Pathbase: a database of mutant mouse pathology

Abstract

Pathbase is a database that stores images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis. Images of normal mouse histology and strain-dependent background lesions are also available. The database and the images are publicly accessible (http://www.pathbase.net) and linked by anatomical site, gene and other identifiers to relevant databases; there are also facilities for public comment and record annotation. The database is structured around a novel ontology of mouse disorders (MPATH) and provides high-resolution downloadable images of normal and diseased tissues that are searchable through orthogonal ontologies for pathology, developmental stage, anatomy and gene attributes (GO terms), together with controlled vocabularies for type of genetic manipulation or mutation, genotype and free text annotation for mouse strain and additional attributes. The database is actively curated and data records assessed by pathologists in the Pathbase Consortium before publication. The database interface is designed to have optimal browser and platform compatibility and to interact directly with other web-based mouse genetic resources.

The Challenges of Defining Oral Cancer: Analysis of an Ontological Approach

“…As a comprehensive ontology of human anatomy, the FMA includes terms that represent the structural organization of the human body from the macromolecular to macroscopic levels. The types of malignant neoplasms found in the mouth region can be linked through FMA to other comprehensive terminologies related to cancer such as Mouse Pathology [47], and Cancer Research and Management ACGT Master Ontology [48]. Currently, we are developing a standardized vocabulary for the surgical pathology domain and we are planning to link the mouth region cancer terminologies to that vocabulary.…”

Using bio-ontologies as data annotation, integration & analytical tools at the Mouse Genome Informatics resource

“…In parallel, efforts are underway to decompose pre-coordinated MP terms into computable logical definitions (crossproducts) and render the PATO-style and MPO phenotype descriptions interoperable, using PATO in conjunction with orthogonal ontologies of quality-bearing entities [21]. In fact, the MPO has been designed as a cross-product ontology (22) that can hold, for each term, seamless crossreferences to other open biological ontologies (OBO) [23], currently incorporating or associating terms from the GO Biological Process ontology, the Cell-Type (CL) Ontology of the OBO Foundry [24], the Embryonic Mouse Anatomical Dictionary developed by EMAP [25], the Adult MA Dictionary developed by GXD (see below), and the Mouse Pathology ontology (MPATH) developed by Pathbase [26], among others.…”

Untitled

“…The mouse anatomy ontology is also being used to annotate phenotype data for the Eumorphia project [35]. In Pathbase, a database of mutant mouse pathology [36], anatomical attributes of images for mutant postnatal mouse pathology are coded using terms based on the Adult Mouse Anatomical Dictionary. Furthermore, efforts are currently underway to incorporate the adult mouse anatomy ontology into the National Cancer Institute (NCI) Thesaurus, a knowledgebase containing the working vocabularies used in NCI data systems [37].…”