=Paper=
{{Paper
|id=None
|storemode=property
|title=Semantic Integration of the Genome Annotations
|pdfUrl=https://ceur-ws.org/Vol-952/paper_42.pdf
|volume=Vol-952
|dblpUrl=https://dblp.org/rec/conf/swat4ls/KatayamaOKMF12
}}
==Semantic Integration of the Genome Annotations==
https://ceur-ws.org/Vol-952/paper_42.pdf
Semantic integration of the genome annotations
Toshiaki Katayama1, Shinobu Okamoto1, Shuichi Kawashima1, Hiroshi Mori2, and
Takatomo Fujisawa3
1
Database Center for Life Science, Research Organization of Information and Systems ,
Tokyo, Japan
ktym@dbcls.jp, {so,kwsm}@dbcls.rois.ac.jp
2
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo,
Japan
hmori@bio.titech.ac.jp
3
National Institute of Genetics, Research Organization of Information and Systems,
Mishima, Japan
tf@nig.ac.jp
Abstract. Integration of the genome annotations is gaining more importance to
interpret the biological meanings of large scale sequence data produced by the
new sequencing technologies. Because existing annotations from public
databases and literatures varies in terms of both categories and species, the
Semantic Web technology has a great advantage for accumulating those wide-
ranging information without having difficulty in the integration process. During
the BioHackathon 2012, a new ontology to define the location of the
annotations was defined as the Feature Annotation Location Description
Ontology (FALDO). This ontology will be used to integrate annotations from
INSDC (DDBJ/EMBL/GenBank) and UniProt databases, GFF3 formatted files,
and many other bioinformatics resources. In parallel, Database Center for Life
Science (DBCLS) and DNA Data Bank of Japan (DDBJ) has been jointly
developing a RDF-based genome database which consists of the five layers. 1)
RDF-based annotation data store, 2) SPARQL-based query engine, 3) RESTful
API to retrieve genomic information, 4) HTML/CSS-based reusable web
components and 5) integrated Web user interface. Our proposal is to
standardize those layers so that every researcher can jointly use and/or update
distributed genome annotations.
Keywords: genome annotation, database integration, semantic web, ontology
Introduction
Reliable genome annotations are essential for understanding the existing and newly
sequenced organisms. A number of model organism databases have been already
developed for from human to pathogens including prokaryotes. However, thanks to
the rapid evolution of the next generation sequencers, the number and volume of the
2 Toshiaki Katayama1, Shinobu Okamoto1, Shuichi Kawashima1, Hiroshi Mori2, and
Takatomo Fujisawa3
sequenced organisms are growing exponentially. To understand the meaning of this
vast amount of data, the importance of the reference annotation database is increasing.
Even with the existence of many public databases, accumulation of those annotations
is a difficult task because 1) annotations are still hidden in the literatures for most
organisms and annotations of genes often require experimental verifications, 2) data
formats used for the annotations were not always standardized, 3) there are no
standard system to annotate any regions on the genomic sequence with a flexible yet
controlled manner. The first problem requires text mining technologies and
collaboration with biologists, the latter two issues can be resolved if our community
agreed on a common standard. One of those efforts is the Generic Feature Format
(GFF) and the Distributed Annotation System (BioDAS) which were introduced by
the Generic Model Organism Database (GMOD) projects initially developed for the
WormBase, FlyBase and some other model organism databases. Although the GFF
format and the BioDAS protocol have been considered as standards for sharing
genomic annotations, there still are some limitations. One is the lack of semantics in
the GFF format which brought local variations such as the Gene Transfer Format
(GTF). Also, especially for curators, it is very difficult to use the GFF format for
describing sequence features not directly linked with the Sequence Ontology (SO)
terms, or the semantic relations among sequence features such as interactions or
regulations.
Results
To describe the missing semantics in the existing genome annotations or to add
new heterogeneous annotations, we introduced the Semantic Web technology. It
utilizes ontologies consisting of controlled vocabularies and their semantic relations,
for describing objects to be annotated. Initially, we gathered reference knowledge
from existing public data sources such as RefSeq, GFF3, and UniProt. We also
merged annotations for prokaryote genomes from GTPS and MBGD databases and
annotations of animal genomes from the H-inv database. All of those information are
converted into RDF format and stored in a dedicated triple store. Along with this
development, we are also developing a common genome annotation ontology.
During the NBDC/DBCLS BioHackathon 2012 held in Japan, developers of life
science databases and applications gathered and agreed on to develop new ontology
for describing locations of the objects. As a result, the Annotation Location
Description Ontology (FALDO) was proposed and we converted the locations and
positions of all annotations stored in our triple store to comply with this new standard.
Our proposed new RDF-based genome database is consisted of the five layers. 1)
RDF-based annotation data store, 2) SPARQL-based query engine, 3) RESTful API
to retrieve genomic information, 4) HTML/CSS-based reusable web components and
5) integrated Web user interface (Figure 1). To make the database generic as much as
possible for any organisms, we introduced the following design principles.
First, to identify any object in the database, data provider must assign a unique URI
for any object in the dataset. However, designing well-formatted URIs for every
heterogeneous object without any confusion is a difficult task. Therefore, for this
Semantic integration of the genome annotations 3
purpose, we recommend to use unique URIs based on the Universally Unique
Identifiers (UUIDs). Because a UUID can be independently and locally generated
which will not collapse with the other ID in theory. One might think blank nodes in
the RDF can be also applicable for this purpose, however, the use of UUID-based
URIs can assure that the annotation for any object can be globally identifiable.
Second, we recommend to use existing ontologies such as Sequence Ontology
(SO) and FALDO to identify the type and location of the annotated object on the
sequence.
Third, it is recommended to develop a new ontology for each dataset which
describes data source specific annotations such as the Feature/Qualifier used in the
INSDC databases, specific tags in the H-inv database or the GFF3O ontology for the
GFF3 data format. Then, each ontology should be linked with the new common
genome annotation ontology so that users can use existing reasoning tools to generate
interoperable triples which are subjected to be consumed by the genome database
interface.
Figure 1. Layers of the RDF-based semantic genome database.
Discussions
We are still in a very early stage of the development. Therefore, we are inviting
collaborators for standardizing each of the five layers within the life science
community so that every researcher can jointly use and/or update distributed genome
annotation databases.