Revision as of 20:12, 13 March 2014

Previous Years

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

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

?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

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, Postgres, 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

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)

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

@@ Line 51: / Line 51: @@
 * ?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
+**Clone wiki from PaulD: http://wiki.wormbase.org/index.php/WormBase_Model:Clone#Class_contents_WS242
-http://wiki.wormbase.org/index.php/WormBase_Model:Clone#Class_contents_WS242
 * Database Future Mtg report