<?xml version="1.0" encoding="UTF-8" ?>
<data>
  <organism>Saccharomyces cerevisiae</organism>
  <path>.\data</path>
  <files>
    <input>
      <SBO>sbo_id.txt</SBO>
      <GO>go_id.txt</GO>
      <EC>EC.txt</EC>
      <PubMed>PubMed_IDs.txt</PubMed>
      <PMC>PMC_IDs.txt</PMC>
    </input>
    <output>
      <GO>go_terms.txt</GO>
      <SBO>sbo_terms.txt</SBO>
      <KEGG>
        <enzyme>EC.txt</enzyme>
        <compound>CPD.txt</compound>
        <gene>SCE.txt</gene>
        <enzyme_name>EC_name.txt</enzyme_name>
        <compound_name>CPD_name.txt</compound_name>
        <gene_name>SCE_name.txt</gene_name>
        <enzyme2compound>EC_CPD.txt</enzyme2compound>
        <enzyme2gene>EC_SCE.txt</enzyme2gene>
      </KEGG>
      <UMLS>umls_terms.txt</UMLS>
      <PubMed>PubMed_index.txt</PubMed>
      <PMC>PMC_index.txt</PMC>
      <HTML>
        <PubMed>PubMed.html</PubMed>
        <PMC>PMC.html</PMC>
        <items>20</items>
        <max>100</max>
      </HTML>
      <bibtex>
        <PubMed>PubMed.bib</PubMed>
        <PMC>PMC.bib</PMC>
      </bibtex>
    </output>
    <tmp>
      <GO>ajaxGO.xml</GO>
      <UMLS>queryUMLS.xml</UMLS>
      <terms>termsUMLS.xml</terms>
      <PubMed>PubMed_IDs.txt</PubMed>
      <PMC>PMC_IDs.txt</PMC>
    </tmp>
    <template>
      <UMLS>queryUMLS.xml</UMLS>
    </template>
  </files>
  <database>
    <driver>org.postgresql.Driver</driver>
    <url>jdbc:postgresql://********</url>
    <username>********</username>
    <password>********</password>
  </database>
  <pubchem>
    <driver>org.postgresql.Driver</driver>
    <url>jdbc:postgresql://********</url>
    <username>********</username>
    <password>********</password>
  </pubchem>
  <UMLS>
    <dbYear>2007AA</dbYear>
    <language>ENG</language>
    <host>umlsks.nlm.nih.gov</host>
  </UMLS>
  <params>
    <keywords>(((brewer OR baker OR budding) AND yeast) OR ((S OR Saccharomyces) AND cerevisiae)) AND (enzyme OR reaction OR substrate OR product) AND (kinetic OR parameter OR constant OR concentration OR rate)</keywords>
    <weights>
       <EC>60</EC>
      <CPD>30</CPD>
      <SCE>10</SCE>
      <!--  ...  -->
      <RN>80</RN>
      <GO>20</GO>
      <!--  ...  -->
      <PATH>50</PATH>
       <SBO>50</SBO>
    </weights>
  </params>
  <options>
    <database>PMC</database>
    <search>yes</search>
    <export>
      <HTML>yes</HTML>
      <bibtex>yes</bibtex>
      <fullText>yes</fullText>
      <tags>
      </tags>
    </export>
    <menu>
      <start>1 - Get terms</start>
      <end>8 - Export results</end>
    </menu>
  </options>
</data>
