OBD:SPARQL-InSitu
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Introduction: A SPARQL Endpoint for a database of annotated gene expression
This document describes a SPARQL endpoint for a database containing annotated images of gene expression in fruitfly embryogenesis. The images depict the actual expression of genes at a microscopic level using a technique called insitu hybridisation. The results were recorded in a relational database, and the images were annotated using the fly anatomy ontology.
The relational database and experiments are described in this journal article (open access):
A description of the database and traditional CGI interface can be found here:
D2RQ Mapping
I mapped the relational schema to RDF using D2RQ. The mapping is an extension of the mapping of the Gene Ontology database schema (described in OBD:SPARQL-GO).
The temporary URL for the SPARQL endpoint is:
Please read on before exploring randomly!
Images
The images show the anatomical localisation of gene expression in embryogenesis. All the images were captured using high resultion digital photography as part of the BDGP fruitfly insitu project. Each image has its own URL. We use the following prefix:
@prefix insitu <http://www.fruitfly.org/insituimages/insitu_images/thumbnails>
For example, the following are images depicting expression of the gene 'sim' in the mesectoderm anlage:
We use the Mindswap digital media ontology to represent both images themselves and the relationship between the image and the biological entities depicted therein:
@prefix dm: <http://www.mindswap.org/2005/owl/digital-media#> .
At this point we do not capture any metadata on the image itself. The plan is to use the nascent OBI (ontology for Biomedical Investigations) for microscopy and image orientation details. For those interested in the imaging itself, information can be found at:
Currently we capture the image type (always dm:Image) and the depiction relation; for example (in n3):
insitu:img_dir_22/insitu22070.jpe
a dm:Image ;
dm:depicts [
# <representation of gene expression events go here>
]
Biological Reality
The image represents a biological process - the coordinated expression of multiple genes in particular parts of the developing fly, at specific developmental stages. I will discuss the locations first, then the genes.
Instances of body parts are represented using classes from the fly_anatomy ontology. This ontology consists of a subsumption hierarchy (is_a/subclass), mereotopological relations (part_of/has_part) and ontogeneic relations (develops_from).
You can download fly_anatomy in OWL from
Currently the only part of the ontology that is available through the d2rq mapping on this server is the rdfs:label (changed: inherits mappings from OBD:SPARQL-GO). This is useful as all the class URIs are non-descriptive numeric IDs. For example, to get the URI of the class representing the mesectoderm anlage (a region of the embryo that is the precursor of many other body parts including brain cells), you can issue the following query:
SELECT * WHERE {
?LocClass rdf:type owl:Class ;
rdfs:label 'mesectoderm anlage'
}
This should return the ID/URI:
Note the class URIs all have http://www.purl.org/obo/owl as a prefix. This may change in future.
Human-readable details of this class can be found using a traditional (ie non-RDF/SPARQL/OWL based), web interface:
We also use an ontology of developmental stages, acessable using the same kind of queries.
Each image depicts an instance of a population of genes being expressed (as RNA molecules, which are then detected using insitu hybridization). There is some complex biology going on, but we can use a minimal representation that retains fidelity on the underlying biological reality as follows. The n3 snippet below shows an example. The rdfs:labels have been added for clarity, but are not actually produced by the mapping:
<http://www.fruitfly.org/insituimages/insitu_images/thumbnails/img_dir_22/insitu22070.jpe> a dm:Image ; dm:depicts [ rdfs:label "instance of coordinated expression of sim genes in the mesectoderm anlage" ; a oban:CoordinatedGeneExpression ; oban:has_participants_from bdgp:RE54280 ; ro:located_in [ a fly_anatomy:mesectoderm_anlage ] ro:during [ a fly_devel:stage7-8 ] ]
(note in the actual rdf/n3 obtained via the mapping, the class URIs would be non-descriptive numbers. I cheat and use the labels and URIs here for clarity)
bdgp:RE54280 is the URI for one of the RNA products of the sim gene (quick biology lession: genes are transcribed by the machinery of the cell to make RNA molecules, which can themselves encode proteins. Often large numbers of genes of identical types are switched on, ie transcribed at timed points during development)
The coordinated expression event is located as a particular (unlabeled) location, and a particular (unlabeled) developmental stage, and has participants drawn from a specific types of gene.
Currently we do not use bNodes for the unnamed instances, but we could. As an aside, we note that in representing biological instances we frequently have unlabeled instances.
Currently we do not encode the relations between specific genes, transcripts and proteins. However, it's possible to query for gene products using the gene as an alternate label:
SELECT * WHERE {
?gp skos:altLabel 'sim'
}
You can see all the relations for this entity here:
We recognise there is an actual ontological, non-lexical relationship between a gene and its product; however, treating these as labels is simplest for this demo.
Additional ontologies
Classes and relations have been temporarily defined in the oban ontology. CoordinatedGeneExpression will eventually be defined using a combination of the OBO upper ontology and the Gene Ontology representation of gene expression.
MORE DETAILS TO FOLLOW
Applications
It would be nice to demonstrate how a semantic web application could make use of this endpoint without any pre-programmed domain knowledge. Query by SPARQL will only interest a few.
Disco: Hyperdata Browser
Disco is "A simple browser for navigating the Semantic Web". For more information, see:
Disco can be used to navigate a web of data resources. Start off with a location instance:
Then follow to an expression instance; eg:
http://spade.lbl.gov:2021/resource/expression/10
You can then see an image depicting that expression event.
Or, alternatively, start off with all location instances of type "trunk mesoderm anlage":
Tabulator
Tabulator; enter a resource directly; eg:
The default display isn't so informative, but I'm probably using tabulator wrong:
What Next?
It would also be good to show how two or more resources can be integrated via SPARQL. I have a separate database (the Gene Ontology Database) which is wrapped with D2RQ which gives functional information on the genes used here. If there are applications that can do this, I could wrap more resources (or make them available via other SPARQL endpoints, eg through Sesame). There is no shortage of biological databases out there in need of integration!
For me the interesting part of the semantic web is the 'semantic' part. To me this must include some kind of logical entailment. Here are the kinds of entailment I would want to use:
SUBSUMPTION
The classes in the anatomical ontology are arranged in a subclass hierarchy. For example, 'sensory neuron' is a kind of 'neuron'. This means that if I am searching for events that are located at the neuron, I want to find events that are explicitly asserted to be located at the 'sensory neuron'.
This would require some simple fragment of RDFS entailment
MEREOLOGICAL
Anatomical classes stand in part_of relationships to one another (the ontology will also soon include other spatial relations). For example, neuron part_of nervous system, so I want queries for events in the nervous system to return events asserted to be in the neuron. The part_of relation is transitive. Because the class-level relations are encoded in owl (using owl:someValuesFrom) we need some fragment of OWL entailment here (unless we use some kind of TBox-in-ABox pattern and use RDFS instance-level transitivity. But even so we will likely want to use role-chains and other fragments of OWL)
OTHER
If an image depicts an event, and that event takes place in a location, then the image also depicts that location. The dm ontology does not state this semantics for depicts, and even if it did, supporting this would require either SWRL or OWL2 (role chains)
I think these entailment are important. Currently someone searching for
images of insects would not find my images. This is because I have not
explicitly encoded these to be images depicting insects. I have
asserted them to be images depicting biological processes that take
place in a part of an organism which is a kind of insect. The person
or application formulating this query would have to know this in
advance and construct the query accordingly. This seems antithetical
to the vision of the semantic web.
I am aware that implementing these kinds of entailments in a web context is challenging, to say the least. In fact it seems that there may be something of a dichotomy emerging between RDF folks who have large distributed datasets and want minimal OWL semantics and those working solely in an ontology development environment and want to cram the most into OWL whilst keeping it practical for mid sized ontologies...
I have a proposed solution that will work for my complex entailments and large datasets, at the expense of the "web" part of the SW. I will outline it here.
The relational database I am wrapping with D2RQ already has the deductions I need pre-computed in a deductive closure. I can actually solve my use cases above with simple SQL queries and thus also in the corresponding SPARQL endpoint. The question is, how should I expose this?
One option is to implement rdf:type as if it were querying the implied graph; I could do the same thing for dm:depicts
For example, the following query over the implied graph
SELECT * WHERE {
?im digitalmedia:depicts ?loc .
?loc rdf:type ?loctype .
?loctype rdf:type owl:Class ;
rdfs:label 'embryo'
}
would include in its result set results from the following quesry over the asserted graph:
SELECT * WHERE {
?im digitalmedia:depicts ?ex .
?ex oborel:located_in ?loc .
?loc rdf:type ?loctype .
?loctype rdf:type owl:Class ;
rdfs:label 'mesectoderm anlage'
}
But if all queries are over the implied graph, how can I query for asserted triples? SPARQL appears to be completely agnostic wrt details of the underlying graph, whether it is asserted or implied. Sesame/SeRQL provides serql:directType which seems reasonable.
I say my approach is at the expense of the "web" part of the SW because the deductive closures are only computed over a predetermined subset of all possible ontologies. For example, my SPARQL queries may have all kinds of cool entailment over the fly anatomy ontology, but if I do not have in my database a species taxonomy then the fact that "fly subclassOf insect" will not be entailed and my "find me all images of insects" use case will not be solved. From my perspective, this is fine, I can pre-compute on all the ontologies that are required for my use cases. But I'd like to try and be a good semantic web citizen.
It seems my other options are to wait until D2RQ can take care of entailment issues for me (perhaps by integrating with a reasoner), or to hope that this can be done perhaps by some 3rd party endpoint, with something like DARQ integrating the results.
