Chris’s initial plan before beginning work…
Checkout code from NCBO GForge
Developers recommended to use Eclipse
Everything can be run from command line; eventually everything can be run from a RESTy web admin interface.
Run
obd-create-db.pl -h
Then run
obd-reasoner.pl -d obdevo@HOST
This populates the deductive closure
This is just a newline separate list of ontology IDs (teleost_anatomy quality etc) or URLs
(Optional: sources can be loaded later)
OPEN. Is this entirely covered by loading TTO? Do we want to load alternative phyogenetic hypotheses? Metadata on how the tree was arrived at? Branch lengths? How will these be used in queries?
Loading of PhyloXML or NHX files would be easiest for us
Run
obd-exec –format org.obd.parser.NESCENTPhenoteConfigParser
(use NCBO one as a template)
Note that we could write a phenote mapping to org.obo.annotation instead. This is probably the way to go in the long run, but it will slow us in the short term. See Phenote section below
Once the annotations are loaded we run the reasoner again:
obd-reasoner.pl -d obdevo@HOST
This computes the subsumption relations between EQs
TBD: discuss the relation between a higher taxon and phenotypes instantiated by sub-taxa. How to deal with loss?
See also phylogenies above
ROB: fill in generic OBD TomCat instructions here
The web interface is bare bones, but it will allow you to navigate taxon-taxon, taxon-phenotype, phenotype-phenotype, phenotype-taxon
(here phenotype encompasses EQ class expressions as well as individual ontology classes)
Also uses reasoner results in querying
PLAN: set up initial install, demo, discuss further requirements, what is required from API to implement them
For now the easiest way to deal with lifecycle is to recreate the database from scratch. If all primary data is in cvs/svn/ftp we lose nothing, but there is admin overhead etc
Longer term OBD will support incremental loading
Medium term the entire load cycle can be automated, so long as everything is configured:
This is the file here: http://obo.cvs.sourceforge.net/obo/obo/website/cgi-bin/annotations.txt?view=log
It is easiest for OBD if all sources are registered.
As noted above, this can be sidestepped in the short term for OBD loading
TBD. Some ideas:
e.g. to do integrate ZFIN genotype-phenotype annotations with evo-debo ones This can be done dynamically with a MultiShard