diff --git a/docs/chado/chado.html b/docs/chado/chado.html deleted file mode 100644 index 2039bfa52247cbd46f2b1c4054f44462f34e5ae8..0000000000000000000000000000000000000000 --- a/docs/chado/chado.html +++ /dev/null @@ -1,230 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> -<html> - <head> - <meta content="text/html; charset=ISO-8859-1" - http-equiv="content-type"> - <title>Artemis - Chado database</title> - </head> - <body> - <a href="http://www.sanger.ac.uk/Software/Artemis/"><b>Artemis</b></a> and - <a href="http://www.sanger.ac.uk/Software/ACT/"><b>ACT</b></a> can be used - to connect to <a href="http://www.gmod.org/"><b>Chado</b></a> databases. - They are being developed to read and write to the database and perform the - same functions as the standard Artemis and ACT. - - <h2>Connecting to a Chado Database</h2> - The following java flags are used when running Artemis when connecting to a - database. These options currently are all needed. - <ol> - <li><b><pre>-DChado</pre></b> - this is used to get Artemis to look for the database. - The address of the database (hotname, port and name) can be conveniently - included as follows: - <br><pre>-DChado="hostname:port/test?username"</pre> - So that these details are already completed in the popup login pane. - <br><br> - <img src="login.gif" align="middle" alt="login"/> - <br> - </li> - <li><b><pre>-Djdbc.drivers=org.postgresql</pre></b> - this is used to define the <a href="http://jdbc.postgresql.org/"> - JDBC postgres driver - </a>. - </li> - <li><b><pre>-Dibatis</pre></b> - use the <a href="http://ibatis.apache.org/" title="iBatis">iBATIS</a> - Data Mapper - </li> - </ol> - <br> - So the command line will look someting like this example: - <pre> ./art -DChado="localhost:2996/test?tjc" -Dibatis \ - -Djdbc.drivers=org.postgresql.Driver</pre> - - <h2>Reading From the Database</h2> - On a successfull login in a database and file manager window will open up. - The database manager will dislay "Database Loading...". The organisms - in the database with residues are shown in a expandable tree. Double - clicking on the sequence names opens them up in Artemis. - <br><br> - <img src="databasemanager.gif"/> - <p> - A sequence can be opened in Artemis from the command line (without going - through the database manager). This is done by supplying a command line argument - with the organism and chromosome (or source feature): - <br><pre>Pfalciparum:Pf3D7_09</pre> - and optionally a range can be included to just display features within it: - <br><pre>Pfalciparum:Pf3D7_09:92000..112000</pre> - this could be used in combination with the <i>-Doffset=base</i> flag (<i>e.g. - -Doffset=10000</i>) to open Artemis at a particular section of a sequence - - <p> - To reduce the number of transactions to the database, all of the sequence is - read into Artemis. This includes most of the feature qualifiers. There are some - qualifiers (ortho/paralog and similarity qualifiers) that lazily load their data - as and when it is needed, <i>i.e.</i> when opened for viewing in the gene builder. - This lazy loading improves the performance of reading data from the database - for sequences with a large number of features. - - - <h2>iBatis Database Mapping</h2> - <a href="http://ibatis.apache.org/" title="iBatis">iBatis</a> data mapper - framework has been used to facilitate the communication with the database - from Artemis. It uses XML descriptors to couple the SQL statements with the - Java objects that Artemis understands. The XML maps are in the '<i>artemis_sqlmap</i>' - in the Artemis distribution. These are divided up into files based on the - Chado table names. - <p> - The SQL statements can be seen in the Artemis <a href= - "http://www.sanger.ac.uk/Software/Artemis/manual/launch-window.html#LAUNCH-WINDOW-OPTIONS-SHOW-LOG"> - Log Viewer</a> window:<br> - <img src="logviewer.gif" width="100%"/> - <br><br>This is mainly useful for debugging and tracking problems with reading - from and writing to the database. Artemis uses - <a href="http://logging.apache.org/log4j/">log4j</a> to produce logging - and the configuration file for this is in the file '<i>etc/log4j.properties</i>'. - - <h2>Gene Representation</h2> - Below is an illustration of how the feature are stored in Chado - in the Sanger PSU. - <p> - <center><b><i>Gene Model</i></b> - <br> - <img src="chado_gene_model.gif"/></center> - <p>The names (in red) are the internal database uniquenames. These names are - automatically generated by the gene builder from an ID provided by the - user. <i>N.B.</i> in our data model UTRs are represented as distinct from - exons. - <h3>Gene Building</h3> - A gene can be created in Artemis (or ACT) by highlighting a base range and selecting - from the '<i>Create</i>' menu the '<i>Gene Model From Base Range</i>' option. - This prompts for a unique ID and this corresponds to the names in the above - gene model representation. The basic consituent features are created; <i>i.e.</i> - gene, transcript, CDS and polypeptide. <i>N.B.</i> Artemis joins the exon - features and repesents them as a CDS feature. These are shown on the frame - lines in the feature display window. - <p> - A gene builder for a selected gene feature can be opened from the '<i>Edit</i>' menu - by selecting the '<i>Selected Feature in Editor</i>' option or simply using the '<i>E</i>' - shortcut key. - <center><p><b><i>The Artemis Gene Builder</i></b><br> - <img src="editor.gif"></center> - <p>There are two distinct parts to the gene builder window. The top part shows - the <b><i>gene hierarchy and structure</i></b>. The bottom part shows the - <b><i>annotation</i></b> associated with one of the constituent features. - These two parts of the gene builder are described below. - <ol> - <li><b>Gene Hierarchy and Structure</b><br> - The top left hand side is a tree structure of the gene model. To the right - of this is a graphical representation of the features. A feature can be selected - from either the tree or the graphical view. The annotation for the selected - feature is displayed in the bottom part of the gene builder. - <p>Structural changes can be carried out in the graphical view. The feature ends - can be dragged to adjust their coordinates. On right clicking on this area there - is a popup menu for adding and deleting features in the gene model. - <center><p><b><i>Editing the Gene Model In the Gene Builder</i></b><br> - <img src="genebuilder2.gif" border="1"></center> - <p> - Additional transcripts can be added from here. The checkbox to the right of - the above CDS is used to hide and show the associated CDS in the Artemis - feature display. This can make structural edits clearer for multiple transcripts. - <p> - <li><b>Annotation</b><br> - There are 4 (Properties, Core, Controlled Vocabulary and Match) sections in - the annotation part of the gene builder. These are described below. These can - be viewed in a scrollable view or in a tabbed view. There is a check box at - the bottom of the gene builder to change between these views. - <p> - <ul> - <li><b>Properties</b><br> - This contains properties such as the synonyms, time last modified and the - internal ID. Synonyms are added as a controlled vocabulary (these are in - a cv named '<i>genedb_synonym_type</i>'). - - <center><p><b><i>Properties section</i></b><br> - <img src="Properties.gif" border="1"></center> - - </li><p> - <li><b>Core</b><br> - The core annotation contains any other annotation that does not fit into the - other sections. <i>E.g.</i> comments, literature, Dbxref. Hyperlinks are - provided for SWALL, EMBL, UniProt, PMID, PubMed, InterPro and Pfam, and opening - up a local browser. - </li><p> - <li><b>Controlled Vocabulary (CV)</b><br> - The CV module in Chado is concerned with controlled vocabularies or ontologies. - Therefore, Chado can use the biological ontologies and this makes it very - expressive. - <p> - This section in the gene builder provides a form for adding and deleting GO, - controlled curation, product, Riley class annotation. CV terms are added by - clicking the 'ADD' button. When adding a term to a feature the user is - prompted for the CV name and then keyword. The term to be added is then - selected from a drop down list of terms containing the word or phrase. - To further assist in finding the CV term from the list, typing in the - text will start to autocomplete and scroll to the first matching term. - - <center><p><b><i>CV section</i></b><br> - <img src="CV.gif" border="1"></center> - - <p>GO terms are selected from molecular_function, biological_process - or cellular_component CV's. - - <p>Products are stored in Chado as a CV (<i>i.e.</i> in cvterm in - a cv named '<i>genedb_products</i>'). - - <p>Other generic controlled curations can be found by Artemis and shown - if their CV name in Chado is prefixed with '<i>CC_</i>' (<i>e.g.</i> - CC_controlledcuration, CC_workshop). These then appear in a drop down - list when adding CV terms to a feature. - - <p>Adding new terms to the database can also be done from this section. - In the drop down selection of CV's there is an 'Add term...' option. - This opens an input panel for new terms. - <center><p><b><i>Adding a new CV term</i></b><br> - <img src="addterm.gif"></center> - </li><p> - <li><b>Match</b><br> - This section allows the user to add ortholog/paralog links to other genes - in the database. - <p> - The ortholog/paralog tables provide links for opening the gene editor or - an Artemis window for each entry. The '<i>VIEW</i>' button opens a - separate Artemis displaying the gene ortholog or paralog and the - surrounding features. - <p> - In addition similarity qualifiers can be added here from matches to - blast and fasta searches carried out in Artemis. These are added - from the Artemis Object Editor. - </li> - </ul> - </ol> - - <h3>Writing To The Database</h3> - When a feature or qualifier is changed, added or deleted the '<i>Commit</i>' button (on - the top tool bar) changes colour to red. Changes in Artemis only get written back to the - database when this button is clicked. - <center><p><b><i>Commit Button</i></b><br> - <img src="commit.gif" border="1"></center> - <p> - There is also an option under the '<i>File</i>' menu to '<i>Commit To - Database</i>'. Note in ACT there is no commit button and the '<i>Commit To - Database</i>' menu option is used to write back to the database. - <p> - If there is an error during the commit then Artemis will provide the option to - force commit. This means it will commit what it can. Naturally this can be potentially - problematic. Therefore, <b>commiting back to the database frequently is encouaged</b>. - Any errors are reported in the log viewer. - - <h3>Community Annotation</h3> - Multiple users can launch Artemis and query the database. This has been stress - tested and used in the malaria re-annotation exercise with 30+ Artemis clients - connecting to the database. - <p> - Artemis records the time a features was last modified (<i>timelastmodified</i>). Before - changing a feature it will check this time stamp against the database record of the - <i>timelastmodified</i>. - If the corresponding feature in the database has changed by another user it will - ask whether to continue with the commit process. - </body> -</html>