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VFB_schema_IDs
IDs on VFB
OWL IDs.
All OWL entities (inclusing classes and individuals) are identified by a URI. For most purposes, VFB code shortens this to a short-form ID: The bit after the last '/'. We currently use two flavor of URI:
http://purl.obolibrary.org/obo/FBbt_\d{8}
http://www.virtualflybrain.org/owl/VFB_\d{8}
(\d{8} is Perl RegEx for 8 digits)
We happen to use the first of these for anatomical classes and the second we use mostly for anatomical individuals. However, we should resist the temptation to use FBbt as shorthand for class and VFB as shorthand for individual in JavaDoc.
External DB IDs
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FlyBase
feature IDs
Genes:Fbgn\d{7}
Transgenes: FBti\d{7}, FBtp\d{7}FBti and FBtp are important as we use them as keys for third party beans for stacks identified by their transgene expression, as well as to link to FlyBase. Question: what keys are used for third party beans identified by the anatomical structure they depict, e.g. clones, FlyCircuit neurons.
pub Ids: FBrf\d{7}
An argument, along with a miniref string, in the constructor of PubBean -
BrainTrap IDs
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Clusters
Clusters are actually individuals with VFB ids, but for lookup purposes are keyed on FLyCircuit exemplar name <check></check>
Relationship of IDs to Beans
Much information displayed on VFB is first packaged into 'beans' which are then queried for the relevant content using JSP. We currently have 4 flavors of Bean driving the site:
PubBean
OntBean
Constructors: OntBean(); OntBean(java.lang.String fbbtId)
Presumably all current usage involves an FBbt ID, but better to call this arg 'OwlClassID'? Or, given its extension, OwlEntityID ?
OntBeanIndividual
extends OntBean
Constructors: OntBeanIndividual(java.lang.String fbbtId)
Presumably all current usage involves a VFB ID for an individual. Assuming constructor inherited, best name for arg might be OWLEntityID
ThirdPartyBean
Constructors: ThirdPartyBean(); ThirdPartyBean(java.lang.String fbId, java.lang.String remoteId, java.lang.String resourceName, java.lang.String thumbName, java.lang.String stackName, java.lang.String baseUrl, java.lang.String thumbUrl, java.lang.String stacksBaseUrl, java.lang.String descr)
Lots of IDs in here, mostly coming from lookup tables in the VFB DB. Presumably fbID is used internally as key - corresponds to FBti\d{7} or FBtp\d{7}
Discussion
David,
see my addition to the specs document:
https://docs.google.com/document/edit?id=1ubIQpDR_W1Ql_62o3tGEMXtuB_C3Pc9o5sqm2PQWLyA#bookmark=id.7boh3j97xcuk
N
On 26/05/13 12:13, David Osumi-Sutherland wrote:
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
Hi Nestor,
Writing from my phone so can't update doc yet.
Just want to try to correct a persistent misunderstanding. I DO NOT want to display term info for the parent class. One obvious problem with trying to do that is that there could be more than 1. I want you to display Term Info stored with the OWL individual. This includes a list of parent classes whichcan currently be accessed via OntIndividual.getType. I keep asking, without getting an answer, what ID you are using for third party beans for clones and flycircuit neurons. This surely is the VFB id of the individual. If it is, then surely you cam use this to roll an OntBeanIndividual. If not, what ID are you using and are you sure it will be unique in the context of displaying multiple stacks?
Cheers,
David
On 27 May 2013, at 11:23, "Nestor Milyaev" nmilyaev@users.sf.net wrote: