A

An anatomy ontology that describes 3500+ structures seen throughout mouse embryo development. The list is hierarchically organised in various 'part-of' relationships in a directed acyclic graph e.g. hindgut endoderm is part of the hindgut, hindgut is part of the gut, or an alternative view: hindgut endoderm is part of gut endoderm, gut endoderm is part of the gut. The part-of relationships allow flexibility when querying or mining data (e.g. genes expressed in the hindgut endoderm, are also expressed in the gut endoderm or the gut and can be retrieved when any of these terms are used for query). Numerous common synonyms are also included (e.g. mesencephalon = midbrain), allowing either term to be used for query. It differs from the EMAP Anatomy Ontology in that it constitutes just one list for all structures seen throughout development and is NOT overtly divided into 26 separate lists, one for each Theiler stage of development. Thus, it lacks an overt temporal aspect. The full list of terms in the Abstract Mouse can be viewed here.
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An alternative form of a gene (one member of a pair) that is located at a specific position on a specific chromosome.
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The building blocks of proteins. Structurally they consist of a central carbon atom bonded to four different groups (a hydrogen, a carboxyl group (-COOH), an amino group (-NH2) and a variable chain which confers the identity to the specific amino acid. 20 different amino acids are found within proteins: Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine and Valine.
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A commercially available software platform for visualising and manipulating 3D image data. http://www.amiravis.com/
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A Y-shaped protein on the surface of B cells that is secreted into the blood or lymph in response to an antigenic stimulus, such as a bacterium, virus, parasite, transplanted organ or immunisation, and that neutralises the antigen by binding specifically to it.
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A substance that when introduced into the body, stimulates the production of an antibody. It can be a protein.
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Refers to the strand of a DNA molecule whose sequence is complementary to the strand represented in mRNA, or an RNA molecule complementary to the strand that is normally processed into mRNA and translated. The complementary strand to the anti-sense strand is called the sense strand. In situ hybridisation probes, used to detect the present of sense transcript, are anti-sense.
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A computer application (program) that has limited features, requires limited memory resources, and is usually portable between operating systems. They generally 'piggy-back' on another program - for example JavaTreeView is an Applet and requires a web-browser to be already running when it is launched (in this case from a button on a web-page). It then uses the memory and other features of the web-browser application to run it.
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B

The commercial distributor of OPT scanners and accompanying 3D image data visualisation software and also providing a pay-per-use OPT scanning service. http://www.bioptonics.com/.
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Basic Local Alignment Search Tool - An algorithm that finds regions of local similarity between biological sequences. The program compares nucleic acid or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
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Boolean operations are used in Boolean logic, which is a system for logical operations. It was named after George Boole, who first defined an algebraic system of logic in the mid 19th century. The three most basic Boolean logic operators are AND, OR and NOT. Applied to sets of data, they can be visualised in Venn Diagrams:

AND	OR	NOT
orange region = genes expressed in brain AND gut	orange region = genes expressed in brain OR gut	orange region = genes expressed in brain, NOT gut

C

A staging system for human embryos. Stages are based on the external and/or internal morphological development of the embryo, and are not directly dependent on either age or size. The human embryonic period proper is divided into 23 Carnegie stages. Criteria beyond morphological features include age in days, number of somites present, and embryonic length. Named after the Carnegie Institution, Washington DC, where collecting and classifying of human embryos began in the early 1900s. http://embryology.med.unsw.edu.au/wwwhuman/Stages/Allst.htm
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A structural and functional unit of organisms. It is the smallest unit of an organism that is classified as 'living'. Eukaryotic cells contain membrane-bound compartments in which specific metabolic activities take place. Most important among these is the presence of a nucleus, a membrane-delineated compartment that houses the eukaryotic cell's genomic DNA.
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A structural unit within a eukaryotic nucleus that carries genes. A chromosome consists of a long, continuous strand of DNA and associated proteins.
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A computer application or system that accesses a remote service on another computer system (the server), by way of a network.
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In HUDSEN, the term 'clipboard' is used to refer to a group of entries that you have compiled from one or more results lists. Each item on the clipboard is one HUDSEN entry and the clipboard is stored on your computer - this functionality uses cookies. You can compare the contents of your clipboard to the contents of a results list from a search to produce a list of HUDSEN :IDs for entries (a) that are found in both lists (i.e. the Boolean function AND) or (b) the HUDSEN:IDs of the entries in your current results list that are not found in the clipboard contents (i.e. the Boolean function NOT).
NOTE: the HUDSEN clipboard is not the same as the clipboard on your Windows or Mac computer - i.e. you cannot simply paste items from the HUDSEN clipboard into another computer program. The collection function will replace the clipboard in 2009 and allow great flexibility in performing Boolean operations between 2 or more sets of data.
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A method developed by EMAGE to calculate the degree of spatial similarity (using the Jaccard Index) between any number of spatial patterns (spatially annotated onto the same EMAP virtual embryo model), hierarchically cluster the similarity values, and present the data as a tree showing spatial relatedness between the gene expression patterns using a modified version of JavaTreeView. More information on CLUSTER.
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Coming in 2009 - In EMAGE, the term 'collection' is used to refer to a group of EMAGE entries. Each item in the collection is one EMAGE entry. Logging in will allow you to make one or more collections, and to perform boolean comparisons between two or more collections by many aspects of the entries (e.g. gene, stage, detection reagent, spatial annotations, text annotations etc), or to add aspects of the entries within one collection into a combined query term (e.g. ALL the genes or stages or spatial annotations or text annotations in the collection). The content of your collections will be stored on our central server. You will be able to assign different view privileges (e.g. private, for your friends, public etc) to allow for either private use or data exchange. Similar to the clipboard, but it has more functionalities.
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Parcels of text sent by a server to a Web client (usually a browser) and then sent back unchanged by the client each time it accesses that server. Cookies are used for authenticating, session tracking , and maintaining specific information about users such as their site preferences or the contents of their electronic shopping carts. In HUDSEN, we use cookies to store your clipboard (of entries) on your computer.
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A non-profit organisation devoted to expanding the range of creative work available for others legally to build upon and share. The organisation has released several copyright licenses known as Creative Commons licenses. These licenses, depending on the one chosen, restrict only certain rights (or none) of the work. http://creativecommons.org/
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Carnegie stage of (human) embryo development
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D

Distributed Annotation System - defines a communication protocol used to exchange biological annotations. It is motivated by the idea that such annotations should not be provided by single centralised databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualisation, which is done by DAS clients. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. http://www.biodas.org/
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days after intercourse (post coitum - Latin for: 'after intercourse')
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DNA Data Bank of Japan. http://www.ddbj.nig.ac.jp/. Part of the INSDC.
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A general term used in HUDSEN to denote the reagent that has been used to detect gene expression in an assay. i.e. either a probe (as used in in situ hybridisation), antibody (as used in immunohistochemistry) or a reporter gene under the genetic control of the organism (as used in in situ reporter assays).
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DOI - a permanent identifier given to a digital document, which is not related to its current location. A typical use of a DOI is to give a scientific article a unique identifying number that can be used by anyone to locate details of the paper, and often an electronic copy. In this way it functions as a 'permalink'. Unlike the URL system used on the Internet for web pages, the DOI does not change over time, even if the article is relocated (provided the DOI resolution system is updated when the change of location is made). http://www.doi.org/
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Deoxyribonucleic acid. The nucleic acid of which the genome (in the nucleus) is made.
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see: Digital Object Identifier
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A staging system for mouse embryos - specifically over the period from just before gastrulation to the beginning of organogenesis. This period is divided into 9 stages that are based on the morphological development of the embryo and features that are visible using a light microscope. Named after Karen Downs and Tim Davies (Department of Zoology, University of Oxford, UK) who defined these stages in PO strain (Pathology Oxford) embryos. see: Downs, K & Davies, T. (1993) "Staging of gastrulating mouse embryos by morphological landmarks in the dissecting microscope." Development. 118(4):1255-66.
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days post conception
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E

embryonic day of development
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One of 3 embryonic 'germ layers': the endoderm, ectoderm and mesoderm. These layers later develop into certain bodily systems. The ectoderm develops into the brain, skin, nails, the lens of the eye, the retina and the nervous system. Formed during gastrulation.
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Edinburgh Mouse Atlas of Gene Expression.
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The Edinburgh Mouse Atlas Project - the combined research projects of Dr Duncan Davidson and Prof Richard Bladock. Resources provided by EMAP are the EMAP Anatomy Atlas of Mouse Development and the EMAGE Gene Expression Database. See also: http://www.emouseatlas.org/
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A set of 3D images, representing virtual model mouse embryos at different (Theiler) stages of development. The model embryos are made of voxels stacked in 3D space. Each voxel has a grey value associated with it and each voxel's place in the 3D image is defined by its X,Y,Z co-ordinates. Sections can be cut in any plane through the 3D models to visualise internal structures using a number of computer programs (MAPaint, JAtlas Viewer). All models have been made from images taken from one mouse (C57BL/6 x CBA F1) embryo. Depending on the actual model, the 3D image have been made using one of two methods: (a) Optical Projection Tomography, or (b) by initially embedding the embryo in either plastic or wax and taking histological sections (section thickness = 2microns for plastic embedded samples and 7 microns for wax embedded). A digital photograph is then taken of every section, and these digital images are stacked and aligned to create a 3D image. Some embryo models have anatomical domains delineated within them. As there are separate 3D models at different stages of development, there is an overt spatio-temporal aspect.
The EMAP 3D virtual embryos are used as the template for EMAGE spatial annotations that describe sites of gene expression in the developing mouse embryo.
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A structured list of 13,000+ terms that describe visible anatomical structures in the developing mouse embryo. The ontology is arranged in 26 separate lists (one for each Theiler Stage of development). The lists at each stage are hierarchically organised in various 'part-of' relationships in a directed acyclic graph e.g. hindgut endoderm is part of the hindgut,hindgut is part of the gut, or an alternative view: hindgut endoderm is part of gut endoderm, gut endoderm is part of the gut. The part-of relationships allow flexibility when querying or mining data (e.g. genes expressed in the hindgut endoderm, are also expressed in the gut endoderm or gut and can be retrieved when any of these terms are used for query). Numerous common synonyms are also included (e.g. mesencephalon = midbrain), allowing either term to be used for query. It differs from the Abstract Mouse in that it is divided into 26 separate lists, one for each Theiler stage of development, whereas the Abstract Mouse is 'collapsed' across time to produce one list. Thus, it has an overt temporal aspect.
The EMAP anatomy ontology is used as a template to denote text annotations that describe sites of gene expression in the mouse embryo, as produced by both EMAGE and GXD.
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A resource describing the anatomy of the mouse embryo. It contains two main aspects - a set of virtual 3D embryos at different Theiler stages of development, and the associated EMAP anatomy ontology. The 3D models and terms in the ontology are linked by 3D domains defined within each model that correspond to specific terms in the ontology. The EMAP Atlas is the scaffold that houses the text and spatial-based descriptions of gene expression patterns in EMAGE.
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European Molecular Biology Laboratory http://www.embl.org/. Part of the INSDC.
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(from Greek: lit. "that which grows,") a multicellular eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination.
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One of 3 embryonic 'germ layers': the endoderm, ectoderm and mesoderm. These layers later develop into certain bodily systems. The endoderm develops into the inner linings of the digestive tract, as well as the linings of the respiratory passages. It also forms many glands, such as the liver and pancreas. Formed during gastrulation.
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"arising from within" a system, the opposite of exogenous.
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A software system which produces and maintains automatic annotation on many eukaryotic genomes. Ensembl produces data and software used to analyse and present the data. http://www.ensembl.org/
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A searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer. http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
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One entry = one specimen stained for the expression of one gene/protein at one point in embryonic development. Associated with each entry are details of the detection reagent, the specimen, sites of expression (denoted by both text annotation and spatial annotation), the names and details of the data submitter/source and relevant links to other data either in EMAGE or several external databases.

A localised region on the surface of an antigen that is capable of eliciting an immune response and of combining with a specific antibody to counter that response.
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A cell or organism with membrane-bound, structurally discrete nucleus and other well-developed subcellular compartments. Eukaryotes include all organisms except viruses, bacteria, and blue-green algae.
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"coming from outside" a system. Opposite of endogenous.
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Part of a gene whose sequence is present in a mature mRNA after splicing. See also intron.
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See: gene expression
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F

File Transfer Protocol. A protocol associated with the transfer of digital information on the internet between client computers and file servers. Files may be transferred, downloaded, and uploaded individually or in batch form.
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G

A phase early in the development of animal embryos, during which the morphology of the embryo is dramatically restructured by cell migration. It is during gastrulation that the 3 'germ layers' are produced: ectoderm, mesoderm and endoderm.
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The NIH (National Institutes of Health, USA) genetic sequence database, an annotated collection of all publicly available DNA and RNA sequences. http://www.ncbi.nlm.nih.gov/Genbank/index.html
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A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism.
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An approach that is used to introduce insertional mutations across the mammalian genome. It is performed with gene trap vectors whose principal element is a gene trapping cassette consisting of a promoterless reporter gene and/or selectable genetic marker flanked by an upstream 3’ splice site (splice acceptor; SA) and a downstream transcriptional termination sequence (polyadenylation sequence; polyA). When inserted into an intron of an expressed gene, the gene trap cassette is transcribed from the endogenous promoter of that gene in the form of a fusion transcript in which the exon(s) upstream of the insertion site is spliced in frame to the reporter/selectable marker gene. Since transcription is terminated prematurely at the inserted polyadenylation site, the processed fusion transcript encodes a truncated and non-functional version of the cellular protein and the reporter/selectable marker.
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Transcriptional activity of a gene resulting in one or more RNA products and, usually, following translation, one or more protein products.
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The total genetic information of a cell or organelle. In eukaryotes, "genome" usually refers to nuclear DNA rather than to mitochondrial or chloroplast DNA.
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genotype

green fluorescent protein.
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Graphics Interchange Format, a data compression format used initially by CompuServe to compress and transfer graphic images for screen display. The format is commonly used for transferring graphics files on the internet.
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Gene Expression Database at MGI. http://www.informatics.jax.org/expression.shtml
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H

heterozygous

hierarchical clustering

A type of clustering (i.e. the classification of objects into different groups, or more precisely, the partitioning of a data set into subsets (clusters), so that the data in each subset share some common trait - usually proximity according to some defined distance measure). Hierarchical algorithms find successive clusters using previously established clusters. Hierarchical algorithms can be agglomerative ("bottom-up") or divisive ("top-down").
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homozygous

The Human Developmental Studies Network (HUDSEN) Project (www.HUDSEN.org). HUDSEN is created and maintained by the Human Developmental Genetics (HDG) group in the Institute of Human Genetics at Newcastle University. The HDG group are involved in a variety of projects including DGEMap, HDBR, and NG Embryo. For more information, please see the relevant websites.
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A set of 3D images, representing virtual model human embryos at different Carnegie stages of development. The model embryos are made of voxels stacked in 3D space. Each voxel has a grey value associated with it and each voxel's place in the 3D image is defined by its X,Y,Z co-ordinates. Sections can be cut in any plane through the 3D models to visualise internal structures using a number of computer programs (MAPaint, JAtlas Viewer). All models have been made from images taken from one human embryo using Optical Projection Tomography. Some embryo models have anatomical domains delineated within them. As there are separate 3D models at different stages of development, there is an overt spatio-temporal aspect.
The HUDSEN 3D virtual embryos are used as the template for spatial annotations that describe sites of gene expression in the developing human embryo.
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hybridisation (of nucleic acids)

I

See: immunohistochemistry
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A method of identifying cell types based on the binding of antibodies to specific components (most often proteins) of the cell. Immunohistochemistry of embryonic material requires a sample of tissue that is chemically preserved or 'fixed'. The sample can be whole or it can be sliced extremely thinly, so that it is approximately one cell thick, then the sample is fixed onto a glass slide. Antibodies against specific antigens are added to the sample on the glass slide, and the antibodies bind wherever the antigens are present. Excess antibody is then washed away. The antibodies that remain bound to the cell have labels on them that either fluoresce (glow) or undergo a chemical reaction that makes them visible by microscope. It can be used for assaying gene expression (specifically translation) in situ.
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in the original position (Latin for: 'in place'). In biology, within the organism.
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A technique permitting identification of particular deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequences while these sequences remain in their original location in the cell. A cell or tissue is treated with a fixative and then exposed to a labeled (by either radioactivity, small molecules such as digoxigenin or fluorophores) single-stranded nucleic acid probe that hybridises specifically with the targeted nucleic acid sequence (by virtue of base-pairing betwen the sense and anti-sense strands). Excess probe is washed away, and the probe that remains bound to the cell is visualised by detecting the label on it. It can be used for assaying gene expression (specifically transcription) in situ.
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An assay type that uses mice containing a targeted mutation in which a reporter gene has replaced an endogenous gene. The two most common reporter genes are lacZ and green fluorescent protein. It is used a technique for assaying gene expression in situ.
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International Nucleotide Sequence Database Collaboration - collaboration between DDBJ, EMBL, and GenBank to share and maintain nucleic acid sequence data. http://www.insdc.org/
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intron

in vitro

in vivo

See: in situ hybridisation
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See: in situ reporter
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J

A java program for selecting and viewing virtual sections from woolz format 3D images. Since any arbitrary section plane can be chosen, it can be used to explore the internal space of these 3D images. http://genex.hgu.mrc.ac.uk/Software/JavaTools/JAtlasViewer/intro.html
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An object-oriented programming language that is platform independent (the same Java program runs on all hardware platforms without modification). Developed by Sun Microsystems, Java is widely used on the Web for both client and server processing. http://www.java.com/
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An Open Source, Java-based, extensible viewer originally developed for visualisation of clustered (e.g. by hierarchical, K-means methods etc) Microarray Data in the PCL or CDT format. http://jtreeview.sourceforge.net/
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A file formatted in the colour graphics compression format devised by the Joint Photographic Experts Group and having the filename extension jpg. The JPEG standard uses a ‘lossy' data compression method in which some data is sacrificed (lost) to achieve greater compression. JPEGs are widely used on the internet and are especially suited for photographs and other graphics with continuous tones, as compared to GIFs, which are better suited to rendering line art and graphics with large masses of solid colour.
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K

An assay type that uses mice containing a targeted mutation in which a reporter gene has replaced an endogenous gene. The two most common reporter genes are lacZ and green fluorescent protein.
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A casual term for a type of targeted mutation in which a loss-of-function allele is produced.
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L

A chemical entity used to tag a probe or antibody, which will enable the probe or antibody to be detected. e.g. radioactive tags such as S³⁵ (detected by autoradiography), small molecules such as digoxigenin (detected by secondary antibodies raised against them and conjugated to a reporter enzyme such as alkaline phosphatase), or fluorophores such as fluorescein (detected by fluorescence).
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A free UNIX-type operating system originally created by Linus Torvalds with the assistance of developers around the world. Linux operating systems such as SUSE can be installed on a PC. http://www.linux.org/
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locus

Local Spatial Similarity Search Tool - An algorithm that finds regions of local similarity between biological staining patterns in EMAGE (for example, ISH or IHC staining patterns). The program compares a user defined query region to woolz spatial domains in the EMAGE database and calculates a similarity score of matches using the Jaccard Index. LOSSST can be used to infer functional relationships between genes with similar localised patterns of expression, as well as help identify members of a synexpression group. More about LOSSST.
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M

Macintosh Operating System 10. Mac OS X is a line of computer operating systems developed, marketed, and sold by Apple Inc, and which has been pre-loaded on all Macintosh computers since 2001. Mac OS X is a Unix-based operating system.
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A computer program for delineating regions in a 3D images that is routinely used in the HUDSEN, EMAP and EMAGE projects. We routinely use it for delineating anatomical regions within the HUDSEN virtual embryo models, or for performing spatial annotations that describe sites of gene expression. It requires a UNIX, Linux or MacOSX operating system and is available on the EMAP Software CD.
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One of 3 embryonic 'germ layers', the endoderm, ectoderm and mesoderm. These layers later develop into certain bodily systems. The mesoderm forms the somites, the notochord, and the mesenchyme, which give rise to the muscles, circulatory and excretory systems of the body. Formed during gastrulation.
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An RNA molecule that is the product of transcription of a gene, after that molecule has been spliced and polyadenylated, that can be translated into a protein product.
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see: Mouse Genome Informatics
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Micro RNAs (miRNAs) are a group of noncoding RNA molecules, generally 21 to 24 nucleotides in length, which are usually cleaved from a larger hairpin-containing RNA (itself often processed from some portion of mRNA). miRNAs are conserved through evolution, and their abundance and expression patterns are suggestive of diverse regulatory roles.
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Minimum Information Specification For In Situ Hybridisation and Immunohistochemistry Experiments. This specification details the minimum information that should be provided when publishing, making public, or exchanging results from visual interpretation-based tissue gene expression localisation experiments such as in situ hybridisation, immunohistochemistry, in situ reporter genetic experiments, etc.. Compliance to this standard is expected to provide researchers at other labs enough information to reproduce the experiment and/or to fully evaluate the data upon which results are based. It was modeled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. See http://dx.doi.org/10.1038/nbt1391
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An antibody produced by cells cultured in vitro that have their origin in a single antibody-producing cell and which is therefore of a single molecular type, in contrast to the polyclonal antibodies normally found in the serum of an immunised animal.
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Develops and maintains the 'model organism' database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data. http://www.informatics.jax.org/
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see: Messenger RNA.
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An individual carrying a mutation or term applied to a gene or phenotype altered by mutation.
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mutation

Any permanent change in the nucleotide sequence of DNA. Examples include chromosome rearrangements (i.e. where there is a change in how the genome is arranged into its constituent chromosomes) and point mutations (the changing of one nucleotide for another).
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N

National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/. Part of the INSDC.
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An experiment not conducted as part of a screen. The experimental conditions are usually optimised (e.g. to allow maximal binding between a detection reagent and the target molecule in situ).
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DNA or RNA. Each of these compounds consists of a backbone of sugar molecules ribose for RNA and deoxyribose for DNA linked by single phosphate groups. Attached to the sugars of the backbone are any of four nitrogenous bases, A, T, C or G for DNA and A, U, C or G for RNA.
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A monomer unit of nucleic acid, consisting of a purine or pyrimidine base, a sugar molecule (ribose or deoxyribose), and phosphate group(s).
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The compartment in a eukaryotic cell that contains the chromosomes. In most types of eukaryotic cells, the nucleus breaks down as chromosomes condense during cell division.
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O

Ontologies are 'specifications of a relational vocabulary'. In other words they are sets of defined terms such as those in a dictionary, but the terms are given hierarchical relationships to one another. The terms in a given vocabulary are likely to be restricted to those used in a particular field or domain. For example, in the case of EMAP anatomy ontology, the terms all refer to anatomical structures.
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see: Optical Projection Tomography
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An imaging technique to produce 3D images from intact biological samples that may or may not be stained with colorimetric or fluorescent reagents. see http://www.bioptonics.com/
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A group of tissues that perform a specific function or group of functions in an organism.
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A living thing (such as an animal or plant). In at least some form, all organisms are capable of reacting to stimuli, reproduction, growth and maintenance as a stable whole. An organism may be unicellular (i.e. consisting of one cell) or made up of many billions of cells grouped into specialised tissues and organs.
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A period of development of an animal embryo, whereby the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
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P

These relationships are used in the EMAP Anatomy Ontology and the Abstract Mouse to describe how different entities are related to each other. They refer to when one entity is part of another. e.g. the eye is part of the head.
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phenotype

A description of the observable physical state of an individual with respect to some inherited characteristic. Individuals with different genotypes may display the same phenotype.
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An abbreviation for 'picture element' (using the common abbreviation 'pix' for 'pictures'). A single point in a graphic image. Each such information element is not really a dot, nor a square, but an abstract sample. With care, pixels in an image can be reproduced at any size without the appearance of visible dots or squares; but in many contexts, they are reproduced as dots or squares and can be visibly distinct when not fine enough. The intensity of each pixel is variable; in colour systems, each pixel has typically three or four dimensions of variability such as red, green, and blue (RGB) or cyan, magenta, yellow, and black (CMYK).
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Portable Network Graphics. A bitmapped graphics file format endorsed by the World Wide Web Consortium. It is expected to eventually replace the GIF format, because there are lingering legal problems with GIFs. CompuServe owns the format, and Unisys owns the compression method. In addition, GIF is a very basic graphics format that is limited to 256 colours (8-bit colour). PNG provides advanced graphics features such as 48-bit colour, including an alpha channel, built-in gamma and colour correction, tight compression and the ability to display at one resolution and print at another.
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Antibodies that are derived from different B-cell lines. They are a mixture of immunoglobulin molecules secreted against a specific antigen, each recognising a different epitope. These antibodies are typically produced by immunisation of a suitable mammal, such as a mouse, rabbit or goat. Larger mammals are often preferred as the amount of serum that can be collected is greater. An antigen is injected into the mammal. This induces the B-lymphocytes to produce IgG immunoglobulins specific for the antigen. The IgG is purified from the mammal’s serum or the serum is used whole.
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In molecular biology, a nucleic acid that has been labeled either radioactively or chemically that allows the detection of nucleic acids with sequence similarity in a sample by hybridisation. Probes are used to detect DNA on membranes in Southern blots, to detect RNA on membranes in Northern blots, and either DNA or RNA in cytological preparations for in situ hybridisation.
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Important molecules in cells. They perform a variety of functions from structural to enzymatic. While proteins have many diverse functions, all are polymers of 20 possible amino acids. They are produced by the process of translation.
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R

Reference Sequence (RefSeq) database. A non-redundant collection of annotated DNA, RNA, and protein sequences. Each RefSeq represents a single, naturally occurring molecule from one organism. The goal is to provide a comprehensive, standard dataset that represents sequence information for a species. It should be noted, though, that RefSeq has been built using data from public archival databases only. http://www.ncbi.nlm.nih.gov/RefSeq/
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A gene whose product is easily detected and not ordinarily present in an organism or cell type under study that is expressed as part of a DNA construct introduced experimentally. Bacterial beta-galactosidase, whose activity can be detected using a staining reaction, is a commonly used reporter gene, as is green fluorescent protein.
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The EMAGE data warehouse. The datain the repository has been externally sourced and have not yet been scrutinised by an EMAGE curator. They can be accessed by Quick Search only. The mimimum amount of information held for these entries is: Data Source; Gene/Protein assayed; Detection Reagent used; Theiler Stage (usually approximated from the dpc value and not based on actual morphological criteria); the stage given by the data submitter (usually as dpc value, sometimes as numbers of somites); Assay type (ISH/ISR/IHC); Specimen type (WM/section); whether the specimen is wild-type or a mutant (and if a mutant, the allele is indicated); and an image (or set of images) of the specimen.
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Ribonucleic acid. A nucleic acid that is the primary product of gene expression. Chemically, it differs from DNA by the substitution of ribose for deoxyribose in the sugar-phosphate backbone and by the substitution of the base uracil for thymine. RNA is produced by the process of transcription.
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S

screen

A high-throughput gene expression profiling (or 'screening') experiment. Possibly not optimised for the experimental conditions (e.g. to allow maximal binding between detection reagent and the target molecule in situ). Compare to non-screen.
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section

Refers to the strand of a DNA molecule whose sequence is represented in mRNA, or an RNA molecule normally processed into mRNA and translated (rather than the anti-sense or complementary sequence).
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A computer dedicated to providing one or more services over a computer network, typically through a request-response routine to/from client computers. Examples of server applications include file servers, web servers, and the database servers (all of which are used by EMAGE).
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In the developing vertebrate embryo, somites are organised masses of cells of mesodermal type, distributed along the two sides (left and right) of the longitudinally central neural tube. They are transient and go on to form various tissues and organs such as the dermis, skeletal muscle, and vertebrae.
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In HUDSEN: The curation process of using the HUDSEN 3D virtual embryos as a standard framework to denote the sites of gene expression as depicted in images. Different colours in the annotation are used to represent different levels of apparent signal intensity. This converts the inaccessible, yet complex information in the images into a standardised and structured description that is available for database storage and query. An example of spatial annotation being performed using MAPaint. After this process, HUDSEN curators also assign confidence scores relating to the clarity of pattern seen, and the morphological match between each data embryo and the corresponding HUDSEN virtual model used as the spatial template during this process.
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Pertaining to 2D or 3D space.
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Part of the processing of an RNA transcript into mRNA, in which introns are removed enzymatically and exons are retained.
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Structured Query Language. A database computer language designed for the retrieval and management of data in relational database management systems, database schema creation and modification, and database object access control management.
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strain

A specific breeding population of a species, including 'inbred strains', or the progeny of specific crosses, or a mixed population of the species with partially known or unknown genetic background.
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The UniProtKB/Swiss-Prot Protein Knowledgebase is a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and a high level of integration with other databases. Together with UniProtKB/TrEMBL, it constitutes the UniProt Knowledgebase, one component of the Universal Protein Resource (UniProt), a one-stop shop allowing easy access to all publicly available information about protein sequences. http://www.expasy.org/sprot/
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A type of non-random eukaryotic gene organisation. Genes in a synexpression group may not be physically linked, but they are involved in the same process and they are coordinately expressed in a spatio-temporal fashion. It is expected that genes that function in the same process be regulated coordinately. Synexpression groups in particular represent genes that are simultaneously up- or down-regulated, often because their gene products are required in stoichiometric amounts or are protein-complex subunits. It is likely that these gene groups share common cis- and trans-acting control elements to achieve co-ordinate expression.
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T

A type of mutation in which a chromosomal gene is altered by the substitution of a DNA construct assembled in vitro. In mouse, the constructs are usually designed to eliminate gene function; such targeted mutations are often casually referred to as knock outs. Some DNA constructs are designed to alter gene function; such targeted mutations are often casually referred to as knock ins.
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Pertaining to time.
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In HUDSEN: The curation process of using the anatomy ontology as a standard framework to denote the sites of gene expression as described by a data submitter. This converts the (usually) unstructured free-text description of the submitter into a standardised and structured description that is available for database storage and query. See an example.
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A staging system for mouse embryos. Stages are based on the external and/or internal morphological development of the embryo, and are not directly dependent on either age or size. The mouse embryonic period proper is divided into 26 Theiler stages. Criteria beyond morphological features include age in days, number of somites present, and embryonic length. Named after Karl Theiler, a Swiss embryologist (1920-2007) who defined the stages in C57BL/6 x CBA (F1) embryos. Download his book for free from the EMAP Mouse Atlas Website.
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Tagged Image File Format. A widely used bitmapped graphics file format developed by Aldus and Microsoft that handles monochrome, gray scale, 8-and 24-bit colour. TIFF allows for customization, and several versions have been created, which does not guarantee compatibility between all programs.
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tissue

An organisational level of cells intermediate between cells and a complete organism. Hence, a tissue is an group of cells, that together carry out a specific function in the organism.
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transcript

transcription

transgenic

A mouse that contains DNA that has been inserted randomly into the genome. The inserted DNA or gene sequence (the transgene) may or may not be derived from mouse.
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translation

Theiler stage of mouse embryo development
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U

A gene-centred view of the transcriptome (i.e. all possible transcripts produced from the genome). Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene). http://www.ncbi.nlm.nih.gov/UniGene/
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The Universal Protein Resource (UniProt), a one-stop shop allowing easy access to all publicly available information about protein sequences. http://www.uniprot.org/
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A computer operating system originally developed by AT&T in the late 1960s. Today's Unix systems are split into various branches, developed over time by AT&T as well as various commercial vendors and non-profit organisations. During the late 1970s and early 1980s, the influence of Unix in academic circles led to large-scale adoption of Unix by commercial startups, such as Solaris. Today, in addition to certified Unix systems, Unix-like operating systems such as Linux are common.
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Uniform Resource Locator. In computing, a URL specifies where an identified resource is available and the mechanism for retrieving it. In popular language, a URL is also referred to as a web address (e.g. http://emouseatlas.org).
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V

Vertebrate Genome Annotation (VEGA) database - a central repository for high quality, frequently updated, manual annotation of ' finished' genome sequence for selected vertebrates. http://vega.sanger.ac.uk/
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A three-dimensional pixel. A voxel represents a quantity of 3D data just as a pixel represents a point or cluster of points in 2D data. It is used in scientific and medical applications that process 3D images.
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W

Defined by the World Wide Web Consortium (W3C) as "a software system designed to support interoperable machine-to-machine interaction over a network". They commonly use XML messages that follow the SOAP (a protocol for exchanging XML-based messages over computer networks) standard and have been popular with traditional enterprise. In such systems, there is often machine-readable description of the operations offered by the service written in the Web Services Description Language (WSDL).
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whole-mount

A specimen, that is 'mounted' (or prepared for an experiment) intact, or at least partly intact. More specifically it is used to denote a specimen that has not been sectioned.
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wild-type

either: The phenotype with respect to a given inherited characteristic that is considered to be the "normal" type commonly found in natural populations
or: The allele of a particular gene that confers the phenotype considered to be the "normal" type commonly found in natural populations.
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see: woolz
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see: whole-mount
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The woolz image processing software was developed by the MRC Human Genetics Unit, for fast microscope slide scanning, chromosome image analysis, pattern recognition and a wide range of image processing and analysis problems. The woolz image processing system has been adopted as the standard for EMAP and EMAGE and is used for all the reconstructions and anatomical, gene-expression and spatial domains. This is because the interval coding provides significant computing advantages in a range of image processing functions specifically set operationa (union, intersect etc.), morphological operations (erosion, dilation etc.) and other binary image processing such as distance transforms, skeletonisation, segmentation and labelling. The woolz structures are also compact and in terms of grey-level data minimise memory usage without compression (which in principle can also be applied).
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X

Extensible Markup Language. A general-purpose specification for creating custom markup languages. It is classified as an extensible language because it allows its users to define their own elements. Its primary purpose is to help information systems share structured data, particularly via the Internet, and it is used both to encode documents and to serialise data.
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