Difference between revisions of "WormBase-Caltech Weekly Calls"
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* not looking at OWL yet | * not looking at OWL yet | ||
* will get relationships from Raymond | * 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 | ||
+ | * still working on pipeline | ||
+ | |||
+ | ===Rose alleles=== | ||
+ | * 150,000 new alleles, Mary Ann working on it | ||
+ | * phenotypes were only reported for a small fraction | ||
+ | |||
+ | ===CGC strains=== | ||
+ | Mary Ann received latest update, CGC very busy with new gene engineering technique | ||
=== WB WBook chapters === | === WB WBook chapters === | ||
Main outline [https://docs.google.com/a/wormbase.org/document/d/1l6pExlCMI88pi_-djk8jt7IzNsMDV-nIEY9Z1gBNh-A/edit here] | Main outline [https://docs.google.com/a/wormbase.org/document/d/1l6pExlCMI88pi_-djk8jt7IzNsMDV-nIEY9Z1gBNh-A/edit here] | ||
− | *Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly) [https://docs.google.com/a/wormbase.org/document/d/1mAxrqVIhxDNpkTUBmtu12sAo58pEG763tgASlzy-3JU/ here] | + | *Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly) |
+ | [https://docs.google.com/a/wormbase.org/document/d/1mAxrqVIhxDNpkTUBmtu12sAo58pEG763tgASlzy-3JU/ here] | ||
*Pathways and Processes (Karen) [https://docs.google.com/a/wormbase.org/document/d/1maTRPoIdmbZqfnd-8jZ5dCYPGM2fF6ihk9ZMhjcVL1Y/edit?usp=drive_web here] | *Pathways and Processes (Karen) [https://docs.google.com/a/wormbase.org/document/d/1maTRPoIdmbZqfnd-8jZ5dCYPGM2fF6ihk9ZMhjcVL1Y/edit?usp=drive_web here] | ||
+ | * Sequence feature (Daniela) | ||
+ | |||
+ | ===Micropublication=== | ||
+ | * Hobert- micropublication for expression = small facts, data will never be published (Daniela) | ||
+ | * Community annotation not linked to a publication | ||
+ | * a couple models | ||
+ | ** WB captures submissions blind | ||
+ | ** WB reviews | ||
+ | * need to establish microattributions to increase the value of submissions | ||
+ | * involve semi-peer review through automated feed back to scientists who've worked on the gene, cell, entity, etc. | ||
+ | * need to set up a pilot, to see how popular | ||
=== Picture curation === | === Picture curation === | ||
*for topic curation | *for topic curation | ||
**want to annotate figures with genes | **want to annotate figures with genes | ||
− | **want dynamic display with slide show, different highlighted figures, crowdsourcing | + | **want dynamic display with slide show, different highlighted figures, |
+ | * community voting - crowdsourcing | ||
+ | * WB-blessed image represented through wikipathways | ||
+ | |||
+ | |||
+ | ===Kimberly=== | ||
+ | |||
+ | |||
+ | ===Juancarlos=== | ||
+ | * management of automated descriptions with Ranjana | ||
+ | * phenotype requests through RNAi and allele phenotype | ||
− | * | + | ===Automated descriptions=== |
+ | * playing with pulling out useful data to add to description automation |
Revision as of 20:13, 8 January 2015
Previous Years
2015 Meetings
January 2015
January 8, 2015
Community annotation
- author participation
- Cecilia: still lots of work to process data, need to process data submitted by authors
- old data kept for history and for comparison
- people mess up institution names - is being changed to a controlled vocabulary
- campus addresses also not standardized - organize/create address fields, e.g., street address, mail-code, etc.,
- add example address
- ~10 author submissions a week
- most curation is extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but still needs to be parsed
- how to mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- easy to mine from laboratory, those 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 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
- still working on pipeline
Rose alleles
- 150,000 new alleles, Mary Ann working on it
- phenotypes were only reported for a small fraction
CGC strains
Mary Ann received latest update, CGC very busy with new gene engineering technique
WB WBook chapters
Main outline here
- Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)
- Pathways and Processes (Karen) here
- Sequence feature (Daniela)
Micropublication
- Hobert- micropublication for expression = small facts, data will never be published (Daniela)
- Community annotation not linked to a publication
- a couple models
- WB captures submissions blind
- WB reviews
- need to establish microattributions to increase the value of submissions
- involve semi-peer review through automated feed back to scientists who've worked on the gene, cell, entity, etc.
- need to set up a pilot, to see how popular
Picture curation
- for topic curation
- want to annotate figures with genes
- want dynamic display with slide show, different highlighted figures,
- community voting - crowdsourcing
- WB-blessed image represented through wikipathways
Kimberly
Juancarlos
- management of automated descriptions with Ranjana
- phenotype requests through RNAi and allele phenotype
Automated descriptions
- playing with pulling out useful data to add to description automation