<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
span.EmailStyle18
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:612058536;
mso-list-type:hybrid;
mso-list-template-ids:368500798 134807553 134807555 134807557 134807553 134807555 134807557 134807553 134807555 134807557;}
@list l0:level1
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level3
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l0:level4
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level5
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level6
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
@list l0:level7
{mso-level-number-format:bullet;
mso-level-text:\F0B7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l0:level8
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:"Courier New";}
@list l0:level9
{mso-level-number-format:bullet;
mso-level-text:\F0A7;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Wingdings;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Whilst testing my JEnsembl Java API against the new release 17 of EnsemblGenomes – I noticed that there has been a major reorganisation of the bacterial collections.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Prior to v17, taxonomically-grouped, stably-named collections of species were used: e.g. ‘bacillus’, ‘escherichia_shigella’, ‘staphylococcus’ etc.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>These appear to have been replaced with arbitrarily named collections ‘bacteria_1’ to ‘bacteria_24’, and the species contained in these collections do not seem to be grouped in an obviously systematic way.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Previously I had been able to use the stably named collections as part of a mechanism to provide continuity between release versions of the data, by creating a single ‘Species’ Java object belonging to a stably-named collection, with multiple release versions ( e.g. E.coli K12, part of the ‘escherichia_shigella’ collections with versions 1 through 16). <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The new collection layout breaks this pattern with the main consequence being that this complicates access to different release versions for a given bacterial species (as the actual data will lie in an unpredictably named collection database). <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I therefore need to re-design how the JEnsembl API configuration can achieve bacterial species continuity through releases ( or abandon this feature of JEnsembl for bacteria …)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Could you please provide some details to help me out?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-family:Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Is this change to collection organization finalized?<o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-family:Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Is the distribution of species to collections arbitrary?<o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-family:Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Will the distribution of particular species to particular collections change with each release?<o:p></o:p></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo2'><![if !supportLists]><span style='font-family:Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Will homologies for bacterial genes (proteins) no longer be curated in neither the ‘ensembl_compara_bacteria’ nor the ‘ensembl_compara_pan_homology’ databases?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks for any info<o:p></o:p></p><p class=MsoNormal>Trevor<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'>Trevor Paterson PhD<br></span></b><a href="mailto:trevor.paterson@roslin.ed.ac.uk"><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:blue;mso-fareast-language:EN-GB'>trevor.paterson@roslin.ed.ac.uk</span></a><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'>Bioinformatics <br>The Roslin Institute<br>Royal (Dick) School of Veterinary Studies<br>University of Edinburgh<br>Easter Bush<br>Midlothian<br>EH25 9RG<br>Scotland UK<br><br>phone +44 (0)131 651 9157<br><br></span><a href="http://bioinformatics.roslin.ed.ac.uk/"><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:blue;mso-fareast-language:EN-GB'>http://bioinformatics.roslin.ed.ac.uk/</span></a><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-GB'><br></span><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:navy;mso-fareast-language:EN-GB'><br></span><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:green;mso-fareast-language:EN-GB'>Please consider the environment before printing this e-mail</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><i><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:navy;mso-fareast-language:EN-GB'>The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336</span></i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'><br><b>Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.</b></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'> <o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>