Integrative taxonomy

The BioSomce includes information on the source organism (scientific name and common name), its lineage in the NCBI integrated taxonomy, and its nuclear and (if appropriate) mitochondrial genetic code. It also includes information on the location of the sequence in the cell (e.g., nuclear genome or mitochondrion) and additional modifiers (e.g., strain, clone, isolate, chromosomal map location). 

Fonseca, G., Derycke, S., Moens, T. (2008). Integrative taxonomy in two free-hying nematode species complexes. Biological Journal of the Linnean Society 94,737-753. 

Systematic and integrative taxonomy from chemical ecology... 

In the case of Mediterranean orchids, the morphological similarity of the described species sometimes makes their recognition difficult, notably by stakeholders in conservation efforts. Thus, in 2010, 20.6% of the orchid species found in metropolitan France were considered to be supported by insufficient data by the lUCN, mainly as a result of problems with taxonomic identification [SCH 14]. Using the integrative taxonomy... 

Gibson, C. M., Kao, R. H., Blevins, K. K. and Travers, P. D. (2012). Integrative taxonomy for continental-scale terrestrial insect observations. PLoS... 

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

As a consequence, I would like to develop a working explanation or, perhaps more accurately, a schematic taxonomy for the particular kind of "knowledge-discipline" we find in science. My scheme is explicitly not a sociological model. In contrast, I draw on the notion of the construction of historical identities. In practice, national or ethnic identity may be conflated with professional or disciplinary identity, in a way that actually integrates the notions of "tradition" and "school" with that of our historical understanding of "discipline." In this explanation, the school is best understood by analogy to an extended family rather than to a nuclear group at one site. 

The predilection of bacteria to associate with surfaces is the primary organizing principle of community structure. ZoBell (1943) presented a conceptual model of this organization surfaces concentrate nutrients bacterial attachment to surfaces maximizes concentration gradients and reduces diffusion distances packing cells on surfaces improves retention of extracellular enzymes. Over the next 40 years, the study of attached microbial communities became an integral part of several fields (see Chapter 12). The importance of periphyton, or aufwuchs, in stream metabolism was established (Hynes, 1970 Geesey et al., 1978 Stevenson et al., 1996). Comparative studies of community organization and activity in relation to substratum produced a taxonomy for attached communities epilithon, epiphyton,... 

With increasingly networked, distributed computer systems the risk of deliberate malicious interactions, using software-based tools, became a serious threat. Many-fold related issues like data protection, privacy, integrity, authenticity, and denial of service attacks, viruses, worms etc. lead to a separate community to be established, which is nowadays in the main focus of the public as was safety some time ago (and still is—but only after catastrophic events). This community developed separate standards, methods, taxonomy and ways of thinking. 

The NCBI s Entrez is apowerful database search engine. This integrated search engine provides a menu (http //www.ncbi.nih.gov/Entrez/index.html) offering the user selections to search biomedical literature (PubMed), databases on OMIM, nucleotide sequence, protein sequence, whole genome sequences, 3D macromolecular structures, taxonomy (organisms in GenBank), SNP,... 

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

Although the ET processes represented by reactions 3 and 5 are nonphysiologi-cal, they can provide useful information. Thus, by varying the structure of the flavin it is possible to probe the steric and electrostatic environment of a protein redox center [38, 39]. This can be used as a method for assessing functional relationships between members of a homologous series of redox proteins (kinetic taxonomy). It is also possible to use these reactions to test the functional integrity of a redox center in a site-specific mutant [43]. 

Holsapple, C., and Singh, M. (2000), Electronic Commerce Definitional Taxonomy, Integration, and a Knowledge Management Link, Journal of Organizational Computing and Electronic Commerce, Vol. 10, No. 3. 

Bovea, M.D., Perez-Belis, V., 2012. A taxonomy of ecodesign tools for integrating environmental requirements into the product design process. Journal of Cleaner Production 20,... 

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