VFB_schema_IDs modified by David Osumi-Sutherland

David Osumi-Sutherland — Sun, 26 May 2013 11:23:23 -0000

--- v1
+++ v2
@@ -18,7 +18,7 @@
    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.
+   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](http://kyala.gen.cam.ac.uk/javadoc/uk/ac/ed/vfb/model/PubBean.html)
@@ -26,7 +26,7 @@
 2. BrainTrap IDs

 3. Clusters
-   Clusters are actually individuals with VFB ids, but...
+   Clusters are actually individuals with VFB ids, but for lookup purposes are keyed on FLyCircuit exemplar name 

 ## Relationship of IDs to Beans

VFB_schema_IDs modified by David Osumi-Sutherland

David Osumi-Sutherland — Sun, 26 May 2013 11:13:49 -0000

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

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
Clusters
Clusters are actually individuals with VFB ids, but...

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}

Recent changes to VFB_schema_IDs

VFB_schema_IDs modified by David Osumi-Sutherland

VFB_schema_IDs modified by David Osumi-Sutherland

IDs on VFB

OWL IDs.

External DB IDs

Relationship of IDs to Beans

PubBean

OntBean

OntBeanIndividual

ThirdPartyBean