WormBase-Caltech Weekly Calls
From WormBaseWiki
Previous Years
2014 Meetings
March 6, 2014
Agenda
- ?Construct model
- SPELL
SPELL
- WS242 started to have miRNA datasets; very short probes, not uniquely mapped
- Wen made modifications to SPELL to accommodate
- Wen has started separating datasets from papers
- miRNA analyses have used completely different platforms than protein-coding genes, so requires a different dataset for each
- Wen started loading WB topics into SPELL
- Wen would like assign ~100 papers in SPELL to WB topics
- Wen also modified SPELL script to annotate datasets applicable to specific tissues or cells
- Wen may/will co-opt Juancarlos' SPELL instance for testing
?Construct model
- New ?Construct model will be vetted and approved for early in the WS244 curation cycle
- Some changes to the ?Construct model proposed over last week
- Still discussing how to handle plasmids/vectors, whether they should go in the ?Clone class (there is precedence)
- We should defer to the Sequence Ontology, wherever possible, for definitions and relationships
- We will go ahead with considering including all plasmids and vectors (e.g. AddGene & Fire vectors) to the ?Clone class which can then be referenced within the ?Construct class
- Will change the "Identical_transgene"/"Identical_variation" tags to "Corresponding_transgene"/"Corresponding_variation"
- If necessary, we will consider adding a ?Construct tag to the ?Interaction model to accommodate annotation of constructs used in in vitro physical interaction experiments; this is pending curation of (sufficient amounts of) the relevant data
March 13, 2014
Agenda
- ?Infection_assay model
- ?Construct model (do we need to discuss?)
- From my side there no need to discuss further if we can keep the Clone tag in the ?Construct model and as far as plasmids are continued to be curated in the ?Clone class. -Daniela
- Clone wiki from PaulD: http://wiki.wormbase.org/index.php/WormBase_Model:Clone#Class_contents_WS242
- Database Future Mtg report
Database Meeting Summary
- Write up <https://www.dropbox.com/s/fr9qrsbup9djx4z/DatabaseFutureMeetingatOICR.pdf>.
- Working group from three sites will test candidate technologies against metrics, considerations and requirements and report by Oct 2014.
- Not clear yet whether everyone (in WormBase) will use one universal database technology, or if each site might use different databases
- Site requirements: web speed & performance, model flexibility with regular updates, understandability of modeling language/structure
- Different options: relational, row, column, NoSQL, SQL, object-oriented, graph database (Neo4J), DynamoDB (Amazon NoSQL DB)
- Central database for everyone? Real-time editing and updating, or regular updating/synchronization
- Process will take ~2 years or so
Data visualization with Santiago Lombeyda
- Will play with some potentially straight-forward display options
- Virtual worm renderings made into SVGs for layering and clicking/linking
?Infection_assay model
- Broaden scope to include all types of species-species interaction (?Interspecies_interaction class ???)
- Remove "Modifying_influence" tag and "Required*" tags in favor of "Resistance" and "Hypersensitivity" sets of tags
- If we are going to include many types of species-species interactions, we need to consider how to make tag names that are unambiguous with respect to which species is playing a particular role
- We will talk to parasite curators to see what we want to include in the model
- Ranjana would like to add a concise-description-like text description to genes describing their role in infection
- Will require retroactively making database connections once the ?Infection_assay (or equivalent) model is finalized and implemented (not this upcoming release)
WormBase Topic/Process hierarchy/ontology relationships
- Karen will send around a working OBO file
- Curators can look at which topics should be related to others (via parent-child relationships)
- Also, we can look at trying to tie in to existing GO terms
March 20, 2014
Agenda
- Pad 0s in WBPerson objects. https://github.com/WormBase/website/issues/2522#issuecomment-38077230
- Database discussions
- GO Meeting update
New Database Discussions
- We want speed, efficiency, performance
- Will keep WB 2.0 web architecture
- One big database for everyone?
- Timestamps would not be kept for all annotations (performance, economy issues)
- We still keep "Date_last_updated" and "Curator_confirmed" in ACEDB in the #Evidence hash
- We would want to specify when and where we would want to keep (and track) timestamps
- ACEDB timestamps have been proven useful
Padding WBPerson ID numbers with zeros
- Laboratory search for "Raymond Chan" did not produce the desired/expected results
- WBPerson ID is indexed but not the text string of the affiliated person
- In this case WBPerson98 is listed, but automated searching for the full text person name was affected by the return of many WBPerson98* results
- How much work would be required to change the WBPerson ID padding? Not trivial
- We'll clarify what we think should be the user experience and Abby can decide the best way to fix it
- We should thoroughly go through classes and clarify what fields should be indexed
GO Meeting update (from Paul Sternberg and Kimberly Van Auken)
- Chris Mungall presenting/discussing common annotation tool
- Table view annotator
- Graph view annotator (LEGO/ORION) (example: http://go-genkisugi.rhcloud.com/seed/model/gomodel:goa_human-5323da180000002)
- Tree view, PAINT tool used
- Text, Paper viewer (SAB was excited about)
- Protein-2-GO tool: dumped or restructured/repurposed?
- Protein-2-GO open source? Should be open to further development
- OBO-Edit is not being supported, changes from OBO to OWL format
- Switching from OBO-Edit to Protege (will take time, ~6 months development)
- CANTO (PomBase)
- http://curation.pombase.org/
- Online annotation tool, making use of ontologies
- AMIGO2 now live on GO website
- http://beta.geneontology.org/
- Enrichment analysis (from PANTHER database)
Term Genie
- New tool
- Relies on logical definitions for GO terms
- Web-based form for adding GO annotations when you can create logical definitions (explicit use of defined relationships)
- E.G. response to chemical (when chemical has a ChEBI ID), etc.
- Great for requesting new terms
- http://go.termgenie.org/
- http://code.google.com/p/termgenie/
Disease curation
- FlyBase went live with disease data
- We want to continue to have (and maybe extend upon) our connections/links to and from OMIM
- We could work on WormBase/OMIM portal