Mouse Ontology Resources

This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28). The ontology is represented as a directed acyclic graph (DAG). Anatomical structures are organized spatially and functionally, using 'is a' and 'part of' relationships. The ontology will be used by the Gene Expression Database (GXD) to encode and integrate different types of mouse expression data and by the Mouse Genome Database (MGD) to encode mouse phenotype data pertinent to anatomy. The use of common anatomical terms will facilitate the integration and correlation of expression and phenotype data.

Search or browse the mouse dictionary from: http://www.informatics.jax.org/searches/anatdict_form.shtml

The ontology is available as DAG-EDIT: http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/ anatomy/gross_anatomy/animal_gross_anatomy/mouse

Specific comments on the anatomical dictionary should be sent to:
anatomy@informatics.jax.org

The CBIL Controlled Vocabulary for Anatomy provides a set of hierarchical terms for mouse and human anatomical descriptions. The anatomical vocabulary has been used for annotating sources of gene expression and delineating anatomical structures on mouse brain images. The terms range from anatomical systems at the top (e.g., organ system) to cells. The hierarchy contains both IS-A and HAS-A relationships although these are not specified.
Definitions are not provided however the source of the term is provided along with synonyms in some cases.
The controlled vocabulary is based on a table of anatomy terms taken from the Mouse Gene Expression Database at the Jackson Laboratory (specifically GXD mouse stage 28 - adult; i.e. the Adult Moust Anatomy.) However, it has been extended to incorporate human anatomy and also revised in a number of areas, particularly the haematolymphoid system, based on the 37th edition of Gray's Anatomy. Brain terms have been extensively expanded thanks to the contributions of Dr. Jonathan Nissanov of Drexel University. Cell lines are indicated as children of the cell type that they are derived from.

The CBIL Controlled Vocabulary is freely available at
http://www.cbil.upenn.edu/downloads/RAD/ in 5 files
(controlled-vocab-*.sql) to create and populate tables for a relational
database.

The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth. Its primary purpose is to support the annotation of gene function data (e.g. gene expression patterns and mutant phenotypes). The ontology - currently ~8000 entities - includes all major structures that are visible in conventionally-stained histological sections (i.e. sections from paraffin-imbedded material stained with haematoxylin and eosin), but not domains that are only delineated by gene expression. As part of EMAP, the major named structures are being delineated in three-dimensional voxel models of embryos; this delineation in part defines the corresponding anatomical terms.

The anatomical entities present at each Theiler Stage are connected by part of relationships and organised in a hierarchical tree. Since no single hierarchical arrangement of parts will satisfy all requirements, we are building a directed acyclic graph in which the same basic entities are linked in alternative ways (e.g. to include all the bones as "part of" the skeleton). Underlying the visible stage-by-stage ontology is a stage-independent aggregate of all the anatomical terms, known as the 'abstract mouse'. Stage-dependent entities thus bear instance of relationships to the corresponding stage-independent entity. The EMAP anatomy ontology is implemented as a web-accessible database. It is used by the EMAGE gene expression database and by the MGI. The MGI is developing a complementary anatomical ontology for the adult mouse.

The resource can be viewed interactively at http://genex.hgu.mrc.ac.uk/Databases/Anatomy/ and is available from this site in xml and ascii formats. It is also available as open source at the GOBO site: http://www.geneontology.org/doc/gobo.html

NCI Thesaurus is a description logic cancer vocabulary developed using the Apelon Terminology Development Environment (TDE) and made available to NCI applications through the Apelon Distributed Terminology Server (DTS). The browser http://nciterms.nci.nih.gov accesses the vocabulary through DTS. See http://ncicb.nci.nih.gov, click on Architecture, then Enterprise Vocabulary Services for more detailed information.

Mouse Tissue Type: This is based on the Jackson Laboratories Mouse Tumor Biology Database tissue types pull down list with some structure added and minor modifications made. It is not a true is-a hierarchy at present.

Current Uses:

The Mouse Tissue Type vocabulary currently is in use for the Cancer Models Database and caIMAGE database, and is used to annotate and retrieve both mouse models and pathology images. The Mouse Models of Human Cancer Consortium is the primary user at this time. (See: http://emice.nci.nih.gov).

Future Plans:

The mouse tissue type vocabulary is adequate for current uses, but would need additional editing for future use. Rather than revise the current version, we are investigating whether we can adopt or adapt the adult mouse anatomy under development by Jackson Laboratories and University of Edinburgh.

Accessibility:

The NCI Thesaurus content is open source. XML and flat files are available through the caCORE FTP site: http://ncib.nci.nih.gov, Click on caCORE FTP site at the left bottom corner.

The content can be browsed through the DTS server at http://nciterms.nci.nih.gov

Limited access to the vocabulary is also provided through caBIO. (See: http://ncicb.nci.nih.gov ) or contact us for further information.