MIRIAM - AbsoluteAstronomy.com

MIRIAM is an effort to standardize the annotation and curation process of quantitative models of biological systems . The project produced a set of guidelines suitable for use with any structured format for computational models, as well as the software and services infrastructure, in order to allow different groups to collaborate on annotating and curating computational models in biology.

The idea of "a set of good practice rules" with "some metadata obligatory" was first proposed by Nicolas Le Novère in October 2004 as part of a reflection to develop a common database of models in Systems Biology (that led to the creation of BioModels Database

BioModels Database

BioModels Database is a free and open-source database for storing, exchanging and retrieving published quantitative models of biological interest...

). It was further discussed at a meeting in Heidelberg during ICSB 2004 with representatives of many groups involved in effort to exchange computational models.

MIRIAM is a registered project of the MIBBI (Minimum Information for Biological and Biomedical Investigations).

Standard

MIRIAM Standard is composed of three parts: reference correspondence, attribution annotation, and external resource annotation.

Reference correspondence

The first part specifies that a model must be encoded in a public standardized machine-readable format, clearly related to a single reference description, and must reflect the biological processes listed in the reference description. All quantitative attributes have to be defined, including initial conditions, and the model must be able to reproduce reasonably well the results given in the reference description.

The model must be encoded in a public, standardized, machine-readable format (SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...

, CellML
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology...

, GENESIS
GENESIS (software)
GENESIS is a simulation environment for constructing realistic models of neurobiological systems at many levels of scale including subcellular processes, individual neurons, networks of neurons, and neuronal systems.GENESIS was developed in the Caltech laboratory of Dr. James M...

, ...).
The model must comply with the standard in which it is encoded.
The model must be clearly related to a single reference description. If a model is composed from different parts, there should still be a description of the derived/combined model.
The encoded model structure must reflect the biological processes listed in the reference description.
The model must be instantiated in a simulation: all quantitative attributes have to be defined, including initial conditions.
When instantiated, the model must be able to reproduce all results given in the reference description within an epsilon (algorithms, round-up errors).

Attribution annotation

The second part of the standard deals with the annotation of the model. A model has to provide the citation of the reference description, lists its creators, and be attached to some terms of distribution.

The model has to be named.
A citation of the reference description must be joined (complete citation, unique identifier, unambiguous URL). The citation should permit to identify the authors of the model.
The name and contact of model creators must be joined.
The date and time of creation and last modification should be specified. An history is useful but not required.
The model should be linked to a precise statement about the terms of distribution. MIRIAM does not require "freedom of use" or "no cost".

External resource annotation

Finally, each component of a model must be annotated to allow its unambiguous identification. This annotation is based on a set of standard Unique Resource Identifiers that describe a specific piece of knowledge.

The annotation must permit to unambiguously relate a piece of knowledge to a model constituent.
The referenced information should be described using a triplet {data type, identifier, qualifier}:
- The data type should be written as a Unique Resource Identifier (URI).
- The identifier is analysed within the framework of the data type.
- Data type and identifier can be combined in a single URI: urn:miriam:obo.go:GO%3A0006915, urn:miriam:uniprot:P62158, ...
- Qualifiers (optional) should refine the link between the model components and the piece of knowledge: "has a", "is version of", "is homolog to", etc.

In order to resolve this annotation, the community has to agree on a set of valid URIs and possesses ways of automating their treatment. MIRIAM Resources have been developed for this purpose: allowing the storage of the URIs of the data types and the resolution between them and the physical locations of the pieces of knowledge.

Uniform Resource Identifiers

An important part of the standard consists in the controlled annotation of model components, based on Uniform Resource Identifiers. For more information on the use of those URIs to annotate models, see the specification of SBML Level 2 Version 2 (and above). In order to enable interoperability of this annotation, the community has to agree on a set of recognised data resources. MIRIAM Database (using MySQL

MySQL

MySQL officially, but also commonly "My Sequel") is a relational database management system that runs as a server providing multi-user access to a number of databases. It is named after developer Michael Widenius' daughter, My...

) is an online resource created to catalogue the data resources, their URIs and the corresponding physical URLs, whether these are controlled vocabularies or databases.

Each entry contains a diverse set of details about the resource: official name and synonyms, root URIs (URL and URN forms), patterns of identifiers, documentation, etc. Each data resource can be associated with several physical locations. For instance:

name: Gene Ontology
synonym: GO
pattern: GO:\d{7}$
URI: urn:miriam:obo.go
Locations
- location home: http://www.ebi.ac.uk/ego/
- root URL: http://www.ebi.ac.uk/ego/DisplayGoTerm?selected=$1
- location home: http://www.godatabase.org/cgi-bin/amigo/go.cgi
- root URL: http://www.godatabase.org/cgi-bin/amigo/go.cgi?query=$1
- [...]

Note that MIRIAM URIs take a URN form. For instance the URI representing the enzyme classification is: urn:miriam:ec-code.

Resources

A set of resources have been developed. They are freely available online from the European Bioinformatics Institute

European Bioinformatics Institute

The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...

Website, as well as the whole source code of the project on SourceForge.net

SourceForge.net

SourceForge is a web-based source code repository. It acts as a centralized location for software developers to control and manage open source software development. The website runs a version of SourceForge Enterprise Edition, forked from the last open-source version available...

.

The Website uses an Apache Tomcat

Apache Tomcat

Apache Tomcat is an open source web server and servlet container developed by the Apache Software Foundation...

server to provide an interface for the database. Users are able to perform queries such as retrieving valid physical locations (URLs) corresponding to a given URI (whether a generic data type or a precise piece of knowledge), retrieving all the information stored about a data type (such as its name, its synonyms, links to some documentation, etc.) and immediately get the results in a dynamic way, using AJAX

Ajax

- Mythology :* Ajax , son of Telamon, ruler of Salamis and a hero in the Trojan War, also known as "Ajax the Great"* Ajax the Lesser, son of Oileus, ruler of Locris and the leader of the Locrian contingent during the Trojan War.- People :...

.

Moreover, a programmatic access through Web Services (based on Apache Axis

Apache Axis

Apache Axis is an open source, XML based Web service framework. It consists of a Java and a C++ implementation of the SOAP server, and various utilities and APIs for generating and deploying Web service applications. Using Apache Axis, developers can create interoperable, distributed computing...

and SOAP

SOAP

SOAP, originally defined as Simple Object Access Protocol, is a protocol specification for exchanging structured information in the implementation of Web Services in computer networks...

messages) is available. This API

Application programming interface

An application programming interface is a source code based specification intended to be used as an interface by software components to communicate with each other...

permits not only to resolved model annotations, but also to generate the correct URIs based on resource name and accession numbers. For an easier use of these services, a Java

Java (programming language)

Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

library is also available.

MIRIAM Resources is used by several worldwide projects, like BioModels Database