adapt Ranjana and James' automated gene descriptions for alleles
- Start working on in January
SObA
- Juancarlos making progress on integrating into the WB site
- There are difficulties getting SObA into it's own widget on the gene page
- Conflicts with other settings (javascript / cytoscape) on same page, e.g. Interactions widget (w/Cytoscape viewer)
- Updated cytoscape.min.js version on Interactions viewer
Corresponding author curation
- Juancarlos and Cecilia have worked out a pipeline to capture corresponding authors for each paper
- Once paper editor changes are decided, can go live
WormBook chapters for WormBase
- Each chapter written for users, but we likely want to avoid too much technical jargon
- We do want transparency
- We can separate the chapters into less-technical and more-technical, for easier reading