To created a linked data web of heterogeneous biological data resources, we need not only to de¯ne and create the alignment between related data resources but also to express the knowledge about why data items from di®erent sources are linked with each other and how each data link has evolved, so that scientists can trust the data links provided by the data web. This paper highlights the importance of keeping provenance information about the links between data items from di®erent sources, and proposes the use of named graphs to make a provenance statement about each pair of linked data items and each release of a data web.
The number of biology databases available has increased
rapidly in the recent years [
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To simplify this process, the Image Bioinformatics
Research Group (IBRG)1 of the University of Oxford proposes
the use of subject-speci¯c data webs, which use the Web
as the native platform upon which to integrate access to
datasets relating to particular subjects [
The ¯rst demonstrator data web being developed by IBRG is FlyWeb2, which will integrate the heterogeneous data resources concerning research on fruit °y Drosophila melanogaster. These data resources include FlyTED3 (our local research image repository concerning gene expression in the testis of fruit °ies), BDGP4 (the Berkeley Drosophila Genome Project database concerning gene expression in the Drosophila embryos), FlyBase5 (the global database of genomics information concerning Drosophila), and online research publications on Drosophila gene expressions. The goal of FlyWeb is to allow biologists to obtain information about a Drosophila gene, including the gene expression images of its testis and embryos, without having to hop between the Drosophila data islands on the Web.
To build FlyWeb, we need not only to de¯ne and implement the alignment between Drosophila data resources, but also to maintain the data links between related data items from di®erent sources. This position paper focuses on the second issue, and will analyze the motivation for keeping provenance of the links between related data items and present our proposed solution. 2.
The initial development goals of the FlyWeb Project
include understanding the distributed Drosophila data resources;
creating the alignment between them; and creating a query
service to access the integrated data resources. At the time
1http://ibrg.zoo.ox.ac.uk/
2http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyWeb_
project
3http://www.fly-ted.org/
4http://www.fruitfly.org/
5http://flybase.org/
of the writing, concentrating ¯rst on linking the FlyTED
and BDGP databases, we have achieved:
² Describing the Drosophila testis images in FlyTED
using an extension to the Fly Anatomy Ontology [
These initial works provide the foundation that permits us to align the two data resources and build a lightweight data web. However, the evolving nature of biological databases has motivated us to further consider how to manage the links in FlyWeb, once they have been established. 3.
Data items from di®erent Drosophila data resources are integrated into FlyWeb using references to the original data. Related data items are linked together in FlyWeb using biological knowledge from public genomic databases. Biological knowledge is growing rapidly, and genomic databases are frequently updated. By referencing back to these evolving databases, FlyWeb can synchronize with advances in biological knowledge. However, with each update of such an external resource, some of the links between data items recorded locally within FlyWeb may become obsolete or need to be updated with more links to related data items. We need to provide additional metadata about these data links in order to maintain consistency between FlyWeb and the advancing biological knowledge. This will allow scientists to: ² Trust that the data links established in FlyWeb are valid; ² Trust that the data referenced in FlyWeb are consistent with the latest release of the public databases; ² Trace back the data links established by FlyWeb using previous releases of the public databases, which may previously have been used by the scientists to annotate their own local data.
Thus, for each data link to a pair of data items, we need to record the following provenance metadata: ² The evidence of the link; ² When this link was created, by whom, using which version of which database; ² When this link was updated or deprecated; ² Whether there were any previous links between this pair of data items; ² What previous links between data items became obsolete, and why.
To express this provenance of data links, we propose to use named graphs. 4.
An RDF graph contains a collection of RDF triples. A
named graph is an RDF graph which is assigned a name
in the form of a URI [
In order to provide information about why a pair of related data items are linked together in FlyWeb, or why/when they become no longer linked, we create a named graph for each pair of linked data items. In this position paper, we only consider two types of links between data items, i.e. either they are same as or di®erent from each other. There may be other types of data links in FlyWeb. But the provenance model introduced in this paper is not yet designed for describing all di®erent types of data links.
FlyWeb will be updated whenever a major release of the linked-in Drosophila databases is announced. To provide information about each FlyWeb release and the versions of the public databases upon which each release is based, we will also create a named graph for each release of the FlyWeb.
In this position paper we use TriG as the notation to
de¯ne named graphs. \TriG is a variation of Turtle [
FlyWeb integrates several Drosophila data sources, noted as a, b, c, etc. Each data source is associated with version information. Thus ax indicates version x of data source a.
Each release of FlyWeb (f wg, f wk, etc) will contain a collection of data items, im, in, etc, from di®erent Drosophila data sources. A data item from data source a of version x should be uniquely identi¯ed as im(ax). In f wg, im(ax) will be described by all the metedata from its original data source, as well as by FlyWeb statements about whether it is related to another data item in(bx) from data source bx, or whether im(ax) had previously been linked with in(bx) in a previous release of FlyWeb.
Each release of FlyWeb itself is a named graph, which is associated with information about when it was released, by whom, using which versions of which databases. An example of two such named graphs is given below.
The following two examples show two graphs (see Figure 1). Example 1 tells information about FlyWeb version 1.0 (<dwi:flyweb_r1>) that it was released on \2007-1219" and it was built using FlyTED version 1.0, the BDGP database version \2007-03-09" and FlyBase version 4.3. It also contains a single statement about data items, i.e. the gene <flyted:gene_g1> from FlyTED is the same as the gene <bdgp:gene_g2>6 from BDGP. Example 2 de¯nes a 6The bdgp namespace might not be the actual namespace used by the BDGP SPARQL endpoint. Due to technical maintenance, its server was unreachable when the paper was written. named graph of FlyWeb version 1.1, which was built using the same versions of FlyTED and BDGP as FlyWeb version 1.0, but a di®erent version of FlyBase. Because of this update, gene <flyted:gene_g1> is no longer the same as <bdgp:gene_g2>. :flyweb_r1 { flyted:gene_g1 owl:sameAs bdgp:gene_g2 . :flyweb_r1 dc:created "2007-12-19"^^xsd:date; dc:hasVersion "1.0" ; dc:creator <http://www.datawebs.net/foaf.rdf#ibrg> ; dw:derivedFrom flyted:v1.0 ; dw:derivedFrom <bdgp/2007-03-09> ; dw:derivedFrom <flybase/v4.3> . }
Example 2. Named graph for FlyWeb release 1.1 :flyweb_r2 { flyted:gene_g1 owl:differentFrom bdgp:gene_g2 . :flyweb_r2 dc:created "2008-01-25"^^xsd:date; dc:hasVersion "1.1" ; dc:creator <http://www.datawebs.net/foaf.rdf#ibrg> ; dw:derivedFrom flyted:v1.0 ; dw:derivedFrom <bdgp/2007-03-09> ; dw:derivedFrom <flybase/v5.3> . } 4.2
In each FlyWeb named graph, a collection of named graphs are also created for the data links between pairs of related data items. Each such named graph states: ² Why a pair of data items should be or should no longer be linked; ² When the link was made or released, and by whom; ² Which previous links had been created between this pair of data items; ² What the type the link is: a MappingRelation, either a
concepts will be de¯ned in a data web ontology using the owl:sameAs and owl:differentFrom properties.
Example 3 (see Figure 2) shows a named graph <dwi: mapping_m1> that de¯nes an abstract relationship between the gene from FlyTED (<flyted:gene_g1>) and the gene from BDGP (<bdgp:gene_g2>) and traces this relationship by its two children, both of which are themselves named graphs and de¯ne the actual relationships between these two genes built in di®erent releases of FlyWeb.
The ¯rst child <dwi:mapping_m11> de¯nes that the two genes are synonyms given the evidence of <dwi:evidence_ e1> and that this link was created on \2007-12-19" within the release of <dwi:flyweb_r1>. The second child <dwi: mapping_m12> states that the two genes are not the same given the evidence of <dwi:evidence_e2>, and that this link was created on \2008-01-25" within the release of <dwi: flyweb_r2>.
<dwi:mapping_m12> with the graph <dwi:mapping_m1>, and they are linked together by the property dw:siblingOf. These properties enable us to trace a lineage of the data links between a pair of data items.
Example 3. Named graph for a data link @prefix dw: <http://www.datawebs.net/> . @prefix flyted: <http://id.fly-ted.org/> . @prefix dc: <http://purl.org/dc/elements/1.1/> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix owl: <http://www.w3.org/2002/07/owl#> . @prefix bdgp: <http://www.fruitfly.org/> . @prefix dwi: <http://id.datawebs.net/> . @prefix : <http://id.datawebs.net/> . @prefix rdf:
<http://www.w3.org/1999/02/22-rdf-syntax-ns#> . :mapping_m1 { :mapping_m1 rdf:type dw:MappingRelation . flyted:gene_g1 dw:maps bdgp:gene_g2 . # the first child :mapping_m11 dw:childOf :mapping_m1 ; dw:evidencedBy :evidence_e1 ; dw:createdIn :flyweb_r1 ; rdf:type dw:SameRelation ; dc:creation
"2007-12-19"^^xsd:date . :mapping_m11 {
flyted:gene_g1 owl:sameAs bdgp:gene_g2 .
This section uses the above example datasets to walk through three scenarios to show how the named graphs could help us to manage the data links in FlyWeb in a manner that promotes trust. 5.1
The ¯rst scenario shows how FlyWeb can help users to ¯nd out which data items in FlyWeb are linked to their gene, which is annotated using information from FlyBase release 4.3.
Many biology data compilations are maintained locally by research groups and might not always be kept up-to-date with successive releases of the genomic database FlyBase due to the ending of the projects that funded them. Such local legacy data will have been annotated using information from a now out-of-date version of the public database. Subsequent releases of the public database might have annotated its gene records using di®erent gene names. Occasionally, new biological evidence shows that a particular DNA sequence, formerly thought to be a single gene and given a single gene name, in fact encodes two distinct genes that are then given di®erent names.
Without provenance data, users would not be able to ¯nd
in FlyWeb any data relating to their locally recorded former
gene names, because the genes are now annotated with new
names. In order to prevent this situation in the future, we
provide provenance information for each release of FlyWeb,
to state which versions of the public databases it links to.
This provides the °exibility for the scientists to trace data
links for their legacy data. A SPARQL query [
5.2
This scenario shows how users can navigate information about a Drosophila gene in the latest release of FlyWeb using the version information and the creation date associated with the named graph of each release of FlyWeb. The following SPARQL query will retrieve all the data links from the v1.1. release of FlyWeb.
5.3
One way of allowing users to trace the data links between a pair of related data items is to keep a history of all the data links that have ever existed between them. This means that con°icting statements about the relationship between the same pair of data items might exist in di®erent releases of FlyWeb. In order to explain these con°icts, we provide the evidence information for the data links.
Example 1 and Example 2, describing release1.0 and 1.1 of FlyWeb, contain con°icting statements about the relationships between <flyted:gene_g1> and <bdgp:gene_g2>. In order to explain this con°ict, we need to take the following steps: ² Retrieve all the statements about the data link between <flyted:gene_g1> and <bdgp:gene_g2> from di®erent releases of FlyWeb. This will return all the statements about the graphs <dwi:mapping_m11> and <dwi:mapping_m12> that de¯ne the relationships between the two gene names; ² Compare the statements about these two graphs in order to ¯nd out the di®erences between the two versions of relationships between <flyted:gene_g1> and <bdgp:gene_g2>; ² Present the di®erences resulting from the above comparison step to the users, including their creation date, in which release of FlyWeb they were created, as well as the evidence for explaining why each di®erent relationship existed between <flyted:gene_g1> and <bdgp: gene_g2>.
A SPARQL query for the ¯rst step would be:
WHERE { graph ?g {flyted:gene_g1 ?p1 bdgp:gene_g2 . ?g rdf:type dw:MappingRelation . ?cg dw:childOf ?g .
?cg ?p ?o} }
In this position paper we have analyzed how recording the provenance of data links can help us both maintaining the links between related data items and bringing trust to the data web, by providing evidence for links, or tracing how the data links have been updated and maintained. We have shown the potential of named graphs for expressing this provenance information. The °exibility of RDF named graphs and the RDF query language SPARQL provide the capability for us to query and ¯lter the data links on behalf of the data web users, e.g. by presenting only those links newly created since the previous release of FlyWeb, or those present in a particular earlier release of FlyWeb.
When de¯ning this conceptual provenance model, we have adopted existing vocabulary as much as possible, such as the properties of dc:creation and dc:creator from the Dublin Core Metadata Element Set7. We have also used the dw namespace (http://www.datawebs.net/) to specify the following properties of our own: ² dw:derivedFrom ² dw:evidencedBy ² dw:childOf ² dw:siblingOf ² dw:createdIn ² dw:maps We are planning to include these conceptual properties in a data web provenance ontology, that will include other existing vocabularies about provenance and trust.
In this conceptual model we associated with each data link a dw:evidencedBy property to provide the information about why particular statements were asserted. This will bring trust to the linked data for the scientists, so that they can verify that the links are consistent with scienti¯c knowledge. However, we are still investigating how much information should be provided as evidence for each data link: whether it should contain the actual heuristic used for building the links or a textual description of this heuristic; and how we can make this evidence information more comprehensible for biological researchers.
There is a separate provenance issue that is not discussed
in this position paper, namely the provenance of the data
items themselves. We discussed neither the provenance
information for telling where each data item came from nor
the provenance information that might be associated with a
data item from the individual data resource. These are key
research topics for Semantic Web and provenance for life
sciences [
This work is supported by funding from the JISC (FlyWeb Project to Dr David Shotton; http://imageweb. zoo.ox.ac.uk/wiki/index.php/FlyWeb_project) and from BBSRC (Grant BB/E018068/1, The FlyData Project: Decision Support and Semantic Organisation of Laboratory Data in Drosophila Gene Expression Experiments, to Drs David Shotton and Helen White-Cooper). The FlyTED Database was developed with funding from the UK's BBSRC (Grant BB/C503903/1, Gene Expression in the Drosophila testis, to Drs Helen White-Cooper and David Shotton). Preliminary data web requirements analysis was supported by a JISC grant to Dr David Shotton (De¯ning Image Access Project; http://imageweb.zoo.ox.ac.uk/wiki/index.php/Defining