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<!DOCTYPE article PUBLIC "-//OASIS//DTD Simplified DocBook XML V1.0//EN"
"http://www.oasis-open.org/docbook/xml/simple/1.0/sdocbook.dtd">
<article>
  <section>
    <title>FlyMine version 3.1 - release notes</title>
    
    <itemizedlist>
      <listitem>
        <para>Data - fixes</para>
        <itemizedlist>
          <listitem><para>FIX: <emphasis>D. melanogaster</emphasis> genes from FlyBase and UniProt are now merged correctly.</para></listitem>
          <listitem><para>FIX: Missing orthologues from <emphasis>D. melanogaster</emphasis> to <emphasis>A. gambiae</emphasis> are now loaded.</para></listitem>
        </itemizedlist>
      </listitem>
    </itemizedlist>
  </section>

  <section>
    <title>FlyMine version 3.0 - release notes</title>
    
    <itemizedlist>
      <listitem>
        <para>Data - new and updated</para>
        <itemizedlist>
          <listitem><para>UPDATE: FlyBase <emphasis>D. melanogaster</emphasis> genome annotation updated to release 4.2.</para></listitem>
          <listitem><para>NEW: Microarray gene expression data - currently five experiments run at the FlyChip facility are available.</para></listitem>
          <listitem><para>NEW: Protein domain and family information from InterPro.</para></listitem>
          <listitem><para>NEW: DrosDel deletion data added.</para></listitem>
          <listitem><para>NEW: <emphasis>D. melanogaster</emphasis> genes now have full name and wild type function set.</para></listitem>
          <listitem><para>UPDATE: GO annotation changes:</para>
            <itemizedlist>
              <listitem><para><emphasis>D. melanogaster</emphasis> and <emphasis>C. elegans</emphasis> gene associations are now taken from FlyBase and WormBase respectively.</para></listitem>
              <listitem><para>Gene now has a collection of GOAnnotations, an object which contains the GO term id, name, evidence code and text from 'with' reference if present. If 'with' is a Gene or Protein a reference to the object is added.</para></listitem>
              <listitem><para>GOTerm entries now have a description, namespace ('biological_process', 'cellular_component' or 'molecular_function') and a collection of synonyms.</para></listitem>
            </itemizedlist>
          </listitem>
        </itemizedlist>
        <para>NOTE - this list does not include all updates to the versions of existing data sources - for a full list of versions see the Datasources section on the <ulink url="/">FlyMine home page</ulink>.</para>
        <para />
      </listitem>
      <listitem>
        <para>Data - fixes</para>
         <itemizedlist>
          <listitem><para>FIX: Gene.name is now Gene.symbol, added Gene.name which has a longer text name.</para></listitem>
          <listitem><para>FIX: Transcript.exonCount is now set for all Transcripts.</para></listitem>
          <listitem><para>FIX: Only RepeatRegions predicted by TRF are retrieved for <emphasis>A. gambiae</emphasis> from Ensembl.</para></listitem>
          <listitem><para>FIX: There are no longer links to UniProt with BDGP identifiers.</para></listitem>
          <listitem><para>FIX: Incorrect start and end fields removed from RepeatRegion.</para></listitem>
          <listitem><para>FIX: Removed duplicate synonyms for some Proteins.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>Data - known issues</para>
         <itemizedlist>
           <listitem><para>Five genes are annotated incorrectly in the FlyBase release 4.2 annotation. These are eys, Dimp, cp309, Nev3 and kay. It is a known problem with FlyBase and a fix is progress. In FlyMine the symbols(names) are modified so that they are unique and indicate that there is a problem. Examples are: Dimp-duplicate-symbol-1, Dimp-duplicate-symbol-2 instead of Dimp.</para></listitem>
           <listitem><para>The latest version of InterPro (11.0) is not yet available as a mysql dump so we still have version 10.0.</para></listitem>
           <listitem><para>INDAC microarray oligos were designed to FlyBase version 4.0 transcripts. This means a number now map to old transcripts. These oligos can be queried in FlyMine, however the transcript they are designed to will not have merged with a Gene.</para></listitem>
           <listitem><para>A number of proteins from Uniprot have not merged with FlyBase genes.  This means that for certain genes there are two objects - one from Uniprot with no other information.</para></listitem>
           <listitem><para>Orthologues for Anopheles gambiae did not load.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>Interface - new features</para>
        <itemizedlist>
          <listitem><para>NEW: The start page of FlyMine now has links to a series of 'aspects' which are convenient starting points for the different types of data in FlyMine - such as genomics, protein interactions and gene expression. Each aspect lists relevant data sets in FlyMine, template queries and suggested starting points for queries.</para></listitem>
          <listitem><para>NEW: Template search box added to the front page.</para></listitem>
          <listitem><para>NEW: User templates are now listed on the user's History page.</para></listitem>
          <listitem><para>NEW: Saved bags and saved queries can be renamed from the History page.</para></listitem>
          <listitem><para>NEW: Executed queries are now automatically saved to a 'session history'. The user can permanently save a query from the session history from the History page.</para></listitem>
          <listitem><para>NEW: Saved queries and queries in the session history are now displayed with the date and time at which they were created.</para></listitem>
          <listitem><para>NEW: Saved queries and queries in the session history are now displayed with their starting point and a summary of the fields selected for output.</para></listitem>
          <listitem><para>NEW: You can now edit an existing constraint in the query builder by clicking the blue edit icon next to the constraint.</para></listitem>
        </itemizedlist>
      </listitem>
<commit_msg>update to 4.0<commit_after><?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//OASIS//DTD Simplified DocBook XML V1.0//EN"
"http://www.oasis-open.org/docbook/xml/simple/1.0/sdocbook.dtd">
<article>
  <section>
    <title>FlyMine version 4.0 - release notes</title>
    
        <para>Major changes to layout and content of summary pages. These pages can now display the results of template queries inline to give immediate access to data. The www.flymine.org home page now shows aspect icons and query options. Many other interface improvements. Addition of Arbeitman et al, 2002 Drosophila time course microarray data and human disease gene matches from Homophila.</para>

    <itemizedlist>
      <listitem>
        <para>Data</para>
        <itemizedlist>
          <listitem><para>NEW: microarray data from "Gene Expression During the Life Cycle of <emphasis>Drosophila melanogaster</emphasis>", Arbeitman et al 2002.</para></listitem>
          <listitem><para>NEW: added data human disease gene matches from Homophila (http://superfly.ucsd.edu/homophila/).</para></listitem>
          <listitem><para>NEW: more protein interaction experiments from IntAct - see Protein Interaction aspect.</para></listitem>
          <listitem><para>NEW: Gene now has an "allGoAnnotation" collection that contains the term assigned to a gene plus all the parents of the term. Using this collection to find genes with a particular term will find all genes with that term *and* any with a more specific term.</para></listitem>
          <listitem><para>ENHANCEMENT: MRNA now references threePrimeUTR and fivePrimeUTR.</para></listitem>
          <listitem><para>ENHANCEMENT: <emphasis>D. melanogaster</emphasis> translation symbols now set from FlyBase.</para></listitem>
          <listitem><para>ENHANCEMENT: <emphasis>D. melanogaster</emphasis> chromosome bands now loaded from FlyBase.</para></listitem>
          <listitem><para>UPDATE: <emphasis>D. melanogaster</emphasis> genome annotation updated from 4.2 to 4.2.1.</para></listitem>
          <listitem><para>UPDATE: GO annotation and UniProt proteins updated.</para></listitem>
          <listitem><para>FIX: <emphasis>D. melanogaster</emphasis> regulatory regions from FlyBase now have chromose location.</para></listitem>
          <listitem><para>FIX: <emphasis>D. melanogaster</emphasis> insertion sites and point mutations from FlyBase reference genes correctly.</para></listitem>
          <listitem><para>FIX: <emphasis>A. gambiae</emphasis> genes from ensembl and InParanoid orthlogues now merged correctly.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>Tools</para>
        <itemizedlist>
          <listitem><para>NEW: a graph of interacting proteins on protein summary pages.</para></listitem>
          <listitem><para>NEW: graphs of <emphasis>D. melanogaster</emphasis> time course expression on gene details pages (Arbeitman et al, 2002).</para></listitem>
          <listitem><para>NEW: FASTA retrieval icon to access sequence of all features with sequence.</para></listitem>
          <listitem><para>FIX: insertion sites now displayed correctly on GBrowse.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>User Interface</para>
        <itemizedlist>
          <listitem><para>NEW: Template queries are now viewable inline on object summary pages.</para></listitem>
          <listitem><para>NEW: bags saved in history can now be subtracted from one another.</para></listitem>
          <listitem><para>NEW: Query constraint logic can now be manipulated within the query builder - can constrain A AND B/A OR B.</para></listitem>
          <listitem><para>NEW: Added Run query link to run a query directly from the History page.</para></listitem>
          <listitem><para>NEW: Template queries can now include a choice of several different output formats.</para></listitem>
          <listitem><para>ENHANCEMENT: Template search terms are highlighted in results lists.</para></listitem>
          <listitem><para>ENHANCEMENT: Template building integrated into query builder interface.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>Known issues</para>
      </listitem>

    </itemizedlist>
  </section>

  <section>
    <title>FlyMine version 3.1 - release notes</title>
    
    <itemizedlist>
      <listitem>
        <para>Data - fixes</para>
        <itemizedlist>
          <listitem><para>FIX: <emphasis>D. melanogaster</emphasis> genes from FlyBase and UniProt are now merged correctly.</para></listitem>
          <listitem><para>FIX: Missing orthologues from <emphasis>D. melanogaster</emphasis> to <emphasis>A. gambiae</emphasis> are now loaded.</para></listitem>
        </itemizedlist>
      </listitem>
    </itemizedlist>
  </section>

  <section>
    <title>FlyMine version 3.0 - release notes</title>
    
    <itemizedlist>
      <listitem>
        <para>Data - new and updated</para>
        <itemizedlist>
          <listitem><para>UPDATE: FlyBase <emphasis>D. melanogaster</emphasis> genome annotation updated to release 4.2.</para></listitem>
          <listitem><para>NEW: Microarray gene expression data - currently five experiments run at the FlyChip facility are available.</para></listitem>
          <listitem><para>NEW: Protein domain and family information from InterPro.</para></listitem>
          <listitem><para>NEW: DrosDel deletion data added.</para></listitem>
          <listitem><para>NEW: <emphasis>D. melanogaster</emphasis> genes now have full name and wild type function set.</para></listitem>
          <listitem><para>UPDATE: GO annotation changes:</para>
            <itemizedlist>
              <listitem><para><emphasis>D. melanogaster</emphasis> and <emphasis>C. elegans</emphasis> gene associations are now taken from FlyBase and WormBase respectively.</para></listitem>
              <listitem><para>Gene now has a collection of GOAnnotations, an object which contains the GO term id, name, evidence code and text from 'with' reference if present. If 'with' is a Gene or Protein a reference to the object is added.</para></listitem>
              <listitem><para>GOTerm entries now have a description, namespace ('biological_process', 'cellular_component' or 'molecular_function') and a collection of synonyms.</para></listitem>
            </itemizedlist>
          </listitem>
        </itemizedlist>
        <para>NOTE - this list does not include all updates to the versions of existing data sources - for a full list of versions see the Datasources section on the <ulink url="/">FlyMine home page</ulink>.</para>
        <para />
      </listitem>
      <listitem>
        <para>Data - fixes</para>
         <itemizedlist>
          <listitem><para>FIX: Gene.name is now Gene.symbol, added Gene.name which has a longer text name.</para></listitem>
          <listitem><para>FIX: Transcript.exonCount is now set for all Transcripts.</para></listitem>
          <listitem><para>FIX: Only RepeatRegions predicted by TRF are retrieved for <emphasis>A. gambiae</emphasis> from Ensembl.</para></listitem>
          <listitem><para>FIX: There are no longer links to UniProt with BDGP identifiers.</para></listitem>
          <listitem><para>FIX: Incorrect start and end fields removed from RepeatRegion.</para></listitem>
          <listitem><para>FIX: Removed duplicate synonyms for some Proteins.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>Data - known issues</para>
         <itemizedlist>
           <listitem><para>Five genes are annotated incorrectly in the FlyBase release 4.2 annotation. These are eys, Dimp, cp309, Nev3 and kay. It is a known problem with FlyBase and a fix is progress. In FlyMine the symbols(names) are modified so that they are unique and indicate that there is a problem. Examples are: Dimp-duplicate-symbol-1, Dimp-duplicate-symbol-2 instead of Dimp.</para></listitem>
           <listitem><para>The latest version of InterPro (11.0) is not yet available as a mysql dump so we still have version 10.0.</para></listitem>
           <listitem><para>INDAC microarray oligos were designed to FlyBase version 4.0 transcripts. This means a number now map to old transcripts. These oligos can be queried in FlyMine, however the transcript they are designed to will not have merged with a Gene.</para></listitem>
           <listitem><para>A number of proteins from Uniprot have not merged with FlyBase genes.  This means that for certain genes there are two objects - one from Uniprot with no other information.</para></listitem>
           <listitem><para>Orthologues for <emphasis>A. gambiae</emphasis> did not load.</para></listitem>
        </itemizedlist>
      </listitem>

      <listitem>
        <para>Interface - new features</para>
        <itemizedlist>
          <listitem><para>NEW: The start page of FlyMine now has links to a series of 'aspects' which are convenient starting points for the different types of data in FlyMine - such as genomics, protein interactions and gene expression. Each aspect lists relevant data sets in FlyMine, template queries and suggested starting points for queries.</para></listitem>
          <listitem><para>NEW: Template search box added to the front page.</para></listitem>
          <listitem><para>NEW: User templates are now listed on the user's History page.</para></listitem>
          <listitem><para>NEW: Saved bags and saved queries can be renamed from the History page.</para></listitem>
          <listitem><para>NEW: Executed queries are now automatically saved to a 'session history'. The user can permanently save a query from the session history from the History page.</para></listitem>
          <listitem><para>NEW: Saved queries and queries in the session history are now displayed with the date and time at which they were created.</para></listitem>
          <listitem><para>NEW: Saved queries and queries in the session history are now displayed with their starting point and a summary of the fields selected for output.</para></listitem>
          <listitem><para>NEW: You can now edit an existing constraint in the query builder by clicking the blue edit icon next to the constraint.</para></listitem>
        </itemizedlist>
      </listitem>

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