Bibliography

adfa

Array Design File (ADF) format specification - ADF specification.

adfb

Array Design File (ADF) good pratice - ADF good practice, ADF Guidelines, http://www.ebi.ac.uk/~rocca/ADF/ADFGUIDELINES.htm, ADF Checklist, http://www.ebi.ac.uk/~rocca/ADF/ADFchecklist.htm.

adfc

initial Array Design File (ADF) format specification - initial ADF specification, ADF description, http://www.ebi.ac.uk/~rocca/ADF/ADF_Help_v3.htm,FAQ, http://www.ebi.ac.uk/~rocca/ADF/ADF_FAQS.htm.

arr

ArrayExpress- MIAME compliant database, ArrayExpress website, http://www.ebi.ac.uk/arrayexpress.

ebia

EBI - microarray group, EBI microarray group web site, http://www.ebi.ac.uk/microarray.

ebib

European Bionformatics Institute - EBI, EBI web site, http://www.ebi.ac.uk.

ens

Ensembl EnsMart Genome Browser (MartView), http://www.ensembl.org/Multi/martview.

gal

(gal spotter output file format.

go

Gene Ontology, http://www.geneontology.org/GO.current.annotations.shtml.

maga

MicroArray and Gene Expression - MAGE, MAGE website, http://www.mged.org/Workgroups/MAGE/mage.html.

magb

MicroArray and Gene Expression Markup Language - MAGE-ML, MAGE-ML website, http://www.mged.org/Workgroups/MAGE/mage-ml.html.

magc

MicroArray and Gene Expression Markup Language Document document Type Definition - MAGE-ML DTD, OMG MAGE-ML website, http://www.omg.org/technology/documents/formal/gene_expression.htm, last release: 1.1, http://schema.omg.org/lsr/gene_expression/1.1/MAGE-ML.dtd.

magd

MicroArray and Gene Expression Markup Language Document document Type Definition - MAGE-ML DTD, MIAME-ML website, http://mged.sourceforge.net/software/docs.php#MAGEML, last release, http://prdownloads.sourceforge.net/mged/MAGE-ML.dtd.gz.

mage

MicroArray and Gene Expression Markup Language good pratice- MAGE-ML good pratice.

magf

MicroArray and Gene Expression Markup Language specification - MAGE-ML specification, MAGE-ML website, http://www.mged.org/Workgroups/MAGE/mage-ml.html.

magg

MicroArray and Gene Expression Object Model- MAGE-OM, MAGE-OM website, http://www.mged.org/Workgroups/MAGE/mage-om.html, http://mged.sourceforge.net/software/docs.php#MAGEOM.

magh

MicroArray and Gene Expression software toolkit- MAGEstk, MAGEstk website, http://mged.sourceforge.net/software/MAGEstk.php.

mgea

MGED Ontology, MGED Ontology website, MAGE-ML DTD http://www.omg.org/technology/documents/formal/gene_expression.htm http://mged.sourceforge.net/software/docs.php#MAGEML last release http://prdownloads.sourceforge.net/mged/MAGE-ML.dtd.gz http://schema.omg.org/lsr/gene_expression/1.1/MAGE-ML.dtd Microarray Gene Expression Data ontology.

mgeb

MGED Ontology, mailing list, mged-ontologies@lists.sourceforge.net.

mgec

MGED society - Microarray Gene Expression Data society, MGED website, http://www.mged.org.

miaa

MIAMExpress- MIAME compliant submission tool, MIAMExpress website, http://www.ebi.ac.uk/miamexpress.

miab

Minimum information about a microarray experiment - MIAME, MIAME website, http://www.mged.org/Workgroups/MIAME/miame.html, http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v29/n4/abs/ng1201-365.html, MIAME checklist, http://www.mged.org/Workgroups/MIAME/miame_checklist.html, MIAME 1.1 Draft 6, http://www.mged.org/Workgroups/MIAME/miame_1.1.html.

omg

Object Management Group - OMG, OMG website, http://www.omg.org/.

P.C.R. :
Polymerase Chain Reaction, http://allserv.rug.ac.be/~avierstr/principles/pcr.html

CGH :
Comparative Genomic Hybridisation, http://amba.charite.de/cgh/cgh01.html

ChIP :
Binding-site identification by Chromatin-immunoprecipitation, http://www.bio.brandeis.edu/haberlab/jehsite/chip.html

Batch mode :
this mode Allows a limited subset of pdb commands to be started and ran from the command line, without or without the ui. Batch Processing is the en-masse execution of a series of jobs on a computer.

Ontology :
From the Stanford Knowledge Systems Lab:
« An ontology is an explicit specification of some topic. For our purposes, it is a formal and declarative representation which includes the vocabulary (or names) for referring to the terms in that subject area and the logical statements that describe what the terms are, how they are related to each other, and how they can or cannot be related to each other. Ontologies therefore provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary. » Graphical user interface (GUI) :
A program interface that takes advantage of the computer's graphics capabilities to make the program easier to use. Well-designed graphical user interfaces can free the user from learning complex command languages. On the other hand, many users find that they work more effectively with a command-driven interface, especially if they already know the command language.

Validity :
A document is validated, if the data or information given in the document have a correct semantics. Well form :
A document is well formed, if data or information are given in a specified order, are respecting a given document structure.