SRS 8.2 file updates
Updates of SRS files since the release of SRS8.2
This page lists file updates for the folowing SRS8.2 distribution directories:- icarus/db (flatfile/xml parsers, .i .it files)
- icarus/lion/emboss (emboss definition files)
- web/WEB-INF/jsp/views (jsp views)
Updates are also available by ftp (login required) from downloads.biowisdomsrs.com, directory parser/srs82 The updated files are also available as tarball: srs82updates.latest.tar.gz
We also provide a tarball just containing the files which have been updated upto a certain date: srs82updates.DATE.tar.gz from: http://downloads.biowisdomsrs.com/parser/srs82 For detail on the updates available in these tarballs, see the corresponding README.srs82updates.DATE file in that same directory
See README.updates for general information on how to update your SRS installation
There is an rss feed where SRS82 parser updates are announced the moment they are available: http://downloads.biowisdomsrs.com/parser/rss/srsparser82.xml We also announce updates via a mailing list (Important fixes inmediately, small fixes/improvements are usually announced when we make a new srs82updates.DATE.tar.gz file). To subscribe to this mailing list please contact srs_support @ biowisdom.com
| Date | Database | File | Description |
| 2008/08/22 | emboss | icarus/lion/emboss/remap.i icarus/lion/emboss/showalignn.i icarus/lion/emboss/showalignp.i | Fix so showalign and remap will correctly use the colors specified by the user to color sequence regions |
| 2008/08/22 | system genbank embl refseq ddbj | icarus/db/ftseq.is icarus/db/gbemblcommon.is icarus/db/genbank.is | some minor parser improvements |
| 2008/08/19 | chebi | icarus/db/chebidatamodel.i | Fix for a problem where SRS would not always retrieve the matching structure image from lcompound to be displayed with a chebi entry |
| 2008/08/18 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | Changes for release 25 of the reactome database. Note that we have changed the database name as used in the interaction with mysql to Reactome |
| 2008/08/13 | pdb | icarus/db/pdb.i icarus/db/pdb.is | added a new field providing chain Ids (combining entry name and chain designation) |
| 2008/08/12 | uniprot | icarus/db/uniprotvarsplic.is | Change to allow for a change in the header line in uniprot splice variant data (uniprotvarsplice) |
| 2008/08/08 | prisma | icarus/lion/prisma/prismaCheckClasses.i | Fix for a problem where prisma would not pick up an update scheduled to run on Sundays |
| 2008/08/07 | system uniprot ipi | icarus/db/srsgen.i icarus/db/swisscommon.i icarus/db/swissprot.is icarus/db/uniprot.i web/WEB-INF/jsp/views/swissentry/swissentry.jsp | Changes to handle the new format of the DE lines in uniprot. We have added new fields: Name, AltName,Contains, Includes and Flag, but have kept the old Description field in order to query the entire contents of the DE lines. We also added a new synonym finder which uses the Name and AltName fields. Note that the new srsgen.i file needs to be merged with your copy of that file in SRSSITE |
| 2008/08/04 | enzyme | icarus/db/enzyme.i icarus/db/enzyme.is icarus/db/enzyme.it web/WEB-INF/jsp/views/enzymeentry/enzymeentry.jsp | removed the disease (reference to omim) field, as it is no longer used |
| 2008/07/29 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Changes for release 50 of ensembl |
| 2008/07/29 | uniprot ipi | icarus/db/swissprot.is icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i | Changes needed to make sure we correctly link to the enzyme database with the new format of the uniprot description line. You may have to rebuild the links between uniprot_swissprot/trembl and enzyme after applying this update |
| 2008/07/29 | system | icarus/db/dbxref.i icarus/db/href.i | Changes to allow for the new references to BindingDB in uniprot. Please note that you will need to merge href.i and dbxref.i with your copies of these files in SRSSITE |
| 2008/07/28 | iprmatches | icarus/db/iprmatches.is | fix for links to prodom entries in iprmatches |
| 2008/07/02 | kegg | icarus/db/ldrug.i icarus/db/ldrug.is web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp | Added support for the new Source and Component fields in the kegg drugs database (ldrug) |
| 2008/07/02 | chebi | icarus/db/chebi_schema.i | Update for small chebi schema change in release 46 |
| 2008/06/24 | genecards | icarus/db/genecards.i icarus/db/genecards.is web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp | Change to allow for teh mew MilliPore references in GeneCards |
| 2008/06/19 | emboss | icarus/lion/emboss/diffseq.is icarus/lion/emboss/diffseqn.i icarus/lion/emboss/diffseqp.i icarus/lion/emboss/diffseqview.il | Fix for a display problem with the feature files created by diffseq |
| 2008/06/19 | emboss | icarus/lion/emboss/sixpack.i icarus/lion/emboss/sixpack.is | fix for an display issue when more than one sequence is submitted (note that sixpack will only work on the first sequence) |
| 2008/06/18 | blast | icarus/db/blastcommon.i | Fix for a problem with the BlastLoader, which would result in missing values for Blast Evalue and Scores with this loader |
| 2008/06/12 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new hogenom and hovergen hypertext links in uniprot |
| 2008/06/09 | kegg | icarus/db/lenzyme.is | fix for a problem with hypertext links from lenzyme to lcompound |
| 2008/06/06 | chebi | icarus/db/chebidatamodel.i | Better checking for recursion when traversing the chebi ontology, so the drawing of the ontology graph does not end in a loop |
| 2008/06/05 | chebi | icarus/db/chebi.i icarus/db/chebidatamodel.i | Fixed some issues with the ontology tree displayed with chebi entries, and added colorcoding (with a legend) for the relationship between entitities |
| 2008/06/02 | ddbj embl genbank | icarus/db/ddbjrelease.i icarus/db/emblrelease.i icarus/db/genbankrelease.i | Change needed to cope with the increasing sizes of EMBLRELEASE, GENBANKRELEASE and DDBJRELEASE. After applying this update you will have to re-index the primary accession number (pac) field. It is important that you apply this change before you install the next (June 2008) full releases of these databases, as otherwise you will not be able to access all entries |
| 2008/06/02 | ddbj | icarus/db/ddbjnew.it icarus/db/ddbjnewfiles.it icarus/db/ddbjrelease.it icarus/db/ddbjwgs.it | Change to allow for a change in the directory structure of the DDBJ ftp site |
| 2008/06/02 | pdbfinder | icarus/db/pdbfinder.i | Change to make sure that we can launch sequences from pdbfinder as input for analysis tools |
| 2008/06/02 | system kegg | icarus/db/href.i icarus/db/pathway.is | Fixed a parsing issue with the description line in some entries, and changed the hypertext to kegggenes to use a srs83 style url. Note that you will have to merge the updated href.i file with your copy of that file in SRSSITE |
| 2008/05/27 | system | icarus/db/dbxref.i | Change needed to handle the new links to the Candidia Genome Database in uniprot. Please merge the changed dbxref.i file with your copy in SRSSITE |
| 2008/05/27 | system | icarus/db/srsgen.i | reformatted srsgen.i so it matches the layout of srsgen.i after the installation of emboss tools. There are no functional changes |
| 2008/05/14 | system | icarus/db/ftseq.is | Correction for coding error which would break sequence feature retrieval |
| 2008/05/14 | hmmer | icarus/db/hmmpfam.i icarus/db/hmmpfam.is icarus/db/hmmpfam.it | Improvements for the HMMPfam tool - a view showing description, Evalue and Score, and added a searchable description field |
| 2008/05/13 | fasta | icarus/db/fasta.is | Change needed to handle some cases of output from fasta3.5 |
| 2008/05/13 | system | icarus/db/srsgen.i | Change so the Sequence Version field (sv) is also included in an All Identifier search. Note that you will have to merge the updated srsgen.i file with your copy in SRSSITE |
| 2008/05/13 | blast | icarus/db/blastn.i icarus/db/blastp.i icarus/db/blastx.i icarus/db/tblastn.i icarus/db/tblastx.i | Change to make sure blast honours a user request to use ungapped aligments |
| 2008/05/12 | kegg system | icarus/db/kegggenome.i icarus/db/kegggenome.is icarus/db/srsgen.i web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp | Added support for the new ANNOTATION line in kegggenome. Note that you will have to merge the new srsgen.i file with your copy of this file in SRSSITE |
| 2008/05/12 | intact uniprot | icarus/db/intactexperiment.i icarus/db/intactinteraction.i icarus/db/intactinteractor.i icarus/db/uniprotvarsplic.i | Changed the names of the uniprot splice variants database and the various intact databases to all uppercase as mixed case databases names can cause problems when doing databases updates with prisma |
| 2008/05/12 | kegg | icarus/db/kegg_species.i | latest update for kegg species mapping file |
| 2008/05/07 | genbank embl refseq ddbj system | icarus/db/gbemblcommon.is icarus/db/href.i | Added special handling for Korean patent numbers when including a hypertext link to the European patent Office. Note that the new version of href.i needs to be merged with your copy of this file in SRSSITE |
| 2008/05/06 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new nmpdr link in uniprot |
| 2008/04/29 | system | icarus/db/ftseq.is | Change needed to handle a change in the way unknown gaps are specified in EMBL/GenBank/DDBJ Feature tables and contig construction representations |
| 2008/04/24 | go_mysql | icarus/db/gogeneproducts.i | Changed linkidentifiers for some databases. Without this change recent version of gogeneprodcts will not link correctly to uniprot |
| 2008/04/24 | hssp | icarus/db/hssp.is | Some changes to make display of hssp entries in the default view, or any table view faster for entries which contain a large number of sequence references |
| 2008/04/22 | rebase | icarus/db/rebase.i icarus/db/rebase.is icarus/db/rebcomm.is web/WEB-INF/jsp/views/rebaseentry/rebaseentry.jsp | Better handling of rebase where there are multiple entries for the same enzyme - we now combine thes into a single entry, so there are no longer duplicate id warnings when indexing. Also some minor display improvements, and a fix for a spurious parsing error when indexing the commdata (commercial vendors) file |
| 2008/04/22 | system | icarus/util/appl.i | Fix for a problem when using a batch queue system to run a tool on a host on which the SRS partition is not mounted |
| 2008/04/21 | epd | icarus/db/epd.is | removed some obsolete code |
| 2008/04/18 | prisma | icarus/lion/prisma/prismaCheckClasses.i | Change so prisma will honour a defaultBatchCommand if no specific batch command is defined for a task |
| 2008/04/17 | prisma | icarus/lion/prisma/checkDependentDbs.i | Fix for a problem where prisma would not execute a reformat command for a dependend library when the -forceReformat option is specified |
| 2008/04/17 | genecards system | icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp | Updates for version 2.38 of genecards |
| 2008/04/15 | blast fasta system | icarus/db/blast.is icarus/db/blastcommon.i icarus/db/blastgraphicdatamodel.i icarus/db/loader.i icarus/db/psiblast.i icarus/db/psiblast.is icarus/db/psiblast.it web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp | Updates for blast: Fix so the blast graphical view (HomologyView) will behave correctly when browsing through multiple blast results and a fix for a stability problem when doing the same. Brought the psiblast implementation in sync with the other blast programs - all views applicable to blast now also work for psiblast. Note that the new loader.i file must be merged with your copy of this file in SRSSITE |
| 2008/04/09 | prisma | icarus/workflows/checkLocalFiles.i | Change so the fileCountTolerance used by srscheck and prisma is also applied if the nunber of files decreases |
| 2008/04/08 | pdb | icarus/db/pdb.i web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp | Added support for the structure viewers jmol and chime in the pdb entry view. See comments at the top of pdb.i on how to enable jmol |
| 2008/04/01 | prisma | icarus/lion/packages/srsprisma.ip | Change so the prisma installation procedure will no longer hardcode the full path to the icarus include files for the prisma test databases in srsdb.i |
| 2008/04/01 | fasta | icarus/db/fasta.is | Changes needed to handle output from fasta 3.5. Our fasta parser should now be able to handle output generated by fasta 3.3, 3.4 and 3.5 |
| 2008/04/01 | interpro | icarus/db/interpro.is | Fix for an issue with literature reference counting within interpro entries |
| 2008/03/31 | embl refseq | icarus/db/emblcontigs.i icarus/db/emblwgsnew.i icarus/db/emblwgsrelease.i icarus/db/refseqnew.i icarus/db/refseqrelease.i | Correction in the instructions on how to use these files with GCG formatted data. There are no functional changes |
| 2008/03/31 | pathway | web/WEB-INF/jsp/views/pathwayentry/pathwayentry.jsp | Fix for a problem with the imagemap for pathway entries |
| 2008/03/27 | prisma | icarus/lion/prisma/remoteConnection.i | Fix for a problem with recursive traversion of directories on a remote ftp site |
| 2008/03/27 | prisma | icarus/lion/prisma/prismaArchive.i icarus/lion/prisma/prismaCheckMain.i | Fix to ensure we remove old content from the current report directory, and an extra check so prisma will not accidentally wipe out all prisma directories |
| 2008/03/26 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new ProMEX hypertext link in uniprot. Note that you will have to merge the new versions of href.i and dbxref.i with your copies in SRSSITE |
| 2008/03/26 | prisma | icarus/lion/prisma/prismaCheckMain.i | Fix to ensure we remove old content from the prisma reports |
| 2008/03/20 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Changes for ensembl release 49 |
| 2008/03/19 | interpro | icarus/db/interpro.i | Added a link between interpro and refseqp |
| 2008/03/19 | pfam | icarus/db/pfama.it icarus/db/pfamb.it icarus/db/pfamc.it icarus/db/pfamseed.it icarus/db/swisspfam.it | Added code so prisma can set the release number after a data update |
| 2008/03/19 | pfam | icarus/db/pfamhmm.i | Correction for sorting pfamhmm by description |
| 2008/03/19 | kegg | icarus/db/kegg_species.i | Latest version of the kegg species mapping file. Note that if you have prisma, and use it to update the kegggeeome database, it will create this file automatically |
| 2008/03/18 | chebi | icarus/db/chebidatamodel.i | Fixes for a few hypertext link problems in chebi entry display |
| 2008/03/14 | chebi | icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebidatamodel.i web/WEB-INF/jsp/views/chebientry/chebientry.jsp | Changes for release 42 of chebi. A mass and charge field have been added |
| 2008/03/13 | genecards | icarus/db/genecards.is | Change so we do not include the synomyn origin (EG/HGNC) in the synonym index |
| 2008/03/12 | go_mysql kegg reactome system | icarus/db/goterms.i icarus/db/lcompound.i icarus/db/reactome.i icarus/db/srsgen.i | Added an internal link for reactome, and moved some field definitions from reactome.i, goterms.i and lcompound.i to srsgen.i for increased stability during srssection. Note that you will have to merge the new srsgen.i with your version of that file in SRSSITE |
| 2008/03/10 | prisma | icarus/lion/prisma/generateCalendar.i | Workaround for a case where the calender generation mechanism gets confused by daylight savings time |
| 2008/03/10 | emboss | icarus/lion/emboss/prettyplotn.i icarus/lion/emboss/prettyplotp.i icarus/lion/emboss/restover.i | removed options which are no longer valid in EMBOSS 5.0 |
| 2008/03/05 | system | icarus/util/colicarus.i | Change so hypertxt links from displayed icarus files to the SRS documentation work again |
| 2008/03/05 | embl genbank refseq ddbj medline | icarus/db/emblcommon.i icarus/db/genbankcommon.i icarus/db/medlinecommon.i | Changes needed to handle the increasing growth of several indices in EMBL, GenBank and Medline. Applying these changes requires re-indexing and will cause major disruption. Please read instructions in http://downloads.biowisdomsrs.com/parser/srs82/UPDATE.20080503 before applying these updates |
| 2008/02/29 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new 2d-ecoli and phosphosite hypertext references. Note that you will need to merge the new versions of dbxref.i and href.i with your copies of these files in SRSSITE |
| 2008/02/28 | prisma | icarus/lion/prisma/decisionReport.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/inspectReport.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/prismaGuiCal.i icarus/lion/prisma/report_resources/images/DecisionReport_up.png icarus/lion/prisma/report_resources/images/PrismaReport_up.png icarus/lion/prisma/report_resources/images/QualityReport_up.png icarus/lion/prisma/report_resources/images/QuickReference.gif icarus/lion/prisma/report_resources/images/UsageReport_up.png icarus/lion/prisma/report_resources/images/backMainPage_down.png icarus/lion/prisma/report_resources/images/backMainPage_up.png icarus/lion/prisma/report_resources/images/bwfavicon.ico icarus/lion/prisma/report_resources/images/loadersTest_up.png icarus/lion/prisma/report_resources/images/toolsTest_up.png icarus/lion/prisma/report_resources/images/viewReport_up.png | Fixes for various minor inconsistencies with images in prisma reports |
| 2008/02/21 | emboss | icarus/lion/emboss/sixpack.is | fix to prevent sixpack indexing to hang on an empty results file, which in some cases can bring down an SRS server |
| 2008/02/14 | medline | icarus/db/medlinecommon.i | The 2008 release of medline has 16880015 entries, which is about 100000 more than can be accomodated by the 3 byte id space we allocate by default for a database. The result is that for the final 100000 entries in medlinerelease, wrong entries (from the beginning of the database are returned). The updated medlinecommon.i file will correct this, allocating 4 bytes for entry identifiers. Note that you must re-index both medlinerelease and medlinenew for this to take effect. Note that after applying this update, and while re-indexing is in progress, the old indices will still be working, so there is no need to take medline offline (unless you are concerned about those 100000 wrong entries) |
| 2008/02/07 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new world-2dpage link in uniprot |
| 2008/02/01 | uniprot ipi | icarus/db/swissprot.is | Change to make sure that we can still extract the EC number from the uniprot description line after the description line structure changes announced for late February (see http://beta.uniprot.org/docs/sp_soon.htm). The new structure should not cause problems for the current handling of the description line in SRS, but once the data in the new format is available, we will provide additional changes to take advantage of the new structure |
| 2008/02/01 | system | icarus/db/srsgen.i | Fix for a problem when trying to use sequence tools with pdb sequences. Note that with this change the long name of the pdb sequence field changes from Sequence to FtSequence. Please merge the new srsgen.i file with your copy in SRSSITE |
| 2008/01/31 | go_xml | icarus/db/go.i | Added an internal link (go_children/go_parent) to allow querying the go hierarchy using the hierarchical link operators >_ and >^. For this link the information of both the "Is a" and "Part off" fields are combined in a new parentId field |
| 2008/01/29 | prisma | icarus/lion/prisma/localcopyPhase.i | Fix for a problem with dependent databases when a local re-indexing is done |
| 2008/01/25 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new pdbsum and vectorbase links in Uniprot. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE |
| 2008/01/18 | emboss | icarus/lion/emboss/tmap.i icarus/lion/packages/emboss.ip | Changed the TMAP tool (EMBOSS) to take alignments as input. Note that if you have already installed EMBOSS, you have to change the association of TMAP from sequence data input to alignment data input. This is easiest done by editing SRSSITE/packChanges.i, and change "PROTSEQ_DATA.applications.app:$TMAP_APP" to "PROTALI_DATA.applications.app:$TMAP_APP". |
| 2008/01/18 | kegg | icarus/db/pathway.is | Fixes for some issues with image maps when multiple pathway images are displayed |
| 2008/01/17 | system genbank embl refseq ddbj | icarus/db/dbxref.i icarus/db/gbemblcommon.is icarus/db/href.i | Added hypertext links for imgt/gene-db dbxrefs, and suppressed hypertext links for imgt/lims from refseq, as the values currently used in refseq do not provide a usefull way for linking. Note that you will need to merge the new versions of dbxref.i and href.i with your versions of these files in SRSSITE |
| 2008/01/17 | kegg | icarus/db/pathway.is | Fix to remove the duplicate display of map numbers |
| 2008/01/14 | system | logs/logcount.i logs/logcount.is logs/logscript.i logs/loguse.i logs/loguse.is | Some improvements to SRS usage logging. Reports created by running logscript.i are now stored in SRSROOT/logs/reports, and the old usage files are archived in SRSROOT/logs/archive. The usage reports now also include usage per user (with anonymous usage grouped by IP number, and usage by IP number |
| 2008/01/04 | system | icarus/db/srsgen.i | correction for a file definition which was causing erooneous warnings in prisma |
| 2008/01/03 | genecards kegg | icarus/db/genecards.i icarus/db/kegg_images.i icarus/db/lenzyme.i | Added searchnames to some hidden helper libraries so prisma will not throw confusing error messages about missing data files for these |
| 2008/01/03 | geneseq | icarus/db/aageneseqtar.it icarus/db/nageneseqtar.it | Change to make sure prisma will download geneseq tar files, even if the size of the file has not changed |
| 2008/01/02 | pdbfinder | icarus/db/pdbfinder.i icarus/db/pdbfinder.is web/WEB-INF/jsp/views/pdbfinderentry/pdbfindersequence.jsp | Added support for the new compound lines in the chains subsections. Note that after this update you will have to index the new chaincompound field. |
| 2007/12/20 | prisma | etc/runPrisma | Added SRSFLAGS setting preservation for use with integrated config file updates |
| 2007/12/20 | kegg | icarus/db/pathway.i | Changed .Z to .gz to fix a few error/info messages |
| 2007/12/14 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i | Update for release 48 of ensembl |
| 2007/12/12 | prisma | icarus/workflows/checkLocalFiles.i icarus/workflows/coreCheckClasses.i icarus/workflows/moveIndicesPhase.i | Fixes for some issues when complete offline data/index sets are found by srscheck or prisma. SRS would not remove obsolete online data files, and would also try to use obsolete filenames from the off-line data directory for link index building. We also added additional integrity checking for the offline data/index sets found. |
| 2007/12/11 | blast hmmer printscan prositesearch tacg emboss | icarus/db/bl2seq.i icarus/db/hmmbuild.i icarus/db/hmmpfam.i icarus/db/hmmsearch.i icarus/db/printscan.i icarus/db/prositesearch.i icarus/db/psiblast.i icarus/db/restrictionmap.i icarus/lion/emboss/antigenic.i icarus/lion/emboss/backtranseq.i icarus/lion/emboss/biosedn.i icarus/lion/emboss/biosedp.i icarus/lion/emboss/btwisted.i icarus/lion/emboss/cai.i icarus/lion/emboss/chaos.i icarus/lion/emboss/charge.i icarus/lion/emboss/checktrans.i icarus/lion/emboss/chips.i icarus/lion/emboss/compseqn.i icarus/lion/emboss/compseqp.i icarus/lion/emboss/consn.i icarus/lion/emboss/consp.i icarus/lion/emboss/cpgplot.i icarus/lion/emboss/cpgreport.i icarus/lion/emboss/cusp.i icarus/lion/emboss/cutseqn.i icarus/lion/emboss/cutseqp.i icarus/lion/emboss/dan.i icarus/lion/emboss/degapseqn.i icarus/lion/emboss/degapseqp.i icarus/lion/emboss/descseqn.i icarus/lion/emboss/descseqp.i icarus/lion/emboss/diffseqn.i icarus/lion/emboss/diffseqp.i icarus/lion/emboss/digest.i icarus/lion/emboss/distmatn.i icarus/lion/emboss/distmatp.i icarus/lion/emboss/dotmatchern.i icarus/lion/emboss/dotmatcherp.i icarus/lion/emboss/dotpathn.i icarus/lion/emboss/dotpathp.i icarus/lion/emboss/dottupn.i icarus/lion/emboss/dottupp.i icarus/lion/emboss/dreg.i icarus/lion/emboss/einverted.i icarus/lion/emboss/eprimer3.i icarus/lion/emboss/eprimers.i icarus/lion/emboss/equicktandem.i icarus/lion/emboss/est2genome.i icarus/lion/emboss/etandem.i icarus/lion/emboss/extractseqn.i icarus/lion/emboss/extractseqp.i icarus/lion/emboss/freakn.i icarus/lion/emboss/freakp.i icarus/lion/emboss/fuzznuc.i icarus/lion/emboss/fuzzpro.i icarus/lion/emboss/fuzztran.i icarus/lion/emboss/garnier.i icarus/lion/emboss/geecee.i icarus/lion/emboss/getorf.i icarus/lion/emboss/helixturnhelix.i icarus/lion/emboss/hmoment.i icarus/lion/emboss/iep.i icarus/lion/emboss/infoalignn.i icarus/lion/emboss/infoalignp.i icarus/lion/emboss/infoseqn.i icarus/lion/emboss/infoseqp.i icarus/lion/emboss/isochore.i icarus/lion/emboss/marscan.i icarus/lion/emboss/maskseqn.i icarus/lion/emboss/maskseqp.i icarus/lion/emboss/matchern.i icarus/lion/emboss/matcherp.i icarus/lion/emboss/megamerger.i icarus/lion/emboss/merger.i icarus/lion/emboss/msbarn.i icarus/lion/emboss/msbarp.i icarus/lion/emboss/needlen.i icarus/lion/emboss/needlep.i icarus/lion/emboss/newcpgreport.i icarus/lion/emboss/newcpgseek.i icarus/lion/emboss/octanol.i icarus/lion/emboss/palindrome.i icarus/lion/emboss/pasteseqn.i icarus/lion/emboss/pasteseqp.i icarus/lion/emboss/patmatdb.i icarus/lion/emboss/patmatmotifs.i icarus/lion/emboss/pepcoil.i icarus/lion/emboss/pepinfo.i icarus/lion/emboss/pepnet.i icarus/lion/emboss/pepstats.i icarus/lion/emboss/pepwheel.i icarus/lion/emboss/pepwindow.i icarus/lion/emboss/pepwindowall.i icarus/lion/emboss/plotconn.i icarus/lion/emboss/plotconp.i icarus/lion/emboss/plotorf.i icarus/lion/emboss/polydotn.i icarus/lion/emboss/polydotp.i icarus/lion/emboss/preg.i icarus/lion/emboss/prettyplotn.i icarus/lion/emboss/prettyplotp.i icarus/lion/emboss/prettyseq.i icarus/lion/emboss/pscan.i icarus/lion/emboss/recoder.i icarus/lion/emboss/remap.i icarus/lion/emboss/restover.i icarus/lion/emboss/restrict.i icarus/lion/emboss/revseq.i icarus/lion/emboss/seqmatchalln.i icarus/lion/emboss/seqmatchallp.i icarus/lion/emboss/seqretn.i icarus/lion/emboss/seqretp.i icarus/lion/emboss/showalignn.i icarus/lion/emboss/showalignp.i icarus/lion/emboss/showorf.i icarus/lion/emboss/showseqn.i icarus/lion/emboss/showseqp.i icarus/lion/emboss/shuffleseqn.i icarus/lion/emboss/shuffleseqp.i icarus/lion/emboss/sigcleave.i icarus/lion/emboss/silent.i icarus/lion/emboss/sixpack.i icarus/lion/emboss/splittern.i icarus/lion/emboss/splitterp.i icarus/lion/emboss/stretchern.i icarus/lion/emboss/stretcherp.i icarus/lion/emboss/supermatchern.i icarus/lion/emboss/supermatcherp.i icarus/lion/emboss/syco.i icarus/lion/emboss/tfscan.i icarus/lion/emboss/tmap.i icarus/lion/emboss/transeq.i icarus/lion/emboss/trimest.i icarus/lion/emboss/trimseqn.i icarus/lion/emboss/trimseqp.i icarus/lion/emboss/unionn.i icarus/lion/emboss/unionp.i icarus/lion/emboss/vectorstrip.i icarus/lion/emboss/watern.i icarus/lion/emboss/waterp.i icarus/lion/emboss/wobble.i icarus/lion/emboss/wordcount.i icarus/lion/emboss/wordmatchn.i icarus/lion/emboss/wordmatchp.i icarus/lion/emboss/installEmboss.i | Added a default entryview which is needed for pdf export to work |
| 2007/12/11 | kegg | icarus/db/kegggenome.it | fix to make sure that prisma has permission to unpack the kegggenome tarball |
| 2007/12/10 | ccds | icarus/db/ccds.i icarus/db/ccds.is web/WEB-INF/jsp/views/ccdsentry/ccdsentry.jsp | Added a status field, handling of the match_type column in the mouse data, and more robust behaviour when there are format changes |
| 2007/12/03 | ddbj | icarus/db/ddbjnew.i | correction for a wrong link definition between ddbjnew and genbankwgs |
| 2007/11/29 | kegg | icarus/db/kegggenes.is | Fix for an error in an earlier update, whch caused some indices to remain empty. After applying this fix please re-index kegggenes_na and kegggenes_aa, and rebuild the links to these databases |
| 2007/11/27 | kegg | icarus/db/keggorthology.is | Change to improve indexing of external refences in the class field |
| 2007/11/19 | unilib | icarus/db/unilib.is | Fixe for a unilib query results display problem |
| 2007/11/19 | genecards go_mysql | icarus/db/genecards.i icarus/db/gogeneproducts.i icarus/db/goterms.i | reweight some link definitions to get more reliable linking from goterm to embl/genbank |
| 2007/11/14 | kegg | icarus/db/kegg_species.i icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i icarus/db/lcommon.is icarus/db/lenzyme.is web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp | Added support for the new structure field in kegggenes, fixed a minor parsing problem for lenzyme, and updated the kegg species mapping file |
| 2007/11/14 | prisma | icarus/lion/prisma/dbSync.i | Fixed a problem with keeping remote file timestamps |
| 2007/11/13 | system | icarus/db/loader.i icarus/db/views.i | Added a jalview view for databases containing sequence alignments, and made a change so that saving a PDB entry using the CompleteEntry view results in indeed getting the full data file. Note that the new views.i and laoder.i file need to be merged with your copies of these files in SRSSITE |
| 2007/11/08 | genecards system | icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp | Added a product/service section to the entry display, which includes the new Genetex lines and Abcam lines. Also allow for the new DiscoverX line, but this is not yet used in the entry display. Note that you will have to merge the new href.i file with your copy in SRSSITE |
| 2007/11/08 | blocks | icarus/db/blocks.is | correction for alignment display |
| 2007/11/07 | kegg | icarus/db/kegggenome.i | Change to make sure the entryview for kegggenome does not show up in the list of views applicable to a query result |
| 2007/11/06 | cath | icarus/db/cath.i icarus/db/cath.is | Change needed to handle case sensitive ID values in cath. Note that we now use the extended cath code as primary identifier |
| 2007/11/06 | entrezgene system | icarus/db/entrezgene.is icarus/db/href.i | Change to allow for hypertext links to uniprot and ccds in the reference sequence section of the entry display. Please note that you need to merge href.i with your copy in SRSSITE |
| 2007/11/05 | cath | icarus/db/cath.i icarus/db/cath.is icarus/db/cath.it web/WEB-INF/jsp/views/cathentry/cathhierarchy.jsp | Changes to make sure the latest version of cath is downloaded by prisma, and a parser correction for version 3.1 |
| 2007/11/02 | medline | icarus/db/medline.i icarus/db/medlinenew.i icarus/db/medlinerelease.i icarus/db/medlineupdates.i | Added parts to the indexing of the links between medline and embl/genbank, so building these links will be done faster |
| 2007/11/02 | geneseq | icarus/db/geneseq.is | fix for indexing/display of the WPI number |
| 2007/11/01 | intact | icarus/db/intactcommon.is icarus/db/intactinteraction.i | corrections for the pdbid field and the link to reactome |
| 2007/11/01 | reactome | icarus/db/reactome.i icarus/db/reactome_schema.i | update for reactome version 22, and corrections for various link definitions |
| 2007/10/31 | system uniprot | icarus/db/dbxref.i icarus/db/uniprot.i icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i | Added support for the new refseq link in uniprot, including an indexed link between uniprot and refseqp (which will have to be build after applying this update). Note that the new dbxref.i file needs to be merged with your copy of this file in SRSSITE |
| 2007/10/31 | prints rebase | icarus/db/prints.i icarus/db/rebcomm.i | removed sorting from some fields which do not provide single values to sort on |
| 2007/10/30 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensemblproteinmodel.i | Updates for ensembl release 49, and some improvements for the display of the protein for ensembl transcripts |
| 2007/10/25 | geneseq | icarus/db/geneseq.is | fix needed to display all keywords when there are multiple keyword lines |
| 2007/10/09 | prisma | icarus/lion/prisma/prismaCheckClasses.i | Fix for problem regarding CPU timimngs returning a non interger value during reporting phase |
| 2007/10/08 | system uniprot ipi | icarus/db/href.i icarus/db/swissprot.is | Updated hypertext links for HGNC database |
| 2007/09/27 | chebi | icarus/db/chebi_schema.i | Schema update for Chebi release 37. There are no major changes |
| 2007/09/26 | prisma | icarus/lion/prisma/configurePrisma.i | fix for a problem when reconfiguring prisma meta update settings |
| 2007/09/24 | system | icarus/db/srsgen.i | Added BL2SEQ to DNASEQ_DATA and PROTSEQ_DATA so BL2SEQ appears in the applications drop down menu |
| 2007/09/21 | genecards | icarus/db/genecards.i | Added defaultEntryView to BIOALMA subentry database |
| 2007/09/20 | genecards | icarus/db/genecards.i | Added a list view for BioAlma to show data in tabular form |
| 2007/09/19 | prisma | etc/runPrisma | Added fix to keep SRSPRISMADATE sane when updating config files in a prisma run |
| 2007/09/17 | genbank refseq ddbj | icarus/db/genbank.is | Change needed to generate an entry creation date for entries which do not have a submission date |
| 2007/09/17 | prisma | icarus/workflows/moveIndicesPhase.i | Change to make sure the timestamp on indices/caches/sortsets are set when they are moved on line. This prevents srs from wanting to rebuild those when there is no need for it. This was happening in cases where the non-default mod timestamp is used for checking |
| 2007/09/14 | genbank refseq ddbj | icarus/db/genbankcommon.i | Fix for a problem which could cause the references to be printed twice when looking at a text entry |
| 2007/09/12 | genecards | icarus/db/genecards.i web/WEB-INF/jsp/views/genecardsentry/genecardsbioalma.jsp | Added an entry view for BioAlma sub-entry data. Also modified the sub-entry Id ranges so they more accurately reflect data size. The change in sub-entry Id ranges will require Genecards to be re-indexed. |
| 2007/09/10 | pdbfinder | icarus/db/pdbfinder.it | Added explanation of the ATOM and SEQRES fields |
| 2007/09/10 | geneseq | icarus/db/aageneseqsupp.i icarus/db/nageneseqsupp.i | Added napatent and aapatent concepts to Geneseq supp databases |
| 2007/09/07 | embl genbank refseq ddbj system | icarus/db/emblcommon.i icarus/db/emblnew.i icarus/db/emblnewfiles.it icarus/db/emblrelease.i icarus/db/gbemblcommon.is icarus/db/general.it | Changes for release 92 of EMBL. These include a number of new fields for all databases in EMBL format: FtStart and FtEnd can be used to query for features with start/end in a give range, FtRange can be used to find features which overlap with a range. We also added a field for EcNumber, DbXref and Locustag in the feature table. Applying these changes will cause disruption, as the new fields need to be indexed. We suggest you apply these changes with the next full update of EMBL, due soon. Also make sure your srsgen.i file is up to date |
| 2007/09/05 | genbank embl refseq ddbj | icarus/db/gbemblcommon.is | Fix for indexing problems for the ftrange field for single nucleotide features, and inproved the hypertext link from refseqp to refseq via the coded_by feature qualifier |
| 2007/09/05 | refseq | icarus/db/refseqnew.i icarus/db/refseqrelease.i | Reduced the chunksize for indexing, as some file containing large chromosomal entries are starting to require more memory |
| 2007/09/04 | system | icarus/db/getftseq.i | Fix for a problem which caused nested feature sequence feature retrieval to fail on some platforms |
| 2007/08/30 | transfac | icarus/db/tffactor.is | Minor fix for sequence comment html link |
| 2007/08/29 | genbank refseq ddbj | icarus/db/genbank.is | Minor fix to stop eating the first digit off date in the credate production. You will need to re-index the credate field |
| 2007/08/24 | prisma | icarus/lion/prisma/dbSync.i | Fixed a problem for keeping remote file dates after downloads when keepFileDates is set |
| 2007/08/23 | geneseq | icarus/db/geneseq.is | Added a space between consecutive GO identifiers to improve web display |
| 2007/08/21 | genbank embl refseq ddbj system | icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i icarus/db/general.it icarus/db/srsgen.i | Added a number of new fields to the sequence features for data in genbank format: FtStart and FtEnd can be used to query for features with start/end in a give range, FtRange can be used to find features which overlap with a range. We also added a field for EcNumber and LocusTag in the features tables, and expanded the data fields to provide both submission and latest udpate dates. Applying these changes will cause disruption, as the new fields need to be indexed, and we suggest you apply this change with the next release of genbank. Note that the new copy of srsgen.i needs to be merged with your copy in SRSSITE |
| 2007/08/21 | entrezgene | icarus/db/entrezgene.is | Correction for a change in the entrezgene data: the Gene source id has moved to a different xml tag |
| 2007/08/21 | refseq | icarus/db/refseqnew.i icarus/db/refseqrelease.i | Made sure the recently added feature view also works for refseqnew and refseqrelease |
| 2007/08/20 | unigene | icarus/db/unigene.i | Removed links definition for SwissProt databases, added definition for UNIPROT virtual database |
| 2007/08/20 | go_xml | icarus/db/go.it | Updated GO ftp location to point ftp.geneontology.org |
| 2007/08/16 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Some minor changes for ensembl version 46 |
| 2007/08/15 | embl | icarus/db/emblnew.it icarus/db/emblnewfiles.it | Change to make sure prisma also picks up deleted annotated contigs |
| 2007/08/14 | pdb | icarus/db/pdb.i icarus/db/pdb.is web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp web/WEB-INF/jsp/views/pdbentry/pdbmodres.jsp | Added support for the MODRES fields in the Entry view |
| 2007/08/14 | pdb | icarus/db/pdb.is | Added translation for 2 letter na codes so sequence appears in views |
| 2007/08/14 | web/WEB-INF/jsp/views/pdbentry/pdbhetatoms.jsp | Corrected speelling of centre to center so web interface recognises it | |
| 2007/08/13 | pdb | web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp web/WEB-INF/jsp/views/pdbentry/pdbhetatoms.jsp | Added support for the Heterogen atom data |
| 2007/08/13 | ensembl_mysql | web/WEB-INF/jsp/views/ensemblproteinentry/proteinrefs.jsp | Correct formatting for non-named protein domain list feature table |
| 2007/08/10 | pdb | icarus/db/pdb.is | Added support for multiple entries in SPRSDE line |
| 2007/08/09 | clustalw | icarus/db/clustalw.i icarus/db/clustalwcommon.i icarus/db/nclustalw.i | Added support for clustalw2. Uncomment ClustalIter_Option and relevant command in apllication files to enable. Ensure location and name of clustalw program is correct |
| 2007/08/03 | pdb | icarus/db/pdbmodel.it | Correction for the searchname used by prisma for pdbmodel on the download site |
| 2007/08/01 | cath embl genbank genecards interpro medline refseq | icarus/db/cath.it icarus/db/emblrelease.it icarus/db/genbanknew.it icarus/db/genecards.it icarus/db/interpro.it icarus/db/medlinenew.it icarus/db/refseqnew.it icarus/db/refseqpnew.it | Added a getReleaseCommand, so prisma can set the release number after an update |
| 2007/08/01 | entrezgene | icarus/db/entrezgene.i icarus/db/entrezgene.is | Added a separate field for Gene Onthology IDs |
| 2007/08/01 | go_mysql reactome | icarus/db/gogeneproducts.i icarus/db/reactome.i | Added links to the DDBJ databases |
| 2007/08/01 | domo | icarus/db/domo.it | Change so prisma will download domo from the ebi, as the original download site no longer exists. Note that the domo data is static |
| 2007/08/01 | fasta | icarus/db/fasta.is | Change so the fasta parser can work with results from FastS, FastF and FastM |
| 2007/08/01 | embl | icarus/db/emblnew.it icarus/db/emblnewfiles.it | Change to include the expanded and annotated contig files in the embl updates. |
| 2007/08/01 | system | icarus/db/dbxref.i | Change which allows to make hypertext links to uniprot from EMBL/GenBank feature tables |
| 2007/08/01 | embl | icarus/db/embl.is | Fix for a problem with constructing contig sequences when tincaching is enabled |
| 2007/08/01 | kegg | icarus/db/kegg_species.i | Updated Kegg species mapping file |
| 2007/08/01 | system | icarus/db/standard.is | added a jobname production. This is usefull to find out in which datafile an entry resides |
| 2007/07/31 | prisma | etc/conf/templ-prisma icarus/lion/prisma/configurePrisma.i | Added wsrefresh/clearCache.sh as default post installation command. Note that this will only be picked up with a fresh new installation of prisma |
| 2007/07/31 | geneseq | icarus/db/geneseq.is | Correction for a problem with sequences during indexing |
| 2007/07/30 | pdb | icarus/db/pdb.it icarus/db/pdbmodel.it | Correction for the address of the USA download site |
| 2007/07/27 | geneseq system | icarus/db/aageneseq.i icarus/db/concepts.i icarus/db/geneseq.is icarus/db/nageneseq.i | Changes to incoporate new external links information into Geneseq databases |
| 2007/07/27 | geneseq | icarus/db/nageneseq.i | Fix for GO link from proteinSeq concept to nucleicAcidSeq concept |
| 2007/07/26 | prisma | icarus/workflows/buildPhase.i | Removal of partial indices could couse I/O bottlenecks in some circumstances. To prevent this prisma will now use a batch queueing system (if configured) to distribute these tasks |
| 2007/07/25 | pdb | web/WEB-INF/jsp/views/pdbentry/pdbtext.jsp | Fix for a problem where browser would interpret some PDB content as html tags |
| 2007/07/25 | medline | icarus/db/medlinecommon.i | Fix for a problem which caused EC numbers ending up in the CAS number index |
| 2007/07/24 | genbank refseq ddbj | icarus/db/genbank.is icarus/db/genbankcommon.i | Added EC Number and Molecular Weight as fields to refseqp |
| 2007/07/24 | embl genbank refseq ddbj | icarus/db/embl.i icarus/db/emblnew.i icarus/db/emblrelease.i icarus/db/emblwgs.i icarus/db/emblwgsnew.i icarus/db/emblwgsrelease.i icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.i icarus/db/genbanknew.i icarus/db/genbankrelease.i icarus/db/genbankwgs.i icarus/db/refseq.i | Added a new view (FeatureView) for sequence features |
| 2007/07/24 | affymetrix | icarus/lion/affymetrix/affyannot.i | Change weights on some links to prevent unwanted link paths in ceratin link queries |
| 2007/07/24 | pdb | icarus/db/pdb.it icarus/db/pdbmodel.it | Changes to allow prisma to download the newly remdiated PDB datafiles. The changes have no effect in SRS but you may need to check that external software (like structure viewers) is compatable with the new data. See http://remediation.wwpdb.org/ for more information. Note that by default we download pdb from the ebi (European) site. If you wish to download from the US site, please edit the file, commenting out/in the relevant lines |
| 2007/07/24 | ddbj | icarus/db/ddbj.i icarus/db/ddbjnew.i icarus/db/ddbjrelease.i icarus/db/ddbjwgs.i | Reorganised links, and added a new view for sequence features. Note that you also need to update gbemblcommon.i and gbemblcommon.is |
| 2007/07/23 | geneseq | icarus/db/geneseq.is | Change to provide more information in fasta headers with geneseq sequences |
| 2007/07/18 | uniprot ipi | icarus/db/swissprot.is | Change to allow for the use of a "n" in EC numbers (expected to appear in in uniprot in the near future) |
| 2007/07/17 | system | icarus/db/dbxref.i icarus/db/href.i | Added support for the new phargkb link in uniprot. Note that the new dbxref.i and href.i files need to be merged with your copies of these files in SRSSITE |
| 2007/06/28 | system | icarus/db/mesh.it | Change to make sure we only download the desc.xml file for the mesh database (mesh is used as a hidden database to provide synonyms) |
| 2007/06/28 | iprmatches | icarus/db/iprmatches.i icarus/db/iprmatches.it web/WEB-INF/jsp/views/iprmatchesentry/iprmatchesentry.jsp web/WEB-INF/jsp/views/iprmatchesentry/iprmatcheslist.jsp web/WEB-INF/jsp/views/iprmatchesentry/iprmatchestable.jsp | Changes to handle the new format of the iprmatches data, found in the match_complete.xml file which comes with release 15.1 of interpro. The changes are incompatible with the old match.xml file which came with earlier releases, you have to make sure you have the new datafile in place when you apply this fix, and re-index iprmatches |
| 2007/06/28 | chebi | icarus/db/chebi_schema.i | Updated schema for chebi release 34. There are no significant changes |
| 2007/06/27 | emboss | icarus/lion/emboss/emboss.is | Added optionality to the ln production to account for the abscence of an end of line character at the end of the file |
| 2007/06/25 | system | icarus/db/standard.is | Minor fix so iword1a production will index the character 0. |
| 2007/06/22 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensemblgene.i icarus/db/ensembltranscript.i | Correction for the links from ensembl to entrezgene |
| 2007/06/21 | embl | icarus/db/embl.is | Change to allow for multiple genome projects, as is allowed in EMBL 91 |
| 2007/06/20 | prisma | icarus/workflows/linkPhase.i | Fix for a problem where in some cases prisma would not build link indices for a newly indexed database |
| 2007/06/20 | embl | icarus/db/emblnew.it icarus/db/emblnewfiles.it | Fix for a problem where prisma would not remove obsolete files for the emblnew database |
| 2007/06/19 | uniprot | icarus/db/uniprotvarsplic.is | Fixed problem with no entryName being specified |
| 2007/06/18 | system | icarus/db/dbxref.i icarus/db/href.i | Added a few new hypertext links for uniprot. Note that dbxref.i and href.i need to be merged with your copies of these files in SRSSITE |
| 2007/06/18 | genecards | icarus/db/genecards.is | Fix for wrong hypertext link to ensembl |
| 2007/06/15 | prisma | icarus/lion/prisma/inspectReport.i | Another fix to increase stability for quality report generation |
| 2007/06/15 | prisma | icarus/lion/prisma/dbSync.i | Change so prisma will pick up the correct Email address used for anonymous logins from the prisma config file |
| 2007/06/14 | ensembl_mysql | icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i | Small changes for ensembl release 45 |
| 2007/06/13 | uniprot | icarus/db/uniprotvarsplic.is | Added hypertext link to uniprot entry in description line |
| 2007/06/13 | kegg | icarus/db/lcommon.is | Fix for a harmless parsing error thrown when build readlinks from lenzyme |
| 2007/06/13 | kegg | icarus/db/kegggenes.is | Fix for a problem where the kegggenes databases would contain some duplicate accession numbers as a result of wrong species assignments |
| 2007/06/12 | uniprot ipi | icarus/db/swissprot.is | Fix for Splice variant href in comments field so it appears in the complete entry as well as the entry view |
| 2007/06/12 | uniprot ipi | icarus/db/swissprot.is | Fix to correct problems with IsoId href not correctly linking |
| 2007/06/08 | uniprot ipi | icarus/db/swissprot.is | Added hypertext links for the Web Resources in the comment field |
| 2007/06/07 | chebi | icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebidatamodel.i web/WEB-INF/jsp/views/chebientry/chebientry.jsp | Changes to allow for some recent schema changes and fixes for various display problems |
| 2007/06/07 | kegg | icarus/db/lcompound.i |
