Difference between revisions of "WormBase-Caltech Weekly Calls"
Line 119: | Line 119: | ||
* Xiaodong is writing up an abstract, will send around before submission | * Xiaodong is writing up an abstract, will send around before submission | ||
* Xiaodong will run a curation tutorial for Chinese speakers | * Xiaodong will run a curation tutorial for Chinese speakers | ||
+ | |||
+ | |||
+ | ==Jan 22== | ||
+ | === ad hoc curation of tier III species (Mary Ann)=== | ||
+ | WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis? | ||
+ | http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf | ||
+ | |||
+ | === Complex Gene Loci (Mary Ann) === | ||
+ | e.g. lin-15A/lin-15B | ||
+ | |||
+ | unc-17/cha-1 | ||
+ | |||
+ | We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g. lin-15A lin-15B complex loci. | ||
+ | |||
+ | nb. Maybe hard to discuss w/o Paul Davies. | ||
+ | |||
+ | ===micropublication=== | ||
+ | *Daniela starting to work on author submission forms | ||
+ | *Requirements? Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene |
Revision as of 19:43, 22 January 2015
Contents
Previous Years
2015 Meetings
January 2015
January 8, 2015
Community annotation
- author participation
- Cecilia: still lots of work, need to manually process data submitted by authors
- old data kept for history and for comparison
- people mess up institution names - institution field on submission form being changed to a controlled vocabulary
- campus addresses also not standardized - will organize/create address fields, e.g., street address, mail-code, etc.,
- add example address
- ~10 author submissions a week
- most curation involves extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but information still needs to be parsed
- can we mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- (1) easy- people associated with a laboratory, (2) difficult- people not in a registered lab
Cross-product development
Raymond
- embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers
- wants to move to OWL now; comment is that obo relationships are not directly translatable into OWL
- Uberon has elegans anatomy
Gary
- starting to work with Chris and Karen on developing cross-products, still in exploration phase
- not looking at OWL yet
- will get relationships from Raymond
Sequence feature curation
Daniela, Gary, Xiaodong, Mary Ann are validating papers as positive/negative in curation status form. As soon as ready, Mary Ann/Gary will start curating
Rose alleles
- 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247
- phenotypes were only reported for a small fraction
CGC strains
Mary Ann received latest update, CGC very busy with strains generated through new gene engineering techniques
WB WBook chapters
Main outline here- note this document cannot be edited, people can create their own shared docs for their respective papers
- Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)
- Pathways and Processes (Karen) here
- Expression (Daniela)
Micropublication
- Hobert- micropublication for expression = small facts, which are data that will never be published (Daniela working with Hobert on these)
- Community annotation not linked to a publication
- a couple models for WB dealing with the micropubs
- WB captures all submissions blind and posts them
- WB reviews submission - curators decide which micropubs have value
- need to establish microattributions to increase the value of submissions
- involve semi-peer review through automated fact review requests to scientists who've worked on the gene, cell, entity, etc.
- need to set up a pilot, to get a feel for the amount of participation/work this tool will be
Picture curation
- for topic curation
- want to annotate figures with genes - involves model change
- want dynamic display with slide show, different highlighted figures - need to work with webteam
- community voting - crowdsourcing - need to work with webteam
- WB-blessed image represented through wikipathways
Kimberly
Continuing work on the new GO model
Juancarlos
- management of automated descriptions with Ranjana
- phenotype requests through RNAi and allele phenotype done in december
Automated descriptions
- playing with pulling out useful data to add to description automation (James and Ranjana)
January 15, 2015
New expression objects and pictures
- Cross-species comparison of developmental gene expression
- Have life stage annotation
- Microarray experiments
- Do we have data on significant differences from C. elegans? Can we get the analysis or algorithm?
Neuro anatomy
- 3 ways to access neuro-connectivity data
- ACEDB, Kris Gunsalus' server at NYU (defunct), Nikhil Bhatla's connectivity browser
- We would like to adopt Nikhil's browser (for neural connectivity AND the cell lineage browser); we need to act before it disappears
FPKM RNA-Seq data display
- Should we suggest splitting the data display by tissue, life stage, treatment, etc.?
- Gary Williams is responsible; need to talk to him
Heavy metal toxicity/response
- New topic, all papers have been checked
- Need to send list of relevant genes to Hinxton
- Curators can now flag figures relevant as topic diagrams
Phenotype picture curation
- We will begin to collect pictures for phenotypes
- Will require model changes
Phenotype OA Strain fields
- "Parental strain" autocomplete field added to TAB 2 of Phenotype OA
- Plan is to put parental strains in the Phenotype_info hash
- Natural isolate strains can be directly annotated with phenotype?
BioCuration meeting in April
- Xiaodong is writing up an abstract, will send around before submission
- Xiaodong will run a curation tutorial for Chinese speakers
Jan 22
ad hoc curation of tier III species (Mary Ann)
WBPaper00046176 describes Ctr- genes and alleles (fig 3). Although we do not curate this (and other tier III) species, should we place this information somewhere, on an ad hoc basis? http://tazendra.caltech.edu/~acedb/daniel/00046176_Wei14_temp.pdf
Complex Gene Loci (Mary Ann)
e.g. lin-15A/lin-15B
unc-17/cha-1
We should use existing Gene_cluster model and add new Type tag to differentiate between e.g. rrn Gene cluster and e.g. lin-15A lin-15B complex loci.
nb. Maybe hard to discuss w/o Paul Davies.
micropublication
- Daniela starting to work on author submission forms
- Requirements? Paul says needs sequence - minimal important stuff, sequence, expression pattern, construct, reporter gene