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126 5 Survey of Ontologies in Bioinformatics XML format does not use a DTD, and most of the information is encoded as FASTA text ...

PART II Building and Using Ontologies ...

128 This part addresses how ontologies are constructed and used. One uses on- tologies far more frequently than one creates them ...

6 Information Retrieval 6.1 The Search Process Research is a fundamental activity of knowledge workers, whether they are scienti ...

130 6 Information Retrieval or words, individually or severally. The query is then given to a search in- termediary. In the past ...

6.2 Vector Space Retrieval 131 relational databases. Formal query languages are programming languages specialized for retrieval. ...

132 6 Information Retrieval that contain the word. Note that “of” occurs in more documents than “the,” although the latter occur ...

6.2 Vector Space Retrieval 133 Word Number of occurrences Number of documents the 61735764 7656676 of 56188095 8838209 and 35936 ...

134 6 Information Retrieval is based on a probabilistic cost/benefit approach. The two cost factors asso- ciated with informatio ...

6.2 Vector Space Retrieval 135 can then examine the documents in this order until it is found that the doc- uments are no longer ...

136 6 Information Retrieval If there are N documents in the entire collection, and if M of them contain a particular term T, the ...

6.2 Vector Space Retrieval 137 term frequency, inverse document frequency(TFIDF) weighting scheme. This scheme is by far the mos ...

138 6 Information Retrieval length and has the same direction as v. This vector is obtained by dividing v by its length:|vv|. Th ...

6.2 Vector Space Retrieval 139 It is difficult to map the inflected forms of an English word to a single concept because inflect ...

140 6 Information Retrieval A query is evaluated by computing the inner product of the query vec- tor and each document vector ...

6.3 Using Ontologies for Formulating Queries 141 records, available separately. There are 23,887 cross-references that assist in ...

142 6 Information Retrieval One can use more specific concepts, when more general concepts find too much information. This is k ...

6.4 Organizing by Citation 143 by the initial candidates. Many other refinements can also be employed to improve the set of cand ...

144 6 Information Retrieval In the case of graphs, the entries in a principal eigenvector measure the rel- ative importance of t ...

6.4 Organizing by Citation 145 is the case when a relatively small community uses the same terminology as a much larger communit ...