Phylogenetic Analysis Workflows - User-Level Workflow Design: A Bioinformatics Perspective - page 72

The domain model is based on the sequence analysis services from the Eu-
ropean Molecular Biology Open Software Suite (EMBOSS) [264]. EMBOSS
is a rich collection of freely available tools for the molecular biology user com-
munity. It contains a number of small and large programs for a wide range
of tasks, such as sequence alignment, nucleotide sequence pattern analysis,
and codon usage analysis as well as the preparation of data for presentation
and publication. At the time of this writing, the latest version of EMBOSS
(Release 6.4.0 from July 2011) consists of around 430 tools, some derived
from originally standalone packages. EMBOSS provides a common technical
interface for the diverse tools that are contained in the suite. They can, for
instance, be run from the command line, or accessed from other programs.
What is more, EMBOSS automatically copes with data in a variety of for-
mats, even allowing for transparent retrieval of sequence data from the web.
The tools work seamlessly for a number of different formats and types, and
therefore the domain modeling can focus on the actual service semantics
rather than on technical details of data compatibility.
The interfaces of the EMBOSS tools are described in so-called ACD (Ajax
Command Definition) files, which provideinformation about the inputs and pa-
rameters that are required for the tool invocation. What is more, the ACD files
contain annotations for tools, data and parameters that refer to terms from
the EMBRACE Data and Methods Ontology (EDAM, cf. next section) 1 .This
comprehensive meta-information about the EMBOSS tools facilitates the auto-
mated setup of a PROPHETS domain model for EMBOSS services (cf. [179]).
3.3.1 EMBRACE Data And Methods Ontology
(EDAM)
The EDAM ontology [249, 138, 6] has been developed in the scope of the
EMBRACE (European Model for Bioinformatics Research and Community
Education) project [5] as an ontology for describing bioinformatics databases,
data and tools that are in use in the community. It aims at providing a con-
trolled vocabulary for the diverse services and resources in the Life Science
Semantic Web that is suitable for bridging the gap between mere service
registries and semantically aware service composition methodologies. There-
fore it collects and combines knowledge from various existing resources, for
instance from different web service collections such as the BioMoby registry
[341] and the BioCatalogue [112], and from the myGrid ontology [347].
Importantly, EDAM is not a catalog of concrete services, data, resources
etc., but a provider of terms for the annotation of such entities. Strictly
1 At present, some ACD files contain incorrect, imprecise or inconsistent annota-
tions, and also the EDAM ontology still contains some erroneous relations. As a
consequence, some principally possible workflows are not recognized by the syn-
thesis, and, conversely, some of the returned solutions are actually not possible.
However, as both EMBOSS and EDAM are under active development, these is-
sues will most certainly be solved within the next releases.