Difference between revisions of "WormBase-Caltech Weekly Calls"
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*See if Textpresso can pull out paragraphs (or +/- 4 sentences?) for each sentence to see context | *See if Textpresso can pull out paragraphs (or +/- 4 sentences?) for each sentence to see context | ||
*Can we devise some automation to handle interaction updates? | *Can we devise some automation to handle interaction updates? | ||
| + | |||
| + | |||
| + | |||
| + | == January 12, 2012 == | ||
| + | |||
| + | SVM | ||
| + | *Genetic Interaction SVM | ||
| + | *How well does it work? | ||
| + | *Do we have sentences? | ||
| + | *Kimberly will follow up with Xiaodong | ||
| + | *For HIV papers? | ||
| + | |||
| + | |||
| + | Human Diseases Connections | ||
| + | *Should be on new gene pages | ||
| + | *Browse function not yet fully functional | ||
| + | *Search with autocomplete available | ||
| + | *Table from 2000 Review, human/C. elegans orthologs and diseases - put on website? | ||
| + | *Indexed ACEDB data used for searches; create table from indexed data? | ||
| + | *Textpresso pipeline flags relevant disease papers; can info be added to database? | ||
| + | *?Human_disease model vs tag in ?Gene model? | ||
| + | *Similar discussion to ?Process model discussion | ||
| + | *Let's propose a ?Human_disease model; see what objections/suggestions anyone has (EBI?) | ||
| + | *Will follow the OBO/NCBI human disease ontology | ||
| + | |||
| + | |||
| + | Gloworm links | ||
| + | *Raymond made links from Anatomy pages to Gloworm site | ||
| + | *Can view movie relevant to Anatomy object at Gloworm | ||
| + | *Gloworm seems to only work on Macs (firewalled on Windows, doesn't work at all on Linux) | ||
| + | *Can we add an Apple symbol/logo next to Gloworm links on new site? | ||
| + | **Logo difficult, but we could add a text caveat | ||
| + | **New window opens with links; users should see error and be able to send Bill Mohler a message | ||
| + | |||
| + | |||
| + | Ontology Searches | ||
| + | *Status? | ||
| + | *Gary and Karen talking about fixing/cleaning up Phenotype Ontology | ||
| + | *Would be useful to have a filter on ontology searches | ||
| + | *Phenotype search available now, but no filters | ||
| + | *New search features not likely to be made in near future | ||
| + | *Intermine may be better tool for this | ||
| + | |||
| + | |||
| + | Genetic Interactions | ||
| + | *Rose discussed genetic interaction ontology with BioGRID et al in December | ||
| + | *BioGRID will stick with older terms (at least for now) as SGD and Entrez Gene need to also be on board | ||
| + | *Chris will review older 'Genetic' interactions with new terms as a proof of concept | ||
| + | *Can send results to BioGRID, SGD, and Entrez Gene | ||
| + | |||
| + | |||
| + | GSA markup | ||
| + | *Flybase wants authors to take care of all markup QC | ||
| + | *Pipeline: Author QC -> DJS -> Flybase check | ||
| + | *Flybase has minimal QC Fast service | ||
| + | *Michael added an 'UNDO' button for QC Fast | ||
| + | *Remove author ability to add links? | ||
Revision as of 20:00, 12 January 2012
2011 Meetings
2012 Meetings
January 5, 2012
Interactions patch
- One large scale paper omitted from upload
- Patch sent in; all OK
Integration of 3rd party data
- BioGRID, Gene Orienteer, Interolog database, etc.
- Gene Orienteer
- May only want interactions above a threshold
- Interolog database
- Get gene pages linked to their database
- Display data on gene pages, but keep display distinct?
- FlyBase links out to BioGRID, Interolog
- modEncode Transcription Regulatory Network display/diagrams?
New site release with WS230?
- About 2 months
Textpresso Interaction Sentences
- Now have sentences associated with interactions
- Need to discuss what sentences should be kept as adequate evidence of interaction and placed in remarks
- See if Textpresso can pull out paragraphs (or +/- 4 sentences?) for each sentence to see context
- Can we devise some automation to handle interaction updates?
January 12, 2012
SVM
- Genetic Interaction SVM
- How well does it work?
- Do we have sentences?
- Kimberly will follow up with Xiaodong
- For HIV papers?
Human Diseases Connections
- Should be on new gene pages
- Browse function not yet fully functional
- Search with autocomplete available
- Table from 2000 Review, human/C. elegans orthologs and diseases - put on website?
- Indexed ACEDB data used for searches; create table from indexed data?
- Textpresso pipeline flags relevant disease papers; can info be added to database?
- ?Human_disease model vs tag in ?Gene model?
- Similar discussion to ?Process model discussion
- Let's propose a ?Human_disease model; see what objections/suggestions anyone has (EBI?)
- Will follow the OBO/NCBI human disease ontology
Gloworm links
- Raymond made links from Anatomy pages to Gloworm site
- Can view movie relevant to Anatomy object at Gloworm
- Gloworm seems to only work on Macs (firewalled on Windows, doesn't work at all on Linux)
- Can we add an Apple symbol/logo next to Gloworm links on new site?
- Logo difficult, but we could add a text caveat
- New window opens with links; users should see error and be able to send Bill Mohler a message
Ontology Searches
- Status?
- Gary and Karen talking about fixing/cleaning up Phenotype Ontology
- Would be useful to have a filter on ontology searches
- Phenotype search available now, but no filters
- New search features not likely to be made in near future
- Intermine may be better tool for this
Genetic Interactions
- Rose discussed genetic interaction ontology with BioGRID et al in December
- BioGRID will stick with older terms (at least for now) as SGD and Entrez Gene need to also be on board
- Chris will review older 'Genetic' interactions with new terms as a proof of concept
- Can send results to BioGRID, SGD, and Entrez Gene
GSA markup
- Flybase wants authors to take care of all markup QC
- Pipeline: Author QC -> DJS -> Flybase check
- Flybase has minimal QC Fast service
- Michael added an 'UNDO' button for QC Fast
- Remove author ability to add links?
