Catalyzing Inquiry at the Interface of Computing and Biology
COMPUTATIONAL TOOLS 59 4.2.1 Desiderata, If researcher A wants to use a database kept and maintained by researcher B, the “quick ...
60 CATALYZING INQUIRY 4.2.2 Data Standards, One obvious approach to data integration relies on technical standards that define r ...
COMPUTATIONAL TOOLS 61 Microarray data related to a given cell may be taken by multiple investigators in different labo- ratori ...
62 CATALYZING INQUIRY of these approaches are labor-intensive, and an outstanding challenge in the area of data normalization is ...
COMPUTATIONAL TOOLS 63 Box 4.2 The International Consortium for Brain Mapping (ICBM): A Probabilistic Atlas and Reference System ...
64 CATALYZING INQUIRY calls for the use of object-oriented concepts to develop data definitions, encapsulating the internal deta ...
COMPUTATIONAL TOOLS 65 4.2.6 Data Mediators/Middleware, In the middleware approach, an intermediate processing layer (a “mediato ...
66 CATALYZING INQUIRY databases into models of biological activity. As databases become increasingly annotated with func- tional ...
COMPUTATIONAL TOOLS 67 and colleagues argue that “as models become more sophisticated, so does the representation of the data. A ...
68 CATALYZING INQUIRY A feature of ontologies that facilitates the integration of databases is the use of a hierarchical structu ...
COMPUTATIONAL TOOLS 69 An ontology developed by one subcommunity inevitably leads to interactions with related ontolo- gies and ...
70 CATALYZING INQUIRY Box 4.3 Biological Data and the Semantic Web The Semantic Web seeks to create a universal medium for the e ...
COMPUTATIONAL TOOLS 71 TABLE 4.1 Biological Ontology Resources Organization Descriptions Human Genome Organization (HUGO) Gene H ...
72 CATALYZING INQUIRY By representing working hypotheses, derived results, and the evidence that supports and refutes them in ma ...
COMPUTATIONAL TOOLS 73 readable form and making use of databases of biological data and inferred networks, software based on art ...
74 CATALYZING INQUIRY Although the genomic research community uses annotation to refer to auxiliary information that has biologi ...
COMPUTATIONAL TOOLS 75 sharing. Consistent with the MIAME standards proposed by microarray users, MAML can be used to describe e ...
76 CATALYZING INQUIRY The CCDB contains structural and protein distribution information derived from confocal, mul- tiphoton, an ...
COMPUTATIONAL TOOLS 77 It is also desirable to exploit information in the database that is not explicitly represented in the sch ...
78 CATALYZING INQUIRY terminology, particularly neuroanatomical nomenclature, is vast, nonstandard, and confusing. Ana- tomical ...
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