"... In PAGE 8: ...anually excluded compounds. E.g. in experiment 1 the number of nodes reduces from 13 970 to 2802, the number of edges goes down from 58 119 to 4209. Table2 points out how the time complexity for the pathway search benefits from step 2 of the algorithm. Reducing the number of nodes and edges leads to a significant performance improvement.... In PAGE 8: ... In the case of k = 10, the number of necessary alignments without step 2 is 2672 (see table 2), when step 2 was applied this number reduced to 1766. Table2 shows that the time for the pathway search and the number of generated pathways grow exponentially in k. Limitations PathFinder still has some limitations which we describe in the following paragraphs.... ..."

"... In PAGE 4: ... This higher level organization of our knowledge about functions allows for the integration of biological information about the functions of gene products represented by probes on the array. Pathways: The class Pathways ( Table2 ) is an attempt to capture the interactions and/or connections between gene products and compress this information into 48 known meta- bolic and regulatory pathways or cellular processes. This class provides a categorization of pathways and cellular processes that may be involved in stressful responses and disease state or may be impaired as a result of them.... In PAGE 5: ...metabolism; formation of the extracellular matrix; catecholamine metabolism; respiratory chain; lipid metabolism; membrane transport; vesicular trafficking; urea cycle; trafficking between nucleus and cytoplasm; protein and amino acid metabolism; purine, pyrimidine and pyridine metabolism; iron homeostasis; sulfur metabolism, melatonin synthesis; steroid hormone metabolism 243 Biodegradation of xenobiotics Phase II metabolism of xenobiotics; phase I metabolism of xenobiotics; other processes related to detoxification; ubiquitin pathway 206 Cell growth and death Protein repair and chaperoning; tumorigenic transformations; angiogenesis; apoptosis; necrosis; ras/raf/MEK/ERK pathway; p38 pathway; p53 pathway JNK/SAPK pathway 422 Signal transduction and cell communication Signal transduction; cell communication 91 DNA replication and repair DNA replication; DNA repair 48 Immune and inflammatory responses Immune response; inflammatory response 121 Antioxidation Glutathione metabolism; oxidative metabolism of xenobiotics; peroxisome proliferation 151 Structural components Cell junctions; cytoskeleton; proteasome structure; peroxisome structure; ribosome structure 38 Unknown Unknown ESTs 276 The number of probes on the RT U34 GeneChip assigned to each entity is indicated. Pathways Group: The class Pathways Group separates entities of the class Pathways into larger-categories based on similar properties relating to biological processes ( Table2 ). Entit- ies in the class Pathways Group provide logical connections between biological processes presented by this class to stress response.... ..."

"... In PAGE 23: ...DETERMINANTS OF THE PATHWAYS A multinomial logit model was used to investigate the determinants of the pathways ( Table3 ). The results (together with the descriptive statistics discussed above) imply that different determining and conditioning factors are critical for different pathways.... ..."

"... In PAGE 5: ... We refer to reagents as producers and consumers, depending upon their role within the reaction. Table1 gives the pro- ducers and consumers for reactions in the pathway. The first column names the reaction using the following convention.... ..."

"... In PAGE 5: ... We refer to reagents as producers and consumers, depending upon their role within the reaction. Table1 gives the producers and consumers for reactions in the pathway. The first column names the reaction using the following convention.... ..."

"... In PAGE 5: ... We refer to reagents as producers and consumers, depending upon their role within the reaction. Table1 gives the pro- ducers and consumers for reactions in the pathway. The first column names the reaction using the following convention.... ..."

"... In PAGE 16: ... An exposure pathway can be eliminated if at least one of the five elements is missing and will never be present. Appendix B, Table9 identifies the completed exposure pathways, and Appendix B, Table 10 identifies the potential exposure pathways. ... ..."

"... In PAGE 9: ...ocument source ....................................................................................................... 23 Table 5 Example of non-causal relationships created for use with NORMEX concepts . 44 Table6 Example of NORMEX pathway.... In PAGE 55: ...39 List of Tables Table 5 Example of non-causal relationships created for use with NORMEX concepts . 44 Table6 Example of NORMEX pathway.... In PAGE 64: ... Again a nonparametric One-Sign test was used for this evaluation.46 Results An example of a NORMEX explanatory pathway is given in Table6 . The NORMEX syntax was developed using 6 semantic types, namely (T)op Of Pathway, (O)bservable Analyte, (I)nterpretive Finding, (L)aboratory Finding, and (D)isorder.... In PAGE 64: ... The syntax uses 7 attributes, the use of which is dictated by the semantic types involved in various relationships. NORMEX attributes allowed for particular semantic elements, as well as the specific attributes instantiated for an example, are listed in Table6 . Figure 7 demonstrates a typical explanatory pathway as viewed in the ontology modeling tool.... In PAGE 67: ...51 The top-down specific NORMEX syntax of the example in Table6 is T.... In PAGE 74: ...pplications result in the construction of ontology hierarchies with a single (e.g., IsA) relationship between parent and child concepts. Construction of the single-attribute (explanation) hierarchies in the NORMEX model was based on the mix of the relationships or attributes shown in Table6 . The relationship names used in the NORMEX model were selected with the knowledge that SNOMED only contains relationships that are true at least 98% of the time.... In PAGE 74: ...D. section of the model ( Table6 ) the Disorder concept is related to the Observable Function concept by either the Favors increased or the Favors decreased relationship. The model is designed such that all other relationships exist in a true state.... ..."