Humans: taxonomic classification

First, the taxonomic classification of the TrEMBL entry must be within the known taxonomic range of the PROSITE pattern. For instance, a match of an a priori prokaryotic pattern against a human protein is regarded as false positive and filtered out. 

The eukaryotes are often divided into two kingdoms animals (Animalia) and plants (Plantae). This distinction is blurred in the case of flagellates, which can fall into either kingdom, and some can be classified in both. Further categorization results in the main taxonomic ranks shown in Table 1.6, in which the classification of humans is given as an example. 

The diversity of chemical compounds has been used directly for centuries for direct classification. Initially, these classifications grouped organisms by their use or their danger to humans and said nothing of phylogenetic or evolutionary relationships [WIN 99]. The use of secondary metabolites as taxonomic characteristics developed with the advance of chromatography, giving birth to a research discipline named chemotaxonomy. To undertake taxonomy from secondary metabolites also poses difficulties secondary... 

The two most used statistical measures in information retrieval are precision and recall . Precision is the proportion of the resomces returned that are relevant to the search terms used. Recall is a measure of the munber or resomces returned as a proportion of the number that should have been retmned. If a search has 100% recall and 100% precision it will find all the relevant and only the relevant resomces. The trouble with taking a taxonomic intelligence approach to query expansion is that relevance is not clearly defined. If study SI has deliberately excluded taxon B, but another resource (T2) says B is a synonym of A there is no way of excluding SI from the search results for search term B. Without knowing the classifications used by Si not even a human can know to exclude it. Query expansion increases the likelihood that such results will be inappropriately included before a human can intervene. 

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