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[Gmod-apollo-cmts] CVS: apollo/doc/html userguide.html, 1.277, 1.278
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From: elee <gk...@us...> - 2007-12-22 00:50:59
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Update of /cvsroot/gmod/apollo/doc/html In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv23154 Modified Files: userguide.html Log Message: + Added GFF3 section + Updated Chado section with information on program source filtering Index: userguide.html =================================================================== RCS file: /cvsroot/gmod/apollo/doc/html/userguide.html,v retrieving revision 1.277 retrieving revision 1.278 diff -C2 -d -r1.277 -r1.278 *** userguide.html 19 Dec 2007 22:44:47 -0000 1.277 --- userguide.html 22 Dec 2007 00:50:46 -0000 1.278 *************** *** 34,37 **** --- 34,38 ---- <LI><a href="#ChadoAdapter">Reading data directly from a Chado database</a><BR> <LI><a href="#ReadingGFF">Reading Ensembl GFF files</a><BR> + <LI><a href="#ReadingGFF3">Reading GFF3 files</a><BR> <LI><a href="#Reading_Ensembl_via_ensj">Reading Ensembl schema databases</a><BR> <LI><a href="game-synteny.html">Reading cross-species comparative data in *************** *** 194,197 **** --- 195,200 ---- <LI>Chris Mungall</LI> <li>Colin Wiel</li> + <li>Chris Wilks</li> + <li>Olivier Arnaiz</li> <LI>and all the FlyBase curators</LI> </UL> *************** *** 503,506 **** --- 506,523 ---- (e.g. GFF <-> GAME), in practice this is not foolproof. + <h3><a NAME="ReadingGFF3"></a>Reading GFF3 files</h3> + + <a href="http://www.sequenceontology.org/gff3.shtml">GFF3</a> format is + the current generation of a simple format for transferring genomic annotations. <P> + To read in an GFF3 file, choose the "GFF3 format" option from the data adapter menu. You can type your GFF3 file name in the text box or press the Browse button to bring up a file chooser. You must either provide the sequence data in FASTA format or you will need to have the FASTA data embedded in the GFF3 file. For the first option, make sure that "Embedded FASTA in GFF" is not checked and enter the FASTA file to go with the GFF3 data (you can browse for the file as well). For the second option, make sure that "Embedded FASTA in GFF" is checked. This will disable the "Sequence file" selection. When you're ready, press the OK button and the GFF3 file and sequence data will be read in and the features displayed. + <P> + <center><img SRC="images/gff3-adapter.gif" width=605 height=271></center> + <P>If any of the features in the GFF3 file have types that are not recognized + by Apollo they will be given a default pale yellow color. + This can be changed by right-clicking over the appropriate feature box + in the Types panel (see the <a href="#TypesPanel">types panel </a>section + for details). + <P> + <h3><a name="Reading_Ensembl_via_ensj"></a>Reading Ensembl schema databases</h3> *************** *** 3544,3548 **** change text in the file conf/chado-adapter.xml in order to fill in the chadodb element. Here is an example: ! <pre><!-- Indiana public FlyBase server r3.2 --><br> <chadodb><br> <name>FlyBase Chado Indiana public server r3.2</name><br> <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter><br> <url>jdbc:postgresql://bugbane.bio.indiana.edu:7302/chado_r3.2</url><br> <dbName>chado_r3.2</dbName><br> <dbUser>flybase</dbUser><br> <dbInstance>flybaseInstance</dbInstance><br> <style>fly.style</style><br> <sequenceTypes><br> <type>gene</type><br> <type>golden_path_region</type><br> </sequenceTypes><br> </chadodb><br></pre> Add a similar entry to chado-adapter.xml describing your Chado database. --- 3561,3581 ---- change text in the file conf/chado-adapter.xml in order to fill in the chadodb element. Here is an example: ! ! <pre><code> ! <!-- Indiana public FlyBase server r3.2 --> ! <chadodb> ! <name>FlyBase Chado Indiana public server r3.2</name> ! <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter> ! <url>jdbc:postgresql://bugbane.bio.indiana.edu:7302/chado_r3.2</url><dbName>chado_r3.2</dbName> ! <dbUser>flybase</dbUser> ! <dbInstance>flybaseInstance</dbInstance> ! <style>fly.style</style> ! <sequenceTypes> ! <type>gene</type> ! <type>golden_path_region</type> ! </sequenceTypes> ! </chadodb> ! </code></pre> ! Add a similar entry to chado-adapter.xml describing your Chado database. *************** *** 3581,3585 **** programs, and a list of annotation types in your Chado database. Here is an example: ! <pre><chadoInstanceid="flybaseInstance"><br><br> <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsNam><br><br> <featureCV>SO</featureCV><br> <relationshipCV>relationship type</relationshipCV> <br> <propertyTypeCV>property type</propertyTypeCV><br><br> <genePredictionPrograms> <br> <program>genscan</program> <br> <program>piecegenie</program> <br> </genePredictionPrograms><br><br> <searchHitPrograms><br> <program>sim4</program><br> <program>%blastx%</program><br> </searchHitPrograms> <br> <searchHitsHaveFeatLocs>false</searchHitsHaveFeatLocs><br><br> <oneLevelAnnotTypes><br> <type>promoter</type><br> <type>insertion site</type> <br> <type>transposable_element</type><br> <type>remark</type><br> <type>repeat_region</type> <br> <type>substition</type><br> <type>nucleotide_deletion</type><br> <type>nucletide_insertion</type><br> </oneLevelAnnotTypes><br><br> <threeLevelAnnotTypes><br> <type>gene</type><br> <type>pseudogene</type><br> <type>tRNA</type><br> <type>rRNA</type><br> <type>miRNA</type><br> </threeLevelAnnotTypes><br><br> </chadoInstance><br></pre> clsName is the class name to be used for your Chado instance. There are currently three Chado instance classes: --- 3614,3664 ---- programs, and a list of annotation types in your Chado database. Here is an example: ! ! <pre><code> ! <chadoInstanceid="flybaseInstance"> ! <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsNam> ! ! <featureCV>SO</featureCV> ! <relationshipCV>relationship type</relationshipCV> ! <propertyTypeCV>property type</propertyTypeCV> ! ! <genePredictionPrograms> ! <program>genscan</program> ! <program>piecegenie</program> ! </genePredictionPrograms> ! ! <searchHitPrograms> ! <program> ! <name>blat</name> ! <source>cDNA</source> ! <version>1.3</version> ! </program> ! <program>sim4</program> ! <program>%blastx%</program> ! </searchHitPrograms> ! <searchHitsHaveFeatLocs>false</searchHitsHaveFeatLocs> ! ! <oneLevelAnnotTypes> ! <type>promoter</type> ! <type>insertion site</type> ! <type>transposable_element</type> ! <type>remark</type> ! <type>repeat_region</type> ! <type>substitution</type> ! <type>nucleotide_deletion</type> ! <type>nucletide_insertion</type> ! </oneLevelAnnotTypes> ! ! <threeLevelAnnotTypes> ! <type>gene</type> ! <type>pseudogene</type> ! <type>tRNA</type> ! <type>rRNA</type> ! <type>miRNA</type> ! </threeLevelAnnotTypes> ! ! </chadoInstance> ! </code></pre> ! clsName is the class name to be used for your Chado instance. There are currently three Chado instance classes: *************** *** 3599,3602 **** --- 3678,3691 ---- controlled vocabularies in chado (these tend to vary in different chado instantiations. </p> + <p><program> can be defined in two ways:</p> + <ul> + <li><code><program>program_name</program><code></li> + <li><code><program><br> + <name>program_name</name><br> + <source>data_source</source><br> + <version<data_version</version><br> + </program></code></li> + </ul> + The second format can be used for filtering which data source/version to retrieve from the database (useful for viewing and dumping only a subset of all the data). The <code><version></code> element is optional. <p>genePredictionPrograms is a list of gene prediction programs to query *************** *** 3607,3612 **** have feature locs associated with them in chado (rice has them, fly does ! not). If there are search hit feat locs, the hdbc adapter will ! retirieve out of range hsp/leaves that are associated with in range hits, otherwise it doesn't. </p> <p>oneLevelAnnotTypes and threeLevelAnnotTypes list annotation types --- 3696,3701 ---- have feature locs associated with them in chado (rice has them, fly does ! not). If there are search hit feat locs, the jdbc adapter will ! retrieve out of range hsp/leaves that are associated with in range hits, otherwise it doesn't. </p> <p>oneLevelAnnotTypes and threeLevelAnnotTypes list annotation types |