Difference between revisions of "WormBase-Caltech Weekly Calls"
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=== Community annotation=== | === Community annotation=== | ||
* author participation | * author participation | ||
| − | **Cecilia: still lots of work | + | **Cecilia: still lots of work, need to manually process data submitted by authors |
** old data kept for history and for comparison | ** old data kept for history and for comparison | ||
| − | ** people mess up institution names - | + | ** people mess up institution names - institution field on submission form being changed to a controlled vocabulary |
| − | ** campus addresses also not standardized - organize/create address fields, e.g., street address, mail-code, etc., | + | ** campus addresses also not standardized - will organize/create address fields, e.g., street address, mail-code, etc., |
** add example address | ** add example address | ||
** ~10 author submissions a week | ** ~10 author submissions a week | ||
| − | ** most curation | + | ** 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=== | ===Cross-product development=== | ||
Raymond | Raymond | ||
* embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers | * 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 | + | * wants to move to OWL now; comment is that obo relationships are not directly translatable into OWL |
* Uberon has elegans anatomy | * Uberon has elegans anatomy | ||
| Line 41: | Line 41: | ||
===Sequence feature curation=== | ===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 | + | 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=== | ===Rose alleles=== | ||
| Line 48: | Line 48: | ||
===CGC strains=== | ===CGC strains=== | ||
| − | Mary Ann received latest update, CGC very busy with new gene engineering | + | Mary Ann received latest update, CGC very busy with strains generated through new gene engineering techniques |
=== 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]- 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) | *Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly) | ||
[https://docs.google.com/a/wormbase.org/document/d/1mAxrqVIhxDNpkTUBmtu12sAo58pEG763tgASlzy-3JU/ here] | [https://docs.google.com/a/wormbase.org/document/d/1mAxrqVIhxDNpkTUBmtu12sAo58pEG763tgASlzy-3JU/ here] | ||
| Line 58: | Line 58: | ||
===Micropublication=== | ===Micropublication=== | ||
| − | * Hobert- micropublication for expression = small facts, data will never be published (Daniela) | + | * 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 | * Community annotation not linked to a publication | ||
| − | * a couple models | + | * a couple models for WB dealing with the micropubs |
| − | ** WB captures submissions blind | + | ** WB captures all submissions blind and posts them |
| − | ** WB reviews | + | ** WB reviews submission - curators decide which micropubs have value |
* need to establish microattributions to increase the value of submissions | * need to establish microattributions to increase the value of submissions | ||
| − | * involve semi-peer review through automated | + | * 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 | + | * need to set up a pilot, to get a feel for the amount of participation/work this tool will be |
=== Picture curation === | === Picture curation === | ||
*for topic curation | *for topic curation | ||
| − | **want to annotate figures with genes | + | **want to annotate figures with genes - involves model change |
| − | **want dynamic display with slide show, different highlighted figures | + | **want dynamic display with slide show, different highlighted figures - need to work with webteam |
| − | * community voting - crowdsourcing | + | * community voting - crowdsourcing - need to work with webteam |
* WB-blessed image represented through wikipathways | * WB-blessed image represented through wikipathways | ||
| − | |||
===Kimberly=== | ===Kimberly=== | ||
| Line 80: | Line 79: | ||
===Juancarlos=== | ===Juancarlos=== | ||
* management of automated descriptions with Ranjana | * management of automated descriptions with Ranjana | ||
| − | * phenotype requests through RNAi and allele phenotype | + | * phenotype requests through RNAi and allele phenotype done in december |
===Automated descriptions=== | ===Automated descriptions=== | ||
| − | * playing with pulling out useful data to add to description automation | + | * playing with pulling out useful data to add to description automation (James and Ranjana) |
Revision as of 20:27, 9 January 2015
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)
