Specification of the OReFiL WebAPI

SOAP Interface
REST Interface
Responses
SOAP Request / Response Sample
REST Request / Response Sample

Comments and suggestions are welcome, please send an email to yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp.

Interface Specifications

SOAP

WSDL
- /search/service.wsdl
Entry Point
- /search/api
SOAPAction
- /search/api/GetResourceInfoByQueryTerm
Parameters

Name	Description	Must/Optional	Default Value	Allowable Values
expression	Query String	Must	-	Expression that can be acceptable by IndriRunQuery
max_results	Maximum Number of Result Entries	Must	-	1 - 1000
order	Sort Order	Must	-	`relevance` or `date`
enable_hide_unfetched	Display or Hide of Status 404 URLs	Must	-	`true` or `false`
enable_relevance_feedback	Relevance Feedback	Must	-	`true` or `false`

Errors
- Follows the SOAP error specification as much as possible.
- Internal Server Error may occur unless enough parameters are given.

REST

URI
- /search.xml
Parameters
- Given by GET parameters or POST parameters

Name	Description	Must/Optional	Default Value	Allowbale Values
query	Query String	Must	-	Expression that can be acceptable by IndriRunQuery
count	Maximum Number of Result Entries	Optional	100	1 - 1000
sort_by	Sort Order	Optional	relevance	`relevance` or `date`
hide_unfetched	Display or Hide of Status 404 URLs	Optional	on	`on` or `off`
feedback	Relevance Feedback	Optional	off	`on` or `off`

Errors
- Basically users need to handle errors based on HTTP statuses.
- The error description is given in an XML format as much as possible if there is an error in user parameters.
  - Error description
    - errors: a list of errors
      - error: description of each error
        http_status_code: HTTP status code
        code: application error code
        name: error name
        message: error message
  - Error sample
```
<?xml version="1.0" encoding="UTF-8"?>
<errors>
  <error>
    <http_status_code>400</http_status_code>
    <code>40003</code>
    <name>Orefil::InvalidCountError</name>
    <message>Set integer of 1 or more to `Max Results` value.</message>
  </error>
</errors>
```

Response

Result_Set: Results ( `result_set` if REST )
- query: Query string after applying the default value
  - expression: Query string parameter
  - option: Option parameters
    - max_results: Maximum number of results
    - order: Sort order
    - enable_hide_unfetched: Whether displaying status 404 URLs or not ( true / false )
    - enable_relevance_feedback: Relevane feedback ( true / false )
  - last_index_date: Update time of the index
- status: Status of the result ( SOAP only )
  - code: Status code
  - name: Status name
  - message: Status message
- results: A list of results
  - item: A result ( `result` if REST)
    - id: Online resource ID
    - rank: Rank in the result
    - title: Online resource title
    - updated_at: Update time ( XML Schema format )
    - average_stars: Average rating
    - snippet: Snippet
    - mesh_term_list: A list of MeSH terms
      - item: A MeSH term ( mesh_term if REST )
    - url: Online resource's URL
    - pages: A list of URLs that search for referring links
      - item: Referring link search ( `page` if REST )
        name: Name of the search engine
        url: URL for search
    - papers: A list of URLs that search for citing papers
      - item: Citing paper search ( `paper` if REST )
        name: Name of the search engine
        url: URL for search
    - pmid_list: A ilst of PMIDs that cite the resource
      - item: pmid ( pmid if REST )

Request / Response Sample

Here are samples of requests and their corresponding responses in SOAP and REST.

Request
- Query String: #filreq(DNA.majr #combine(genome))
- Options
  - Maximum Number of Results : 3
  - Sort Order: Relevance
  - Status 404 URLs: display
  - Relevance Feedback: off

SOAP

Request

<?xml version="1.0" encoding="UTF-8"?>

  <SOAP-ENV:Envelope

    xmlns:xsd="http://www.w3.org/2001/XMLSchema"

    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

    xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"

    SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"

    xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/">

      <SOAP-ENV:Body>

        <m:GetResourceInfoByQueryTerm xmlns:m="urn:ActionWebService">

          <expression xsi:type="xsd:string">#filreq(DNA.majr #combine(genome))</expression>

          <max_results xsi:type="xsd:int">3</max_results>

          <order xsi:type="xsd:string">relevance</order>

          <enable_hide_unfetched xsi:type="xsd:boolean">true</enable_hide_unfetched>

          <enable_relevance_feedback xsi:type="xsd:boolean">false</enable_relevance_feedback>

        </m:GetResourceInfoByQueryTerm>

      </SOAP-ENV:Body>

    </SOAP-ENV:Envelope>

Response

<?xml version="1.0" encoding="UTF-8" ?>
<env:Envelope xmlns:xsd="http://www.w3.org/2001/XMLSchema"
    xmlns:env="http://schemas.xmlsoap.org/soap/envelope/"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <env:Body>
    <n1:GetResourceInfoByQueryTermResponse xmlns:n1="urn:ActionWebService"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">

      <return xsi:type="n1:Retrieve..ResultSet">
        <results n2:arrayType="n1:Retrieve..Result[3]"
            xmlns:n2="http://schemas.xmlsoap.org/soap/encoding/"
            xsi:type="n2:Array">
          <item>
            <id xsi:type="xsd:int">4980</id>
            <mesh_term_list n2:arrayType="xsd:string[28]"
                xsi:type="n2:Array">

              <item>Abnormalities, Multiple</item>
              <item>Carbamoyl-Phosphate Synthase I Deficiency Disease</item>
              <item>Chickens</item>
              <item>Chromosome Deletion</item>

              <item>Chromosome Mapping</item>
              <item>Chromosomes, Human, Pair 2</item>
              <item>Computational Biology</item>
              <item>DNA Primers</item>

              <item>Database Management Systems</item>
              <item>Databases, Genetic</item>
              <item>Databases, Nucleic Acid</item>
              <item>Databases, Protein</item>

              <item>Exons</item>
              <item>Genome</item>
              <item>Genome, Human</item>
              <item>Genomics</item>

              <item>Information Storage and Retrieval</item>
              <item>Internet</item>
              <item>Linkage (Genetics)</item>
              <item>Microsatellite Repeats</item>

              <item>Polymorphism, Single Nucleotide</item>
              <item>Proteins</item>
              <item>Proteome</item>
              <item>Proteomics</item>

              <item>RNA, Messenger</item>
              <item>Sequence Alignment</item>
              <item>Software</item>
              <item>Zebrafish</item>

            </mesh_term_list>
            <title xsi:type="xsd:string">UCSC Genome Browser Home</title>
            <pmid_list n2:arrayType="xsd:string[15]"
                xsi:type="n2:Array">
              <item>16888352</item>
              <item>16381938</item>

              <item>12045153</item>
              <item>15216554</item>
              <item>17151077</item>
              <item>16888348</item>

              <item>16372332</item>
              <item>11932250</item>
              <item>16722777</item>
              <item>12519945</item>

              <item>16500937</item>
              <item>17142222</item>
              <item>15554057</item>
              <item>15608236</item>

              <item>16888346</item>
            </pmid_list>
            <snippet xsi:type="xsd:string">Comparative &lt;strong&gt;Genomic&lt;/strong&gt; Analysis Using the UCSC &lt;strong&gt;Genome&lt;/strong&gt; Browser. Comparative analysis of DNA sequence from multiple species can provide insights into the function...sequence from multiple species can provide insights into the function and evolutionary processes that shape &lt;strong&gt;genomes&lt;/strong&gt;. The University of California Santa Cruz (UCSC) &lt;strong&gt;Genome&lt;/strong&gt; Bioinformatics group has developed several tools and methodologies in its study of comparative genomics, many...</snippet>

            <rank xsi:type="xsd:int">1</rank>
            <papers n2:arrayType="n1:Retrieve..Paper[4]"
                xsi:type="n2:Array">
              <item>
                <name href="#id18291200"></name>
                <url xsi:type="xsd:string">http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;chkBMCJournals=true&amp;chkCurrentOpinion=true&amp;drpFromDate=&amp;drpToDate=&amp;chkNSP=true&amp;drpAddedInLast=&amp;drpOrderBy=by+date&amp;drpPerPage=20&amp;drpAbstract=no+abstract&amp;strTempString=&amp;strSearchBoxType=bmc_boolean_results&amp;Search.x=10&amp;jou_id=&amp;Search.x=0&amp;Search.y=0&amp;Search=Search</url>

              </item>
              <item>
                <name href="#id18285850"></name>
                <url xsi:type="xsd:string">http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;ds=jnl&amp;g=s&amp;t=all</url>

              </item>
              <item>
                <name href="#id18277510"></name>
                <url xsi:type="xsd:string">http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.ucsc.edu%2F</url>
              </item>

              <item>
                <name href="#id18264560"></name>
                <url xsi:type="xsd:string">http://scholar.google.com/scholar?hl=en&amp;lr=&amp;q=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;btnG=Search</url>
              </item>

            </papers>
            <average_stars xsi:type="xsd:double">+3.666666666666667</average_stars>
            <url xsi:type="xsd:string">http://genome.ucsc.edu/</url>
            <pages n2:arrayType="n1:Retrieve..Page[2]"
                xsi:type="n2:Array">
              <item>

                <name href="#id18255240"></name>
                <url xsi:type="xsd:string">http://www.google.com/search?hl=en&amp;q=link%3ahttp%3A%2F%2Fgenome.ucsc.edu%2F&amp;btnG=Google+Search</url>
              </item>
              <item>

                <name href="#id18253260"></name>
                <url xsi:type="xsd:string">http://www.altavista.com/web/results?itag=ody&amp;q=link:http%3A%2F%2Fgenome.ucsc.edu%2F&amp;kgs=0&amp;kls=1</url>
              </item>
            </pages>

            <updated_at xsi:type="xsd:dateTime">2008-02-20T00:00:00+09:00</updated_at>
          </item>
          <item>
            <id xsi:type="xsd:int">7142</id>
            <mesh_term_list n2:arrayType="xsd:string[9]"
                xsi:type="n2:Array">

              <item>Chromosome Mapping</item>
              <item>Databases, Genetic</item>
              <item>Gene Expression Profiling</item>
              <item>Genome</item>

              <item>Oligonucleotide Array Sequence Analysis</item>
              <item>Sequence Alignment</item>
              <item>Sequence Analysis, DNA</item>
              <item>Software</item>

              <item>User-Computer Interface</item>
            </mesh_term_list>
            <title xsi:type="xsd:string">UCSC Genome Browser Home</title>
            <pmid_list n2:arrayType="xsd:string[2]"
                xsi:type="n2:Array">
              <item>14681485</item>

              <item>16108715</item>
            </pmid_list>
            <snippet xsi:type="xsd:string">Finding anchors for &lt;strong&gt;genomic&lt;/strong&gt; sequence comparison . Recent sequencing of the human and other mammalian &lt;strong&gt;genomes&lt;/strong&gt; has brought about the necessity to align them , to identify and characterize their commonalities and...Algorithms Amino Acid Motifs Chromosome Mapping Sequence Analysis, DNA User-Computer Interface Databases, Genetic Mice &lt;strong&gt;Genome&lt;/strong&gt; Information Storage and Retrieval Internet Rats Computational Biology Software Models, Genetic Animals Oligonucleotide Array Sequence Analysis Databases, Genetic &lt;strong&gt;Genome&lt;/strong&gt; Gene Expression Profiling Sequence Alignment Software Chromosome Mapping Oligonucleotide Array Sequence Analysis User-Computer Interface Sequence Analysis, ... Nucleic Acid Hybridization Microarray Analysis Genetic Techniques Information Storage and Retrieval Sequence Analysis Chemistry, Analytical...</snippet>

            <rank xsi:type="xsd:int">2</rank>
            <papers n2:arrayType="n1:Retrieve..Paper[4]"
                xsi:type="n2:Array">
              <item>
                <name href="#id18291200"></name>
                <url xsi:type="xsd:string">http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;chkBMCJournals=true&amp;chkCurrentOpinion=true&amp;drpFromDate=&amp;drpToDate=&amp;chkNSP=true&amp;drpAddedInLast=&amp;drpOrderBy=by+date&amp;drpPerPage=20&amp;drpAbstract=no+abstract&amp;strTempString=&amp;strSearchBoxType=bmc_boolean_results&amp;Search.x=10&amp;jou_id=&amp;Search.x=0&amp;Search.y=0&amp;Search=Search</url>

              </item>
              <item>
                <name href="#id18285850"></name>
                <url xsi:type="xsd:string">http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;ds=jnl&amp;g=s&amp;t=all</url>

              </item>
              <item>
                <name href="#id18277510"></name>
                <url xsi:type="xsd:string">http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fwww.genome.ucsc.edu%2F</url>
              </item>

              <item>
                <name href="#id18264560"></name>
                <url xsi:type="xsd:string">http://scholar.google.com/scholar?hl=en&amp;lr=&amp;q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;btnG=Search</url>
              </item>

            </papers>
            <average_stars xsi:type="xsd:double">+3</average_stars>
            <url xsi:type="xsd:string">http://www.genome.ucsc.edu/</url>
            <pages n2:arrayType="n1:Retrieve..Page[2]"
                xsi:type="n2:Array">
              <item>

                <name href="#id18255240"></name>
                <url xsi:type="xsd:string">http://www.google.com/search?hl=en&amp;q=link%3ahttp%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;btnG=Google+Search</url>
              </item>
              <item>

                <name href="#id18253260"></name>
                <url xsi:type="xsd:string">http://www.altavista.com/web/results?itag=ody&amp;q=link:http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;kgs=0&amp;kls=1</url>
              </item>
            </pages>

            <updated_at xsi:type="xsd:dateTime">2008-02-18T00:00:00+09:00</updated_at>
          </item>
          <item>
            <id xsi:type="xsd:int">7515</id>
            <mesh_term_list n2:arrayType="xsd:string[4]"
                xsi:type="n2:Array">

              <item>Computational Biology</item>
              <item>Genomics</item>
              <item>Isochores</item>
              <item>Software</item>

            </mesh_term_list>
            <title xsi:type="xsd:string">UCSC Genome Browser Home</title>
            <pmid_list n2:arrayType="xsd:string[1]"
                xsi:type="n2:Array">
              <item>15215396</item>
            </pmid_list>

            <snippet xsi:type="xsd:string">IsoFinder : computational prediction of isochores in &lt;strong&gt;genome&lt;/strong&gt; sequences . Isochores are long &lt;strong&gt;genome&lt;/strong&gt; segments homogeneous in G+C . Here , we describe an algorithm ( IsoFinder ) running on the web...by each cut . This leads to the decomposition of a chromosome sequence into long homogeneous &lt;strong&gt;genome&lt;/strong&gt; regions ( LHGRs ) with well-defined mean G+C contents , each significantly different from the G...</snippet>

            <rank xsi:type="xsd:int">3</rank>
            <papers n2:arrayType="n1:Retrieve..Paper[4]"
                xsi:type="n2:Array">
              <item>
                <name href="#id18291200"></name>
                <url xsi:type="xsd:string">http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;chkBMCJournals=true&amp;chkCurrentOpinion=true&amp;drpFromDate=&amp;drpToDate=&amp;chkNSP=true&amp;drpAddedInLast=&amp;drpOrderBy=by+date&amp;drpPerPage=20&amp;drpAbstract=no+abstract&amp;strTempString=&amp;strSearchBoxType=bmc_boolean_results&amp;Search.x=10&amp;jou_id=&amp;Search.x=0&amp;Search.y=0&amp;Search=Search</url>

              </item>
              <item>
                <name href="#id18285850"></name>
                <url xsi:type="xsd:string">http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;ds=jnl&amp;g=s&amp;t=all</url>

              </item>
              <item>
                <name href="#id18277510"></name>
                <url xsi:type="xsd:string">http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.cse.ucsc.edu%2F</url>
              </item>

              <item>
                <name href="#id18264560"></name>
                <url xsi:type="xsd:string">http://scholar.google.com/scholar?hl=en&amp;lr=&amp;q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;btnG=Search</url>
              </item>

            </papers>
            <average_stars xsi:type="xsd:double">+3</average_stars>
            <url xsi:type="xsd:string">http://genome.cse.ucsc.edu/</url>
            <pages n2:arrayType="n1:Retrieve..Page[2]"
                xsi:type="n2:Array">
              <item>

                <name href="#id18255240"></name>
                <url xsi:type="xsd:string">http://www.google.com/search?hl=en&amp;q=link%3ahttp%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;btnG=Google+Search</url>
              </item>
              <item>

                <name href="#id18253260"></name>
                <url xsi:type="xsd:string">http://www.altavista.com/web/results?itag=ody&amp;q=link:http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;kgs=0&amp;kls=1</url>
              </item>
            </pages>

            <updated_at xsi:type="xsd:dateTime">2008-02-17T00:00:00+09:00</updated_at>
          </item>
        </results>
        <query xsi:type="n1:Retrieve..Query">
          <option xsi:type="n1:Retrieve..Option">

            <max_results xsi:type="xsd:int">3</max_results>
            <enable_relevance_feedback xsi:type="xsd:boolean">false</enable_relevance_feedback>
            <enable_hide_unfetched xsi:type="xsd:boolean">true</enable_hide_unfetched>
            <order xsi:type="xsd:string">relevance</order>

          </option>
          <expression xsi:type="xsd:string">#filreq(DNA.majr #combine(genome))</expression>
          <last_index_date xsi:type="xsd:dateTime">2008-03-17T15:34:23+09:00</last_index_date>
        </query>
        <status xsi:type="n1:Retrieve..Status">

          <name xsi:type="xsd:string">Orefil::Success</name>
          <code xsi:type="xsd:string">20000</code>
          <message xsi:type="xsd:string">success.</message>
        </status>

      </return>
    </n1:GetResourceInfoByQueryTermResponse>
    <name id="id18291200"
        xsi:type="xsd:string"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">BioMed Central</name>
    <name id="id18285850"
        xsi:type="xsd:string"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">Scirus</name>
    <name id="id18277510"
        xsi:type="xsd:string"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">HighWire Press</name>

    <name id="id18264560"
        xsi:type="xsd:string"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">Google Scholar</name>
    <name id="id18255240"
        xsi:type="xsd:string"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">Google</name>
    <name id="id18253260"
        xsi:type="xsd:string"
        env:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">AltaVista</name>
  </env:Body>

</env:Envelope>

REST

Request

/search.xml?query=%23filreq%28DNA.majr+%23combine%28genome%29%29&count=3&sort_by=relevance&hide_unfetched=on

Response

<?xml version="1.0" encoding="UTF-8"?>
<result_set>
  <query>
    <expression>#filreq(DNA.majr #combine(genome))</expression>
    <option>
      <max_results>3</max_results>
      <order>relevance</order>
      <enable_hide_unfetched>true</enable_hide_unfetched>
      <enable_relevance_feedback>false</enable_relevance_feedback>
    </option>
    <last_index_date>2008-03-04T17:05:26+09:00</last_index_date>
  </query>
  <results>
    <result>
      <id>4980</id>
      <rank>1</rank>
      <title>UCSC Genome Browser Home</title>
      <updated_at>2008-02-20T00:00:00+09:00</updated_at>
      <average_stars>3.4</average_stars>
      <snippet>
        Comparative <strong>Genomic</strong> Analysis Using the UCSC <strong>Genome</strong> Browser. Comparative analysis of DNA sequence from multiple species can provide insights into the function...sequence from multiple species can provide insights into the function and evolutionary processes that shape <strong>genomes</strong>. The University of California Santa Cruz (UCSC) <strong>Genome</strong> Bioinformatics group has developed several tools and methodologies in its study of comparative genomics, many...
      </snippet>
      <mesh_term_list>
        <mesh_term>Abnormalities, Multiple</mesh_term>
        <mesh_term>Carbamoyl-Phosphate Synthase I Deficiency Disease</mesh_term>
        <mesh_term>Chickens</mesh_term>
        <mesh_term>Chromosome Deletion</mesh_term>
        <mesh_term>Chromosome Mapping</mesh_term>
        <mesh_term>Chromosomes, Human, Pair 2</mesh_term>
        <mesh_term>Computational Biology</mesh_term>
        <mesh_term>DNA Primers</mesh_term>
        <mesh_term>Database Management Systems</mesh_term>
        <mesh_term>Databases, Genetic</mesh_term>
        <mesh_term>Databases, Nucleic Acid</mesh_term>
        <mesh_term>Databases, Protein</mesh_term>
        <mesh_term>Exons</mesh_term>
        <mesh_term>Genome</mesh_term>
        <mesh_term>Genome, Human</mesh_term>
        <mesh_term>Genomics</mesh_term>
        <mesh_term>Information Storage and Retrieval</mesh_term>
        <mesh_term>Internet</mesh_term>
        <mesh_term>Linkage (Genetics)</mesh_term>
        <mesh_term>Microsatellite Repeats</mesh_term>
        <mesh_term>Polymorphism, Single Nucleotide</mesh_term>
        <mesh_term>Proteins</mesh_term>
        <mesh_term>Proteome</mesh_term>
        <mesh_term>Proteomics</mesh_term>
        <mesh_term>RNA, Messenger</mesh_term>
        <mesh_term>Sequence Alignment</mesh_term>
        <mesh_term>Software</mesh_term>
        <mesh_term>Zebrafish</mesh_term>
      </mesh_term_list>
      <url>http://genome.ucsc.edu/</url>
      <pages>
        <page>
          <name>Google</name>
          <url>
            http://www.google.com/search?hl=en&amp;q=link%3ahttp%3A%2F%2Fgenome.ucsc.edu%2F&amp;btnG=Google+Search
          </url>
        </page>
        <page>
          <name>AltaVista</name>
          <url>
            http://www.altavista.com/web/results?itag=ody&amp;q=link:http%3A%2F%2Fgenome.ucsc.edu%2F&amp;kgs=0&amp;kls=1
          </url>
        </page>
      </pages>
      <papers>
        <paper>
          <name>BioMed Central</name>
          <url>
            http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;chkBMCJournals=true&amp;chkCurrentOpinion=true&amp;drpFromDate=&amp;drpToDate=&amp;chkNSP=true&amp;drpAddedInLast=&amp;drpOrderBy=by+date&amp;drpPerPage=20&amp;drpAbstract=no+abstract&amp;strTempString=&amp;strSearchBoxType=bmc_boolean_results&amp;Search.x=10&amp;jou_id=&amp;Search.x=0&amp;Search.y=0&amp;Search=Search
          </url>
        </paper>
        <paper>
          <name>Scirus</name>
          <url>
            http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;ds=jnl&amp;g=s&amp;t=all
          </url>
        </paper>
        <paper>
          <name>HighWire Press</name>
          <url>
            http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;andorexactfulltext=and&amp;author1=&amp;pubdate_year=&amp;volume=&amp;firstpage=&amp;src=hw&amp;searchsubmit=redo&amp;resourcetype=1&amp;search=Search&amp;fmonth=Jan&amp;fyear=1844&amp;tmonth=Dec&amp;tyear=2007&amp;fdatedef=1+January+1844&amp;tdatedef=31+Dec+2007
          </url>
        </paper>
        <paper>
          <name>Google Scholar</name>
          <url>
            http://scholar.google.com/scholar?hl=en&amp;lr=&amp;q=http%3A%2F%2Fgenome.ucsc.edu%2F&amp;btnG=Search
          </url>
        </paper>
      </papers>
      <pmid_list>
        <pmid>16888352</pmid>
        <pmid>16381938</pmid>
        <pmid>12045153</pmid>
        <pmid>15216554</pmid>
        <pmid>17151077</pmid>
        <pmid>16888348</pmid>
        <pmid>16372332</pmid>
        <pmid>11932250</pmid>
        <pmid>16722777</pmid>
        <pmid>12519945</pmid>
        <pmid>16500937</pmid>
        <pmid>17142222</pmid>
        <pmid>15554057</pmid>
        <pmid>15608236</pmid>
        <pmid>16888346</pmid>
      </pmid_list>
    </result>
    <result>
      <id>7142</id>
      <rank>2</rank>
      <title>UCSC Genome Browser Home</title>
      <updated_at>2008-02-18T00:00:00+09:00</updated_at>
      <average_stars>3.0</average_stars>
      <snippet>
        Finding anchors for <strong>genomic</strong> sequence comparison . Recent sequencing of the human and other mammalian <strong>genomes</strong> has brought about the necessity to align them , to identify and characterize their commonalities and...Algorithms Amino Acid Motifs Chromosome Mapping Sequence Analysis, DNA User-Computer Interface Databases, Genetic Mice <strong>Genome</strong> Information Storage and Retrieval Internet Rats Computational Biology Software Models, Genetic Animals Oligonucleotide Array Sequence Analysis Databases, Genetic <strong>Genome</strong> Gene Expression Profiling Sequence Alignment Software Chromosome Mapping Oligonucleotide Array Sequence Analysis User-Computer Interface Sequence Analysis, ... Nucleic Acid Hybridization Microarray Analysis Genetic Techniques Information Storage and Retrieval Sequence Analysis Chemistry, Analytical...
      </snippet>
      <mesh_term_list>
        <mesh_term>Chromosome Mapping</mesh_term>
        <mesh_term>Databases, Genetic</mesh_term>
        <mesh_term>Gene Expression Profiling</mesh_term>
        <mesh_term>Genome</mesh_term>
        <mesh_term>Oligonucleotide Array Sequence Analysis</mesh_term>
        <mesh_term>Sequence Alignment</mesh_term>
        <mesh_term>Sequence Analysis, DNA</mesh_term>
        <mesh_term>Software</mesh_term>
        <mesh_term>User-Computer Interface</mesh_term>
      </mesh_term_list>
      <url>http://www.genome.ucsc.edu/</url>
      <pages>
        <page>
          <name>Google</name>
          <url>
            http://www.google.com/search?hl=en&amp;q=link%3ahttp%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;btnG=Google+Search
          </url>
        </page>
        <page>
          <name>AltaVista</name>
          <url>
            http://www.altavista.com/web/results?itag=ody&amp;q=link:http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;kgs=0&amp;kls=1
          </url>
        </page>
      </pages>
      <papers>
        <paper>
          <name>BioMed Central</name>
          <url>
            http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;chkBMCJournals=true&amp;chkCurrentOpinion=true&amp;drpFromDate=&amp;drpToDate=&amp;chkNSP=true&amp;drpAddedInLast=&amp;drpOrderBy=by+date&amp;drpPerPage=20&amp;drpAbstract=no+abstract&amp;strTempString=&amp;strSearchBoxType=bmc_boolean_results&amp;Search.x=10&amp;jou_id=&amp;Search.x=0&amp;Search.y=0&amp;Search=Search
          </url>
        </paper>
        <paper>
          <name>Scirus</name>
          <url>
            http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;ds=jnl&amp;g=s&amp;t=all
          </url>
        </paper>
        <paper>
          <name>HighWire Press</name>
          <url>
            http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;andorexactfulltext=and&amp;author1=&amp;pubdate_year=&amp;volume=&amp;firstpage=&amp;src=hw&amp;searchsubmit=redo&amp;resourcetype=1&amp;search=Search&amp;fmonth=Jan&amp;fyear=1844&amp;tmonth=Dec&amp;tyear=2007&amp;fdatedef=1+January+1844&amp;tdatedef=31+Dec+2007
          </url>
        </paper>
        <paper>
          <name>Google Scholar</name>
          <url>
            http://scholar.google.com/scholar?hl=en&amp;lr=&amp;q=http%3A%2F%2Fwww.genome.ucsc.edu%2F&amp;btnG=Search
          </url>
        </paper>
      </papers>
      <pmid_list>
        <pmid>14681485</pmid>
        <pmid>16108715</pmid>
      </pmid_list>
    </result>
    <result>
      <id>7515</id>
      <rank>3</rank>
      <title>UCSC Genome Browser Home</title>
      <updated_at>2008-02-17T00:00:00+09:00</updated_at>
      <average_stars>3.0</average_stars>
      <snippet>
        IsoFinder : computational prediction of isochores in <strong>genome</strong> sequences . Isochores are long <strong>genome</strong> segments homogeneous in G+C . Here , we describe an algorithm ( IsoFinder ) running on the web...by each cut . This leads to the decomposition of a chromosome sequence into long homogeneous <strong>genome</strong> regions ( LHGRs ) with well-defined mean G+C contents , each significantly different from the G...
      </snippet>
      <mesh_term_list>
        <mesh_term>Computational Biology</mesh_term>
        <mesh_term>Genomics</mesh_term>
        <mesh_term>Isochores</mesh_term>
        <mesh_term>Software</mesh_term>
      </mesh_term_list>
      <url>http://genome.cse.ucsc.edu/</url>
      <pages>
        <page>
          <name>Google</name>
          <url>
            http://www.google.com/search?hl=en&amp;q=link%3ahttp%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;btnG=Google+Search
          </url>
        </page>
        <page>
          <name>AltaVista</name>
          <url>
            http://www.altavista.com/web/results?itag=ody&amp;q=link:http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;kgs=0&amp;kls=1
          </url>
        </page>
      </pages>
      <papers>
        <paper>
          <name>BioMed Central</name>
          <url>
            http://www.biomedcentral.com/search/results.asp?txtSearch1=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;chkBMCJournals=true&amp;chkCurrentOpinion=true&amp;drpFromDate=&amp;drpToDate=&amp;chkNSP=true&amp;drpAddedInLast=&amp;drpOrderBy=by+date&amp;drpPerPage=20&amp;drpAbstract=no+abstract&amp;strTempString=&amp;strSearchBoxType=bmc_boolean_results&amp;Search.x=10&amp;jou_id=&amp;Search.x=0&amp;Search.y=0&amp;Search=Search
          </url>
        </paper>
        <paper>
          <name>Scirus</name>
          <url>
            http://www.scirus.com/srsapp/search?q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;ds=jnl&amp;g=s&amp;t=all
          </url>
        </paper>
        <paper>
          <name>HighWire Press</name>
          <url>
            http://highwire.org/cgi/searchresults?fulltext=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;andorexactfulltext=and&amp;author1=&amp;pubdate_year=&amp;volume=&amp;firstpage=&amp;src=hw&amp;searchsubmit=redo&amp;resourcetype=1&amp;search=Search&amp;fmonth=Jan&amp;fyear=1844&amp;tmonth=Dec&amp;tyear=2007&amp;fdatedef=1+January+1844&amp;tdatedef=31+Dec+2007
          </url>
        </paper>
        <paper>
          <name>Google Scholar</name>
          <url>
            http://scholar.google.com/scholar?hl=en&amp;lr=&amp;q=http%3A%2F%2Fgenome.cse.ucsc.edu%2F&amp;btnG=Search
          </url>
        </paper>
      </papers>
      <pmid_list>
        <pmid>15215396</pmid>
      </pmid_list>
    </result>
  </results>
</result_set>