Difference between revisions of "BBOP OBD visit/Chris notes"

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Chris's initial plan before beginning work...
 +
 
 +
== Setup ==
 +
 
 +
Checkout code from NCBO GForge
 +
 
 +
* OBDAPI
 +
* OBDUI
 +
 
 +
Developers recommended to use Eclipse
 +
 
 +
Everything can be run from command line; eventually everything can be
 +
run from a RESTy web admin interface.
 +
 
 +
* TODO: web admin interface (PUNT)
 +
 
 +
* TODO: add instructions for setting up PATH
 +
 
 +
== Initialization ==
 +
 
 +
=== Core database plus ontologies ===
 +
 
 +
Run
 +
 
 +
obd-create-db.pl -h <HOST> -d obdevo -c obdevo.conf
 +
 
 +
Then run
 +
 
 +
obd-reasoner.pl  -d obdevo@HOST
 +
 
 +
This populates the deductive closure
 +
 
 +
* TODO: create and test obdevo.conf (1 day)
 +
 
 +
This is just a newline separate list of ontology IDs (teleost_anatomy
 +
quality etc) or URLs
 +
 
 +
(Optional: sources can be loaded later)
 +
 
 +
=== Load Phylogenies ===
 +
 
 +
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
 +
 
 +
=== Load annotations ===
 +
 
 +
Run
 +
 
 +
obd-exec --format org.obd.parser.NESCENTPhenoteConfigParser <TAB-FILES>
 +
 
 +
* TODO: write org.obd.parser.NESCENTPhenoteConfigParser (1 day)
 +
 
 +
(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
 +
 
 +
* TODO: add NESCENT specific rules (3+ days) (PUNT)
 +
 
 +
TBD: discuss the relation between a higher taxon and phenotypes
 +
instantiated by sub-taxa. How to deal with loss?
 +
 
 +
See also phylogenies above
 +
 
 +
== Set up UI / REST interface ==
 +
 
 +
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
 +
 
 +
== Annotation and Ontology Lifecycle ==
 +
 
 +
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
 +
 
 +
* TODO: incremental annotation loading support (PUNT)
 +
 
 +
Medium term the entire load cycle can be automated, so long as
 +
everything is configured:
 +
 
 +
* TODO: add NESCENT .tab file location to annotations metadata file
 +
 
 +
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.
 +
 
 +
* TODO: load + reason entire OBD database automatically from config
 +
 
 +
== Phenote integration ==
 +
 
 +
* TODO: write org.phenote.datamodel.NESCENTTaxonPhenotypeMappingDriver (3 days) (PUNT)
 +
 
 +
As noted above, this can be sidestepped in the short term for OBD loading
 +
 
 +
* TODO: write adapter GUI in Phenote
 +
 
 +
== Additional capabilites ==
 +
 
 +
TBD. Some ideas:
 +
 
 +
* evo-devo lenses (Jim/Rob)
 +
* integration with wider phenotype database
 +
e.g. to do integrate ZFIN genotype-phenotype annotations with evo-debo ones
 +
This can be done dynamically with a MultiShard
  
 
[[Category:Informatics]]
 
[[Category:Informatics]]

Latest revision as of 02:31, 25 August 2008

Chris's initial plan before beginning work...

Setup

Checkout code from NCBO GForge

  • OBDAPI
  • OBDUI

Developers recommended to use Eclipse

Everything can be run from command line; eventually everything can be run from a RESTy web admin interface.

  • TODO: web admin interface (PUNT)
  • TODO: add instructions for setting up PATH

Initialization

Core database plus ontologies

Run

obd-create-db.pl -h <HOST> -d obdevo -c obdevo.conf

Then run

obd-reasoner.pl -d obdevo@HOST

This populates the deductive closure

  • TODO: create and test obdevo.conf (1 day)

This is just a newline separate list of ontology IDs (teleost_anatomy quality etc) or URLs

(Optional: sources can be loaded later)

Load Phylogenies

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

Load annotations

Run

obd-exec --format org.obd.parser.NESCENTPhenoteConfigParser <TAB-FILES>

  • TODO: write org.obd.parser.NESCENTPhenoteConfigParser (1 day)

(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

  • TODO: add NESCENT specific rules (3+ days) (PUNT)

TBD: discuss the relation between a higher taxon and phenotypes instantiated by sub-taxa. How to deal with loss?

See also phylogenies above

Set up UI / REST interface

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

Annotation and Ontology Lifecycle

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

  • TODO: incremental annotation loading support (PUNT)

Medium term the entire load cycle can be automated, so long as everything is configured:

  • TODO: add NESCENT .tab file location to annotations metadata file

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.

  • TODO: load + reason entire OBD database automatically from config

Phenote integration

  • TODO: write org.phenote.datamodel.NESCENTTaxonPhenotypeMappingDriver (3 days) (PUNT)

As noted above, this can be sidestepped in the short term for OBD loading

  • TODO: write adapter GUI in Phenote

Additional capabilites

TBD. Some ideas:

  • evo-devo lenses (Jim/Rob)
  • integration with wider phenotype database

e.g. to do integrate ZFIN genotype-phenotype annotations with evo-debo ones This can be done dynamically with a MultiShard