Читать книгу Pathology of Genetically Engineered and Other Mutant Mice - Группа авторов - Страница 24

The move to make scientific data openly discoverable, accessible, and useable has led to the formalization of the principles of open data, known as FAIRsharing [2]. Data has to be free, accessible, interoperable, and reusable. Increasingly databases are trying to comply with the FAIR semantic and access technical requirements as part of data discovery and interoperability, and many databases now provide access computationally through an Application Programming Interface (API) as well as through Hypertext Markup Language (HTML), together with complete data dumps and data reports. Searching using standardized semantics and ontologies provides very powerful ways of searching databases, and for databases such as MouseMine it is possible to use very powerful SPARQL Protocol and RDF (Resource Description Framework) Query Language (SPARQL) queries.

Along with standardization of database structures and access goes formalization of standards, essential for interoperability and data aggregation. Different communities have established specific standards for metadata, minimal information (MI) for reporting (MI standards), and other data structures. These standards and the characteristics of databases can now be found in databases of databases such as the very useful FAIRsharing database. FAIRsharing lists and describes standards used in databases but also the type of data and importantly the species. Currently, FAIR sharing lists 90 databases either dedicated to the mouse or with specifically mouse data [2].

The Re3data repository [3] lists 57 mouse data resources, interestingly with limited overlap with those from FAIRsharing, indicating the usefulness of looking at as many metaresources as possible. Of course, many databases, particularly small but often valuable ones, are not listed in these resource repositories. It is one aim in this chapter to introduce some of these smaller databases that are nevertheless very valuable.

Table 2.1 Websites with information useful for phenotyping mutant laboratory mice.

Website name	Address	Data resource
Alliance of Genome Resources	https://www.alliancegenome.org	Identification of animal models for human disease
Atlas of mouse cardiovascular development	https://www.devbio.pitt.edu/research/atlas‐mouse‐cardiovascular‐development	Atlas of the mouse cardiovascular system using EFIC
Bonebase	http://www.bonebase.org	Variation in bone mass using μCT and histomorphometry for KOMP mice
Emouseatlas	https://www.emouseatlas.org/emap/home.html	Mouse embryonic anatomy and development
GUDMAP	https://www.gudmap.org	Urogenital and prostate development with a collection of immunohistochemical, histological, and immunofluorescence images, and gene expression data
International Mouse Phenotyping Consortium (IMPC)	https://www.mousephenotype.org	Summaries of phenotyping of genetically engineered mice in the KOMP program
Monarch	https://monarchinitiative.org	Identification of animal models for human disease
Mouse Brain Atlas	https://developingmouse.brain‐map.org, https://mouse.brain‐map.org	High‐resolution physical atlases of the adult and embryonic mouse brains
Mouse Genome Informatics	http://www.informatics.jax.org	Large datasets on mice, genetics, inbred strains, mutant lines, etc.
Mouse Genome Informatics SNP Database	http://www.informatics.jax.org/snp	Single nucleotide polymorphisms for inbred strains
MouseMine	http://www.mousemine.org/mousemine/begin.do	Comparative human and mouse data
Mouse Models of Human Cancer Database (MMHCD)	http://tumor.informatics.jax.org/mtbwi/index.do	Mouse models of human cancer data and images
Mouse Phenome Database	https://phenome.jax.org	Variety of data on studies that compare inbred strains
MUTAGENETIX	https://mutagenetix.utsouthwestern.edu	Immunological phenotypes of single gene mouse mutants produced by ENU mutagenesis
National Toxicology Program Neoplastic Lesion Atlas	https://ntp.niehs.nih.gov/nnl/index.htm	Atlas of images and descriptions on nonneoplastic lesions in rats and mice
Noah's Arkive	http://noahsarkive.cldavis.org/cgi‐bin/show_image_info_page.cgi	Images of lesions from many different species
Online Mendelian Inheritance in Man (OMIM)	https://www.ncbi.nlm.nih.gov/omim	Summaries with references on genetic based diseases in humans with reference to animal models
Pathbase, The European Mouse Pathology Database	http://www.pathbase.net	Images of lesions found in mice (spontaneous, genetically engineered, etc.)
PATHBIO	http://www.pathbio.org	Training modules, X‐ray atlas, lymphatic mapping atlas, images of inbred strain specific diseases
Sanger Mouse SNP Database	https://www.sanger.ac.uk/sanger/Mouse_SnpViewer/rel‐1505	Single nucleotide polymorphisms for 36 inbred strains
Skinbase	http://eulep.pdn.cam.ac.uk/~skinbase/index.php	Subdirectory of Pathbase focusing on normal and abnormal skin phenotypes in mice

Many archival databases and some reference resources are very dependent on users to curate, correct uploads, and to give them added value for a community. Databases run for the use of specific communities can provide a high degree of added value at low cost and contribute heavily to scientific sustainability. Image databases especially fall into this category and in particular need new material from experts in the field to constantly expand the resource and accurately curate the material. Pathologists can use these resources as legacy tools for extra photomicrographs they take while working up new models or defining spontaneous diseases in colonies. Such additional images can be referenced in the primary publication as being publicly available on the websites, which usually is very well received by journals and reviewers on future grant applications. Many of the current public repositories will not accept files of the size of zoomable histopathology images and limited user uploads. This, together with payment to commercial repositories is a specific problem for very image intensive histopathology and cell biology data.