SRS 8.1 Parser Updates

Updates of SRS files since the release of SRS 8.1

This page lists file updates for the folowing SRS8.1 distribution directories:RSS Feed

  • icarus/db (flatfile/xml parsers, .i .it files)
  • icarus/lion/emboss (emboss definition files)
  • srstags/srstags/web/views (jsp views)
  • icarus/workflow (srscheck)
  • icarus/lion/prisma (prisma)

If you download files from here, please make sure you install them in the correct SRS directory, and if you download them to a Windows machine, please make sure you do not accidentally insert DOS control characters into the files. (you may want to use the dos2unix utility on your unix box to ensure this).

Updates are also available by ftp (login required) from downloads.biowisdomsrs.com, directory parser/srs81 The updated files are also available as tarball: srs81updates.latest.tar.gz

We also provide a tarball just containing the files which have been updated upto a certain date: srs81updates.DATE.tar.gz from: http://downloads.biowisdomsrs.com/parser/srs81. For detail on the updates available in these tarballs, see the corresponding README.srs81updates.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 SRS81 parser updates are announced the moment they are available: http://downloads.biowisdomsrs.com/parser/rss/srsparser81.xml We also announce updates via a mailing list (Important fixes inmediately, small fixes/improvements are usually announced when we make a new srs81updates.DATE.tar.gz file. To subscribe to this mailing list please contact srs_support@biowisdom.com

Date / DatabasesFiles / Description
2011/11/27: geneticcode Minor change to add in release command for geneticcode
icarus/db/geneticcode.it
2010/10/11: system uniprot ipi Change so our hypertext links to ensembl can use the new simplified unique ID method of accessing the ensembl website (which is needed as uniprot no longer provides the species name in the ensembl reference line). Note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/swissprot.is
2010/10/07: taxonomy Small change in the way the species field is indexed - mainly to prevent virusses ending up with the name of their target as their species name
icarus/db/taxonomy.is
2010/09/28: kegg latest kegg species mapping file. Note that if you use prisma, prisma will generate this file automatically with each kegg update
icarus/db/kegg_species.i
2010/09/21: kegg Change needed as reaction pair field has been removed, and glycan fields is now located in the comments line, and drug references have been added
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/ldrug.i
srstags/srstags/web/views/lcompoundentry/lcompoundlinks.jsp
2010/09/21: kegg Change to suppress a parsing error (caused by a fault in the data) during indexing
icarus/db/pathway.is
2010/09/21: hssp Increased the number of parts used for indexing hssp
icarus/db/hssp.i
2010/09/10: kegg Support added to KEGGGENOME for KEYWORDS field
icarus/db/kegggenome.i
icarus/db/kegggenome.is
srstags/srstags/web/views/kegggenomeentry/kegggenomeentry.jsp
2010/08/13: system Change to allow for the new ProteinModelPortal link in uniprot. Please note that the new versions of href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/08/13: dbest Change to be more tolerant for non-standard characters in est names
icarus/db/dbest.is
2010/08/12: genecards system Update for genecards release 3.03. Please note that after unpacking the genecards tar archive, the data is now located in a subdirectory called old_website. We have modified the unpackcommand used by prisma to create symlinks to the directories in the old_website subdirectory, but if you are not using prisma, or if prisma has already downloaded and unpacked the file, you may have to create the relevant symlinks manually. Also not that the new copy of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecardstar.it
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2010/08/05: imgt Change to allow for longer entrynames, as found in the latest release of imgt
icarus/db/imgt.i
2010/06/18: system Added support for several new ensembl hypertext links in uniprot. Please note that the new version of href.i and dbxref.i will need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/06/01: uniref Change so we build the link between uniref50 and uniref90 in parts, in order to reduce memory usage
icarus/db/uniref90.i
2010/05/21: system interpro iprmatches Updated, added and fixed various hypertext links for interpro and iprmatches. Please note that the new version of href.i needs to ne merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/interpro.is
icarus/db/iprmatches.is
2010/05/13: genecards system Added support for the new LSDB and EPITOMICS lines in genecards. Please note that the new version of href.i needs to be merged with your copy of this file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2010/05/07: kegg latest version of the kegg species mapping file. Note that if you use prisma to keep your data up-to-date prisma will regenerate this file when appropriate
icarus/db/kegg_species.i
2010/05/04: system Added support for the new ucd-2dpage link in uniprot. Please note that you will hevato merge the new version of dbxref.i and href.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/03/29: system Added support for the new conoserver, genolist and mint links in uniprot. Please note that the new versions of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/03/05: system uniprot ipi Added support for the new SUPFAM, ProtClustDB and EuPathDB links in uniprot. Please note that you will have to merge the new versions of href.i and dbxref.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2010/03/03: genpept Change to allow for the fact that genpept is now distributed as multiple files (the single file available before has become too large to handle for the genpept ftp server)
icarus/db/genpeptrelease.it
2010/02/11: system kegg Important change for the kegg genome database. Please see README.KEGGGENOME for full details. Note that the new verson of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genKeggSpecies.i
icarus/db/href.i
icarus/db/kegg_species.i
icarus/db/kegggenome.i
icarus/db/kegggenome.is
srstags/srstags/web/views/kegggenomeentry/kegggenomeentry.jsp
2010/01/26: system uniprot ipi Added support for new db link in Uniprot, to eggNOG. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2010/01/26: genecards Correction for the prisma command which sets the release number of genecards after an update
icarus/db/genecards.it
2010/01/25: kegg Removed a feature which is specific for srs8.2/srs8.3
icarus/db/keggorthology.i
2010/01/21: unigene Re-introduced the exp and rexp fields for unigene, as these fields have re-appeared in the data. After applying this update you will have to index these two fields
icarus/db/unigene.i
icarus/db/unigene.is
srstags/srstags/web/views/unigeneentry/uniggeneral.jsp
2010/01/15: kegg Added support for the new INTERACTION line in the kegg drug database. After applying this update, please re-index ldrug
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2010/01/15: medline The 2010 release of medline contains a newly structured Comments and Correction section. We have now taken advantage of this to add a Comments subentry for medline, which allows searching by pubmed id and comment type (retraction, comment, citation etc). After applying this update you will have to re-index the medline databases.
icarus/db/medline.i
icarus/db/medline.is
icarus/db/medlinecommon.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
icarus/db/medlineupdates.i
srstags/srstags/web/views/medlineentry/medlineentry.jsp
2010/01/11: genecards Change to make sure that prisma will download the correct tar archive for genecards
icarus/db/genecardstar.it
2010/01/06: system kegg Change to allow for the new DISEASE line in the Kegg gene databases. After applying this update please index the new disease field. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
srstags/srstags/web/views/kegggenesentry/kegggenesentry.jsp
2009/12/18: genecards Updates for release 2.41.1 of genecards. Please note that if you use prisma to keep your databases up to data, prisma will download the wrong tar archive if you do no apply these changes. If prisma has already downloaded the wrong tar archive, remove the Genecards.tar.gz file from the data directory to force prisma to download it again.
icarus/db/genecards.is
icarus/db/genecardstar.it
2009/12/14: kegg To allow for the increasing size of kegggenes we changed the link index between kegggenes and taxonomy so it is build in parts
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
2009/12/09: kegg Small change to prevent a parsing error with the new map07222 entry in the kegg pathway database
icarus/db/pathway.is
2009/12/09: kegg Update for the kegg species mapping file. Note that if you use prisma to maintain your databases, this file will be generated automatically by prisma
icarus/db/kegg_species.i
2009/12/08: pfam Change needed to build read-links for pfamc
icarus/db/pfam.is
2009/12/03: pfam Changes for release 24 of pfam. If you have already installed that data release, please re-index all pfam databases after applying these parser updates
icarus/db/pfam.is
icarus/db/pfama.i
icarus/db/pfamc.i
2009/12/03: medline Update for some small dtd changes in the 2010 release of medline. You shoukd preferably apply this update before you index the 2010 release, which is expected to become available mid December
icarus/db/medlinecommon.i
2009/12/01: emboss Minor change to allow colour postscript output for EMBOSS tools that produce colour graphics
icarus/lion/emboss/dotpathn.i
icarus/lion/emboss/dotpathp.i
icarus/lion/emboss/pepnet.i
icarus/lion/emboss/pepwheel.i
icarus/lion/emboss/plotorf.i
icarus/lion/emboss/prettyplotn.i
icarus/lion/emboss/prettyplotp.i
icarus/lion/emboss/syco.i
2009/11/23: kegg Added support for the new METABOLISM field in the kegg drug database
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2009/11/19: kegg Fix for a problem which occurs if the sequence length is missing in the data
icarus/db/kegggenes.is
2009/10/30: kegg Added support for the new literature references in the kegg orthology database. After applying this update, re-index keggorthology, and if you have medline, also build the link indices to medline
icarus/db/keggorthology.i
icarus/db/keggorthology.is
srstags/srstags/web/views/keggorthology/keggorthologyentry.jsp
2009/10/30: kegg Correction for the way authors are indexed/displayed for the kegg genome database
icarus/db/kegggenome.is
2009/10/22: entrezgene system Change to allow for a change in the way links to the reactome database are provided. Please note that the new href.i file needs to merged with your copy of that file in SRSSITE
icarus/db/entrezgene.is
icarus/db/href.i
2009/10/21: kegg latest kegg species mapping file. Note that if you have prisma this file will be automatically re-generated when the kegg databases are updated
icarus/db/kegg_species.i
2009/10/19: pfam Allow for a new line in the pfamA data, and change the download location for the pfam databases to use ftp.sanger.ac.uk
icarus/db/pfam.i
icarus/db/pfam.is
icarus/db/pfama.i
icarus/db/pfama.it
icarus/db/pfamb.i
icarus/db/pfamb.it
icarus/db/pfamc.i
icarus/db/pfamc.is
icarus/db/pfamc.it
icarus/db/pfamhmm.i
icarus/db/pfamhmm.is
icarus/db/pfamhmm.it
icarus/db/pfamseed.i
icarus/db/pfamseed.it
2009/10/15: system Added support for the new genevestigator link in uniprot. Please note that the new dbxref.i and href.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/10/02: entrezgene Added a test which checks if the entrezgene xml file is properly terminated. This will prevent prisma from moving the data online in case the conversion from ASN1 has failed, but the gene2xml program has exited cleanly
icarus/db/entrezgene.it
2009/09/17: refseq Change so prisma will not download the refseq wgs master record files, as these do not contain sequence information
icarus/db/refseqrelease.it
2009/09/15: refseq Change so we build the link between refseqrelease and refseqprelease in parts, as building the link in one part now requires more than 4GB of memory
icarus/db/refseqrelease.i
2009/09/14: interpro Fix for a display problem with interpro entries which have embedded an CDATA tag in the abstract field
icarus/db/interpro.is
2009/09/08: kegg Change to allow for the fact that the kegg drug database is now provided in a separate tar archive
icarus/db/kegg_images.i
2009/09/04: system Change to allow for the new STRING link in the uniprot DR lines. Please note that you wil have to merge the new dbxref.i and href.i files with your versions of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/08/28: system kegg Changes needed for the latest version of the kegg pathway database. There have been significant changes in the way references to other kegg databases are provided, and without this update these will not work in SRS. Note that the new pathway.is file is not backwards compatible with previous versions of the pathway data, so you will need to ensure that no old data is left in your pathway data directories (if you have SRS prisma, prisma will do that automatically). Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE. After applying this update you will have to re-index pathway, and rebuild links to other kegg databases
icarus/db/href.i
icarus/db/pathway.i
icarus/db/pathway.is
2009/08/25: hmmer Corrected the hmmsearch parser as some SRS8.2 specific code had slipped in
icarus/db/hmmsearch.is
2009/08/25: uniprot ipi Fix for a problem with indexing the ID field for uniprot
icarus/db/swissprot.is
2009/08/24: kegg Change so we no longer try to extract gif image files from the pathway tar archive, as pathway has now fully switched to png images
icarus/db/pathwaytar.it
2009/08/04: system Added hypertext link support for the new CTD reference in uniprot. Please note that the new dbxref.i and href.i files need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/07/29: unigene uniprot Change made to unigene, uniprot_swissprot and uniprot_trembl to fix problem with read links
icarus/db/unigene.i
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2009/07/23: homologene system Moved the EntrezGeneId field defintion from homologene.i to to srsgen.i as it is also used for unigene. Please note that the new version of srsgen.i needs to be merged with your copy of srsgen.i in SRSSITE
icarus/db/homologene.i
icarus/db/srsgen.i
2009/07/23: unigene Removed the link between unigene and entrezgene we recently added, as that link was already defined in entrezgene.i
icarus/db/unigene.i
2009/07/21: system uniprot ipi Added support for new UCSC link in Uniprot, and updated links to Gene3D, ArrayExpress, GeneCards, PDBsum. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/swissprot.is
2009/07/21: cath update for the new download site for cath data
icarus/db/cath.it
2009/06/23: unigene Replaced the redundant/obsolete LocusLink field with a EntrezGeneId field, and removed some other fields which are no longer used. After applying this update you may want to rename the unigene loc indices to egid, and remove the pla, exp, rexp, gn and per indices
icarus/db/unigene.i
icarus/db/unigene.is
srstags/srstags/web/views/unigeneentry/sequence.jsp
srstags/srstags/web/views/unigeneentry/uniggeneral.jsp
2009/06/19: system kegg Some more improvements for kegg pathway: added a field for glycan IDs, which are now also hypertext linked in the entry view. Fixed hypertext links in the new Metabolic Pathways entries. Made sure that png image files are unpacked from the pathway tar archive which prisma downloads. Please note that the new version of href.i needs to be merged with your copy in SRSSITE
icarus/db/href.i
icarus/db/pathway.i
icarus/db/pathway.is
icarus/db/pathwaytar.it
2009/06/11: hmmer Change to handle entry IDs which contain a ":"
icarus/db/hmmsearch.is
2009/06/09: hmmer Change to keep hmmsearch hit names short
icarus/db/hmmsearch.is
2009/06/02: medline Change to handle a new layout used for some EC numbers in medline
icarus/db/medline.is
2009/06/01: system Added support for the new PMAP-CutDB link in uniprot. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/05/08: system Added support for the new oma hypertext link in uniprot. Please note that the new version of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/04/30: pdb Change to handle a slight format change in the resolution remark line. After applying this fix, please re-index the resolution (res) field
icarus/db/pdb.is
2009/04/16: system Added support for the new CAZy links in uniprot. Please note that the new dbxref.i and href.i files need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/04/06: prosite Fix to handle a situation in prositedoc where the entry contains two PDOC start lines
icarus/db/prositedoc.is
2009/03/23: genecards system Added support for the new NOVUS line in genecards. Note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2009/03/16: embl implemented a slightly more robust method of identifying the start of an entry in embl
icarus/db/embl.is
2009/03/12: genbank refseq Changes to allow for the new DBLINK link in GenBank. Since this line will replace the existing PROJECT line, we have merged these two, and use the GenomeProject field for its content (this to keep the differences between the EMBL and GenBank implementations in SRS to a minimum
icarus/db/genbank.is
icarus/db/genbankcommon.i
2009/03/11: prints A small parser change for release 39 of PRINTS
icarus/db/prints.is
2009/03/11: clustalw Fix for a problem with the display of sequence names in table views, fixed for a problem where wrong sequence names could be assigned, and improved htmlization of sequence names
icarus/db/clustalw.is
2009/03/10: fasta Fix for a parsing problem with fasta results from databases with more than 2.1 billion residues (this results in a slightly different Library line in the output)
icarus/db/fasta.is
2009/03/09: system Added hypertext link support for the new tcdb and pathway interaction references in uniprot. Note that you will have to merge the new copies of these files with your versions in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/03/09: genbank refseq Changes to allow for the new DBLINK link in GenBank. Since this line will replace the existing PROJECT line, we have merged these two, and use the GenomeProject field for its content (this to keep the differences between the EMBL and GenBank implementations in SRS to a minimum. There is no need to re-index after applying this update.
icarus/db/genbank.is
icarus/db/genbankcommon.i
2009/03/02: genbank refseq Fix for a display issue with complete refseqp entries
icarus/db/genbankcommon.i
2009/02/23: genbank Change so prisma will no download the wgs master record files, as they do not contain sequence information
icarus/db/genbankwgs.it
2009/02/23: dbsts Workaround for a few parsing errors during indexing
icarus/db/dbsts.is
2009/02/13: system Change to handle some uniprot entries which have more than 4000 external library references (DR lines). No re-indexing is required, but the new version of srsgen.i needs to be merged with your copy of this file in SRSSITE
icarus/db/srsgen.i
2009/02/11: system Changes to allow for the new links to Bgee and IPI in uniprotKB. Note that the new dbxref.i and href.i files need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/01/27: system uniprot ipi Changes to allow for the new reference to brenda in UniProt - note that the new href.i and dbxref.i files need to merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2009/01/20: pfam Change to reflect the fact that swisspfam is no longer available for download
icarus/db/swisspfam.it
2008/12/17: system Added support for PRIDE and GeneCards hypertext links in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/12/16: genbank refseq Change to allow for a PrimaryAccession (pac) index of more than 4GB. Note that after applying this change all databases in GENBANK_FORMAT will become inaccesible and require a complete re-index
icarus/db/genbankcommon.i
2008/12/09: embl Change to allow for a PrimaryAccession (pac) index of more than 4GB. Note that after applying this change all databases in EMBL_FORMAT will become inaccesible and require a complete re-index.
icarus/db/emblcommon.i
2008/12/03: embl genbank refseq Some changes to prevent memory problems when indexing large genomic entries: Smaller parts for refseq, and a more efficient parsing of the feature table, as full chromosome entries have well over a million features in the feature table
icarus/db/embl.is
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/refseqnew.i
icarus/db/refseqrelease.i
2008/11/25: dbest Change needed to handle the increasing size of dbest. The comments field (cc) is now larger than 4GB, and the author (aut) field will be in the near future. After applying this update, the existing dbest_cc and dbest_aut indices will become unreadable. We would recommand to remove the existing dbest_cc.* and dbest_aut.* files and re-index.
icarus/db/dbest.i
icarus/db/dbest.is
2008/11/10: kegg system Change to make sure all kegg data is in sync with eachother (when prisma is used to keep the data up-to-date) - we no longer download the individual ligand sets (lenzyme, lcompound, ldrug, lglycan and lreaction), but use the tar archive we download to obtain the images for these datasets (kegg_images). Note that for this to work the off-line data directory for these datasets in srsdb.i needs to be set to the data directory used for the keggimages dataset.
icarus/db/kegg_images.i
icarus/db/lcompound.it
icarus/db/ldrug.it
icarus/db/lenzyme.it
icarus/db/lglycan.it
icarus/db/lreaction.it
icarus/db/srsdb.i
2008/11/10: kegg Change to make sure we can handle some hidden files which may be present in the kegggenome tar archive
icarus/db/kegggenome.it
2008/11/10: dbest dbgss Fix for a problem where SRS might mistake gzipped datafiles for actual datafiles
icarus/db/dbest.i
icarus/db/dbest.it
icarus/db/dbgss.i
icarus/db/dbgss.it
2008/11/10: kegg Latest kegg species mapping file. Note that it you have prisma, this file will be regenrated automatically when the kegggome database is updated
icarus/db/kegg_species.i
2008/11/10: entrezgene added an alternative unpackcommand which strips out the xml indentation for entrezgene - this will save about 35% on diskspace, but will make the raw xml less readable. Edit the file to comment in/out the command you would like to use
icarus/db/entrezgene.it
2008/11/06: system Added support for nextbio and xenbase hypertext links in uniprot - note that the new versions of href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2008/11/06: genecards system Changes for release 2.39 of GeneCards. Note that the new version of href.i needs to merged with your copy in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2008/10/16: uniprot ipi Fix for a problem with displaying subentry IDs
icarus/db/swissprot.is
2008/10/10: go_xml Small change to work around a dodgy data problem in the 20081005 release of go
icarus/db/go.is
2008/10/08: fasta Change to handle a small data output change between fasta3.5.3 and fasta3.5.4
icarus/db/fasta.is
2008/10/06: embl Fix so we do not download the tpa cumulative file ( we use the relevant sections instead ) . Note that for emblnew without emblnewfiles enabled, this also fixes a problem where the tpa/cumulative file was taking precendence over the main new/cumulative file, resulting in missing entries
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2008/10/01: embl removed a blast conversion section which had crept in
icarus/db/emblrelease.it
2008/09/24: system kegg Added internal hypertext links to the kegg orthology database from pathway entries. Note that the new href.i file needs to be merged with your copy in SRSSITE
icarus/db/href.i
icarus/db/pathway.is
2008/09/19: system Added display of comment and consortium with references in the main sequence databases
srstags/srstags/web/WEB-INF/tags/referencetable.tag
2008/09/19: kegg Various changes for lenzyme - removed the no longer present motif and disease fields, and allow for better processing and display of the now highly structured reference field(s) - note that after this update you will have to re-index lenzyme
icarus/db/lenzyme.i
icarus/db/lenzyme.is
srstags/srstags/web/views/lenzymeentry/lenzymeentry.jsp
2008/09/15: embl Change to allow for the TSA (Transcriptome Shotgun Assembly) section
icarus/db/embl.is
2008/09/11: embl Corrections for the annotated contig location and filenames used for deleted entries
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2008/09/10: kegg Changes to allow for the new PRDUCTS field in the kegg drug database
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2008/08/22: emboss Fix so showalign and remap will correctly use the colors specified by the user to color sequence regions
icarus/lion/emboss/remap.i
icarus/lion/emboss/showalignn.i
icarus/lion/emboss/showalignp.i
2008/08/18: reactome 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
icarus/db/reactome.i
icarus/db/reactome_schema.i
2008/08/07: system uniprot ipi 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
icarus/db/srsgen.i
icarus/db/swisscommon.i
icarus/db/swissprot.is
icarus/db/uniprot.i
srstags/srstags/web/views/swissentry/swissentry.jsp
2008/08/04: enzyme removed the disease (reference to omim) field, as it is no longer used
icarus/db/enzyme.i
icarus/db/enzyme.is
icarus/db/enzyme.it
srstags/srstags/web/views/enzymeentry/enzymeentry.jsp
2008/07/29: ensembl_mysql Changes for release 50 of ensembl
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2008/07/29: uniprot ipi 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
icarus/db/swissprot.is
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2008/07/29: system 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
icarus/db/dbxref.i
icarus/db/href.i
2008/07/28: iprmatches fix for links to prodom entries in iprmatches
icarus/db/iprmatches.is
2008/07/02: kegg Added support for the new Source and Component fields in the kegg drugs database (ldrug)
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2008/07/02: chebi Update for small chebi schema change in release 46
icarus/db/chebi_schema.i
2008/06/24: genecards Change to allow for teh mew MilliPore references in GeneCards
icarus/db/genecards.i
icarus/db/genecards.is
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2008/06/12: system Added support for the new hogenom and hovergen hypertext links in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/06/09: kegg fix for a problem with hypertext links from lenzyme to lcompound
icarus/db/lenzyme.is
2008/06/02: embl genbank 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
icarus/db/emblrelease.i
icarus/db/genbankrelease.i
2008/06/02: kegg Fixed a parsing issue with the description line in some entries
icarus/db/pathway.is
2008/05/27: system 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
icarus/db/dbxref.i
2008/05/14: system Correction for coding error which would break sequence feature retrieval
icarus/db/ftseq.is
2008/05/13: fasta Change needed to handle some cases of output from fasta3.5
icarus/db/fasta.is
2008/05/13: blast Change to make sure blast honours a user request to use ungapped aligments
icarus/db/blastn.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/tblastn.i
icarus/db/tblastx.i
2008/05/12: kegg system 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
icarus/db/kegggenome.i
icarus/db/kegggenome.is
icarus/db/srsgen.i
srstags/srstags/web/views/kegggenomeentry/kegggenomeentry.jsp
2008/05/12: kegg latest update for kegg species mapping file
icarus/db/kegg_species.i
2008/05/07: genbank embl refseq system 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
icarus/db/gbemblcommon.is
icarus/db/href.i
2008/05/06: system Added support for the new nmpdr link in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/04/29: system Change needed to handle a change in the way unknown gaps are specified in EMBL/GenBank/DDBJ Feature tables and contig construction representations
icarus/db/ftseq.is
2008/04/17: genecards system Updates for version 2.38 of genecards
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2008/04/01: fasta 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
icarus/db/fasta.is
2008/03/26: system 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
icarus/db/dbxref.i
icarus/db/href.i
2008/03/20: ensembl_mysql Changes for ensembl release 49
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2008/03/18: chebi Fixes for a few hypertext link problems in chebi entry display
icarus/db/chebidatamodel.i
2008/03/14: chebi Changes for release 42 of chebi. A mass and charge field have been added
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
srstags/srstags/web/views/chebientry/chebientry.jsp
2008/03/13: genecards Change so we do not include the synomyn origin (EG/HGNC) in the synonym index
icarus/db/genecards.is
2008/03/05: genbank refseq medline 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/srs81/UPDATE.20080503 before applying these updates
icarus/db/genbankcommon.i
icarus/db/medlinecommon.i
2008/02/29: system 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
icarus/db/dbxref.i
icarus/db/href.i
2008/02/21: emboss fix to prevent sixpack indexing to hang on an empty results file, which in some cases can bring down an SRS server
icarus/lion/emboss/sixpack.is
2008/02/14: medline 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)
icarus/db/medlinecommon.i
2008/02/07: system Added support for the new world-2dpage link in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/02/01: uniprot ipi 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
icarus/db/swissprot.is
2008/01/25: system 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
icarus/db/dbxref.i
icarus/db/href.i
2008/01/18: emboss 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".
icarus/lion/emboss/tmap.i
icarus/lion/packages/emboss.ip
2008/01/18: kegg Fixes for some issues with image maps when multiple pathway images are displayed
icarus/db/pathway.is
2008/01/17: system genbank embl refseq 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
icarus/db/dbxref.i
icarus/db/gbemblcommon.is
icarus/db/href.i
2008/01/17: kegg Fix to remove the duplicate display of map numbers
icarus/db/pathway.is
2008/01/03: geneseq Change to make sure prisma will download geneseq tar files, even if the size of the file has not changed
icarus/db/aageneseqtar.it
icarus/db/nageneseqtar.it
2008/01/02: pdbfinder 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.
icarus/db/pdbfinder.i
icarus/db/pdbfinder.is
srstags/srstags/web/views/pdbfinderentry/pdbfindersequence.jsp
2007/12/14: ensembl_mysql Update for release 48 of ensembl
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
2007/12/11: kegg fix to make sure that prisma has permission to unpack the kegggenome tarball
icarus/db/kegggenome.it
2007/11/29: kegg 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
icarus/db/kegggenes.is
2007/11/14: kegg Added support for the new structure field in kegggenes, fixed a minor parsing problem for lenzyme, and updated the kegg species mapping file
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
2007/11/08: genecards system 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
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2007/11/06: cath Change needed to handle case sensitive ID values in cath. Note that we now use the extended cath code as primary identifier
icarus/db/cath.i
icarus/db/cath.is
2007/11/06: entrezgene Change to allow for hypertext links to uniprot in the reference sequence section of the entry display
icarus/db/entrezgene.is
2007/11/05: reactome Added missing field definition
icarus/db/reactome.i
2007/11/05: cath Changes to make sure the latest version of cath is downloaded by prisma, and a parser correction for version 3.1
icarus/db/cath.i
icarus/db/cath.is
icarus/db/cath.it
srstags/srstags/web/views/cathentry/cathhierarchy.jsp
2007/11/01: reactome update for reactome version 22, and corrections for various link definitions
icarus/db/reactome.i
icarus/db/reactome_schema.i
2007/10/31: system uniprot 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
icarus/db/dbxref.i
icarus/db/uniprot.i
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2007/10/30: ensembl_mysql Updates for ensembl release 49, and some improvements for the display of the protein for ensembl transcripts
icarus/db/ensemblRDB.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensemblproteinmodel.i
2007/10/09: uniprot ipi Removed some debugging code in hypertext link generation
icarus/db/swissprot.is
2007/10/08: system uniprot ipi Updated hypertext links for HGNC database
icarus/db/href.i
icarus/db/swissprot.is
2007/09/27: chebi Schema update for Chebi release 37. There are no major changes
icarus/db/chebi_schema.i
2007/09/25: genbank refseq Correction for an error in the creation date production
icarus/db/genbank.is
2007/09/24: system Added BL2SEQ to DNASEQ_DATA and PROTSEQ_DATA so BL2SEQ appears in the applications drop down menu
icarus/db/srsgen.i
2007/09/17: genbank refseq Change needed to generate an entry creation date for entries which do not have a submission date
icarus/db/genbank.is
2007/09/14: genbank refseq Fix for a problem which could cause the references to be printed twice when looking at a text entry
icarus/db/genbankcommon.i
2007/09/10: pdbfinder Added explanation of the ATOM and SEQRES fields
icarus/db/pdbfinder.it
2007/09/07: embl genbank refseq system 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
icarus/db/emblcommon.i
icarus/db/emblnew.i
icarus/db/emblnewfiles.it
icarus/db/emblrelease.i
icarus/db/gbemblcommon.is
icarus/db/general.it
2007/09/05: genbank embl refseq 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
icarus/db/gbemblcommon.is
2007/09/05: refseq Reduced the chunksize for indexing, as some file containing large chromosomal entries are starting to require more memory
icarus/db/refseqnew.i
icarus/db/refseqrelease.i
2007/09/03: genbank refseq Added credate token, needed for indexing the creation date field in genbank/refseq
icarus/db/genbank.is
2007/08/30: transfac Minor fix for sequence comment html link
icarus/db/tffactor.is
2007/08/23: geneseq Added a space between consecutive GO identifiers to improve web display
icarus/db/geneseq.is
2007/08/23: geneseq Added support for additional external DB links
icarus/db/aageneseq.i
icarus/db/geneseq.is
icarus/db/nageneseq.i
2007/08/21: genbank embl refseq system 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
icarus/db/gbemblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/genbankcommon.i
icarus/db/general.it
icarus/db/srsgen.i
2007/08/21: clustalw Changed srs 8.2 value to valStr for Iterative option
icarus/db/clustalwcommon.i
2007/08/21: entrezgene Correction for a change in the entrezgene data: the Gene source id has moved to a different xml tag
icarus/db/entrezgene.is
2007/08/21: clustalw Fix to remove multiple line breaks that shouldn't be present
icarus/db/clustalw.i
icarus/db/nclustalw.i
2007/08/20: unigene Removed links definition for SwissProt databases, added definition for UNIPROT virtual database
icarus/db/unigene.i
2007/08/20: go_xml Updated GO ftp location to point ftp.geneontology.org
icarus/db/go.it
2007/08/16: ensembl_mysql Some minor changes for ensembl version 46
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2007/08/15: embl Change to make sure prisma also picks up deleted annotated contigs
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2007/08/14: pdb Added support for the MODRES fields in the Entry view
icarus/db/pdb.i
icarus/db/pdb.is
srstags/srstags/web/views/pdbentry/pdbentry.jsp
srstags/srstags/web/views/pdbentry/pdbmodres.jsp
2007/08/14: pdb Added translation for 2 letter na codes so sequence appears in views
icarus/db/pdb.is
2007/08/13: ensembl_mysql Correct formatting for non-named protein domain list feature table
srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp
2007/08/10: pdb Added support for multiple entries in SPRSDE line
icarus/db/pdb.is
2007/08/09: clustalw Added support for clustalw2. Uncomment ClustalIter_Option and relevant command in apllication files to enable. Ensure location and name of clustalw program is correct
icarus/db/clustalw.i
icarus/db/clustalwcommon.i
icarus/db/nclustalw.i
2007/08/03: genbank refseq Correction for an error when indexing the ECnumber and molecular weight field
icarus/db/genbank.is
2007/08/03: pdb Correction for the searchname used by prisma for pdbmodel on the download site
icarus/db/pdbmodel.it
2007/08/01: embl genbank genecards interpro medline refseq Added a getReleaseCommand, so prisma can set the release number after an update
icarus/db/emblrelease.it
icarus/db/genbanknew.it
icarus/db/genbankrelease.it
icarus/db/genecards.it
icarus/db/interpro.it
icarus/db/medlinenew.it
icarus/db/refseqnew.it
icarus/db/refseqpnew.it
2007/08/01: kegg Added a new Chebi ID field
icarus/db/lcompound.i
icarus/db/lcompound.is
2007/08/01: domo Change so prisma will download domo from the ebi, as the original download site no longer exists. Note that the domo data is static
icarus/db/domo.it
2007/08/01: embl Change to include the expanded and annotated contig files in the embl updates.
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2007/08/01: system Change which allows to make hypertext links to uniprot from EMBL/GenBank feature tables
icarus/db/dbxref.i
2007/08/01: embl Fix for a problem with constructing contig sequences when tincaching is enabled
icarus/db/embl.is
2007/08/01: kegg updated kegg species mapping file
icarus/db/kegg_species.i
2007/07/31: geneseq Correction for a problem with sequences during indexing
icarus/db/geneseq.is
2007/07/30: pdb Correction for the address of the USA download site
icarus/db/pdb.it
icarus/db/pdbmodel.it
2007/07/25: medline Fix for a problem which caused EC numbers ending up in the CAS number index
icarus/db/medlinecommon.i
2007/07/24: genbank embl refseq Added ECNumber and Molecular weight for refseqp and added handling of the PRIMARY line in refseq
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/genbankcommon.i
2007/07/24: pdb 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
icarus/db/pdb.it
icarus/db/pdbmodel.it
2007/07/23: geneseq Change to provide more information in fasta headers with geneseq sequences
icarus/db/geneseq.is
2007/07/18: uniprot ipi Change to allow for the use of a "n" in EC numbers (expected to appear in in uniprot in the near future)
icarus/db/swissprot.is
2007/07/17: system 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
icarus/db/dbxref.i
icarus/db/href.i
2007/06/29: chebi schema update for release chebi 34 and fixes for several display problems
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
2007/06/28: system 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)
icarus/db/mesh.it
2007/06/28: iprmatches 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
icarus/db/iprmatches.i
icarus/db/iprmatches.it
icarus/db/iprmatchestable.il
srstags/srstags/web/views/iprmatchesentry/iprmatchesentry.jsp
srstags/srstags/web/views/iprmatchesentry/iprmatcheslist.jsp
2007/06/25: system Minor fix so iword1a production will index the character 0.
icarus/db/standard.is
2007/06/22: ensembl_mysql Correction for the links from ensembl to entrezgene
icarus/db/ensemblRDB.i
icarus/db/ensemblgene.i
icarus/db/ensembltranscript.i
2007/06/21: embl Change to allow for multiple genome projects, as is allowed in EMBL 91
icarus/db/embl.is
2007/06/20: srscheck Fix for a problem where in some cases prisma would not build link indices for a newly indexed database
icarus/workflows/linkPhase.i
2007/06/20: embl Fix for a problem where prisma would not remove obsolete files for the emblnew database
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2007/06/18: system 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
icarus/db/dbxref.i
icarus/db/href.i
2007/06/18: genecards Fix for wrong hypertext link to ensembl
icarus/db/genecards.is
2007/06/14: ensembl_mysql Small changes for ensembl release 45
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2007/06/13: kegg Fix for a harmless parsing error thrown when build readlinks from lenzyme
icarus/db/lcommon.is
2007/06/08: uniprot ipi Added hypertext links for the Web Resources in the comment field
icarus/db/swissprot.is
2007/05/30: genecards Change to allow for the new BIOMOL line in genecards
icarus/db/genecards.is
2007/05/30: kegg Latest version of kegg species mapping file
icarus/db/kegg_species.i
2007/05/30: omim improved (but not perfected) indexing of journal names in omim. Note that due to the nature of the text it is not possible to do it correct for all entries
icarus/db/omim.is
2007/05/29: uniprot ipi After 29 May 2007, uniprot will contain a new evidence field. We have added support for this new field, and also added the EC Number (from the description line) as a separate field
icarus/db/swisscommon.i
icarus/db/swissprot.is
2007/05/29: genecards Fix for a reformatcommand which might fail on linux systems
icarus/db/genecardstar.it
2007/05/25: reactome Change for some schema changes in version 21 of reactome. Note that these files expect the database name to be Reactome21
icarus/db/reactome.i
icarus/db/reactome_schema.i
2007/05/25: genecards Corrected a wrong defintions for the link to goterm
icarus/db/genecards.i
2007/05/25: kegg system The recent change of the kegg download site, with the data for the kegg genes databases located in species specific subdirectories has resulted in very poor update performance by prisma (due to the large number of directories to check, and the poor connectivity to the kegg download site). So we have changed the download strategy to downloads the kegg genes tarball instead. Since this also provides the data for the kegg genome and kegg orthology databases, we also no longer do separate downloads for those. Note that we now no longer have the kegggenesdata and keggorthologydata helper libraries, and we expect the data for the kegggenome and keggorthology databases in the same directory as the kegggenes databases (see the changes is srsdb.i). The actual download process for the tarball is linked to the kegggenome database, so you must enable this library if you want prisma to update the kegggenes databases. Note that this update also requires you to update SRSLION/prisma/pretransPhase.i, otherwise prisma will get the dependies wrong. If you use prisma to udpate your icarus files, or the updateconfig script, please disable the kegggenesdata and keggorthologydata libraries before you do that.
icarus/db/kegggenes.i
icarus/db/kegggenes_na.it
icarus/db/kegggenome.it
icarus/db/keggorthology.i
icarus/db/keggorthology.it
icarus/db/ren_kegggenes.pl
icarus/db/srsdb.i
2007/05/10: entrezgene Change to the entrezgene parser so GO identifiers are indexed in the format GO:1234567
icarus/db/entrezgene.is
2007/05/10: dbest Modification to allow for the display of map submitter information
icarus/db/dbest.i
icarus/db/dbest.is
srstags/srstags/web/views/dbestentry/dbest.jsp
2007/05/03: ensembl_mysql Updates for ensembl release 44. There are some minor schema changes, which do not affect data retrieval/display
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2007/04/25: system Fix for entry names containing things like XXXX_0_XXXX in gcg format files to prevent parsing entering the wrong section of a production
icarus/db/standard.is
2007/04/20: transfac Fixed the binding site parsing so display fnuctions properly
icarus/db/transfaccommon.is
2007/04/16: embl removed a duplicate genomeProject production
icarus/db/embl.is
2007/04/12: geneticcode Removed sorting from name index. Multiple values present due to database updates
icarus/db/geneticcode.i
2007/04/12: kegg The people at Pathway Inc. have reorganised their download area (it now more resembles the academic site). We have changed the .it files for the various kegg databases so we will donwload the correct data. Also a few other changes for fieldnames in lglycan and lreaction, and we allow for the new sequence field in lcompound
icarus/db/kegg_images.i
icarus/db/kegg_species.i
icarus/db/kegggenes_na.it
icarus/db/kegggenome.it
icarus/db/keggorthology.it
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/lcompound.it
icarus/db/ldrug.it
icarus/db/lenzyme.is
icarus/db/lenzyme.it
icarus/db/lglycan.is
icarus/db/lglycan.it
icarus/db/lreaction.is
icarus/db/lreaction.it
icarus/db/pathwaytar.it
srstags/srstags/web/views/lcompoundentry/lcompgeneral.jsp
2007/04/05: system Change to allwo for the new hypertext link to burulist in uniprot. Note that dbxref.i and href.i need to be merged with your copies of these file in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2007/04/03: system uniprot ipi Change in the way we do hypertext links from uniprot to ensembl, ensuring we correctly go either to ensembl data locally in SRS or to the ensembl website. Please merge the new versions of dbxref.i and href.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2007/04/03: entrezgene Change to make sure protein names are displayed in the entrezgene entry
icarus/db/entrezgene.i
icarus/db/entrezgene_dm.i
2007/04/03: go_xml system Correction for hypertext links to evidence identifiers in RGD (RatGenomeDatabase). please merge the new href.i file with your copy of that file in SRSSITE
icarus/db/go.is
icarus/db/href.i
2007/04/03: genecards Updated the link definition for genecars to uniprot to use the uniprot primary accession number. After applying this update, please rebuild the genecards/uniprot link indices ("srsbuild i genecards uniprot_swissprot; srsbuild -i uniprot_trembl")
icarus/db/genecards.i
2007/03/28: system Correction for hypertext links to ensembl. Please merge the new version of href.i with your copy of that file in SRSSITE
icarus/db/href.i
2007/03/28: genbank embl refseq Small change so we no longer loose the end of line character in the display of translations of sequence features
icarus/db/gbemblcommon.is
2007/03/26: kegg Fix for a problem with displaying html-ized GIDs in tables
icarus/db/kegggenes.is
2007/03/21: system uniprot ipi Correcttion for the external hypertext link to merops. Note that the changes in href.i need to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/swissprot.is
2007/03/21: medline Following customer feedback we have added hypertext links to PubMed at the ncbi to our display of medline data.
srstags/srstags/web/views/medlineentry/medlineentry.jsp
srstags/srstags/web/views/medlineentry/medlineresults.jsp
2007/03/21: srscheck Small change in logic to make sure srs does not try to build sort sets for virtual RDB libraries
icarus/workflows/getSystemLibs.i
2007/03/20: kegg Updates species mapping file for the kegg databases
icarus/db/kegg_species.i
2007/03/19: dbest Change to allow for lower case sequence characters
icarus/db/dbest.is
2007/03/19: embl genbank refseq Changes to allow for the GenomeProject field in embl, which will appear in the next release 90, soon available. We made this a searchable field, and also made it searchable for genbank (we were already displaying it for genbank. Note that after applying this update, alltext searches in embl/genbank/refseq will fail due to missing GenomeProject indices. Once the GenomeProject field for all databases in embl or genbank format has been indexed this will work again. You may want to schedule downtime or use an alternative SRS installation to build the GenomeProject indices. You can also edit emblcommon.i and genbankcommon.i to keep the GenomeProject field a non-indexed field. There is a comment in these files indicationg which line needs commenting out for that.
icarus/db/embl.is
icarus/db/emblcommon.i
icarus/db/gbemblcommon.i
icarus/db/genbank.is
icarus/db/genbankcommon.i
2007/03/09: reactome Minor changes for reactome20. Note that reactome.i expects the database to be called "Reactome20"
icarus/db/reactome.i
icarus/db/reactome_schema.i
2007/03/07: kegg Change needed as the Kegg folks have renamed the "ORTHOLOG" field tag to "ORTHOLOGY" for the kegggenes dataset
icarus/db/kegggenes.is
2007/03/07: system Change to allow for the new CYGD reference in the latest release of uniprot
icarus/db/dbxref.i
icarus/db/href.i
2007/03/07: ensembl_mysql Changes for ensembl release 43 and added missing link definitions for the ensemble gene databases
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/exondatamodel.i
2007/03/07: kegg Reversed addition of Remark field definition in this file - already defined in srsgen.i
icarus/db/lreaction.i
2007/03/06: dbest dbgss Change so we use the .gz files for downloads of dbest and dbgss instead of the .Z files
icarus/db/dbest.it
icarus/db/dbgss.it
2007/02/22: system Added support for the new Cornea-2DPAGE, DOSAC-COBS-2DPAGE and REPRODUCTION-2DPAGE in uniprot. Note that the new href.i and dbxref.i files need to be merged with your copies of that file in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2007/02/21: userdna userprotein Increased maxline to 500 to allow for longer header lines
icarus/db/userdna.i
icarus/db/userprotein.i
2007/02/20: kegg Added Remark section for Reactions
icarus/db/lreaction.i
icarus/db/lreaction.is
srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp
2007/02/20: ensembl_mysql emboss Various fixes/improvements for ensembl: Corrected some link definitions, added links to Genbank/DDBJ, added Zebrafish markers, added Affy data for Zebrafish, C.elegans, Chimp and Mosquito. Fixed problems with command line fasta sequence retrieval with transcripts. Some restructuring to make adding new datasets easier
icarus/db/ExonsandIntrons.il
icarus/db/OutputExons.il
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
icarus/db/UTRandCDS.il
icarus/db/ensemblRDB.i
icarus/db/ensemblaffy.i
icarus/db/ensemblcommon.i
icarus/db/ensemblgene.i
icarus/db/ensemblmarker.i
icarus/db/ensemblseq.i
icarus/db/ensembltranscript.i
icarus/lion/packages/emboss.ip
icarus/lion/packages/ensemblRDB.ip
srstags/srstags/web/views/ensemblmarker/marker.jsp
2007/02/19: srscheck Removed icaIsDebug parameter - no longer useable
icarus/workflows/srsCheckMain.i
2007/02/16: srscheck Fix for a problem when using the -user mode of srscheck, resulting in indexfilenames fused to the directory name
icarus/workflows/coreCheckClasses.i
2007/02/13: pdb Change so we no longer see the Broken Pipe error message when indexing pdb
icarus/db/pdb.i
2007/02/09: uniseq Change to correct for a format change which caused the start/end/utr fields to be empty, and fix for a data display issue with the last sequence in a block of ests in the data file
icarus/db/uniseq.is
2007/02/07: uniest Change to allow for refseq style Accession numbers
icarus/db/uniest.is
2007/02/05: kegg Changes to allow for the new Activity field in the kegg drug database
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2007/02/02: uniest unigene uniseq Changes needed to handle uniest entries with tens of thousends of est sequences and the fact that uniseq now has so many entries that the ID structure we use is no longer sufficient. Also a fix so prisma does not download a number of files from the unigene ftp site which result in duplicate entries. Note that after this update you must re-index both unigene and uniest and all links to/from these databases
icarus/db/uniest.i
icarus/db/uniest.is
icarus/db/unigene.it
icarus/db/uniseq.i
icarus/db/uniseq.it
srstags/srstags/web/views/uniestentry/uniestentry.jsp
2007/01/29: kegg Change to the command which removes obsolete pathway files so it does not result in a failure if there are no obsolete files
icarus/db/pathwaytar.it
2007/01/29: kegg updated kegg species mapping file
icarus/db/kegg_species.i
2007/01/25: system Change so prisma will download the 2007 files for mesh
icarus/db/mesh.it
2007/01/25: kegg Changed kegggenes to use only index-links, as on some systems it has become difficults to build read-links
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
2007/01/25: reactome Changes for release 19 of reactome. Note that we expect the database name to be Reactome19. You can modify this by editing reactome.i
icarus/db/reactome.i
icarus/db/reactome_schema.i
2007/01/25: ensembl_mysql Schema and database name changes for ensembl 42 (MySql)
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2007/01/25: kegg latest species mapping file for the kegg databases
icarus/db/kegg_species.i
2007/01/17: genecards Another fix to extend array to 50 elements
icarus/db/genecards.is
2007/01/15: ensembl_mysql Added change for OMIM identifier for linking
icarus/db/ensemblRDB.i
2007/01/15: system Changed Interpro field used in Description View to use DF_Name
icarus/db/loader.i
2007/01/10: system uniprot ipi Change to allow for dip and maizegdb ij the DR lines of uniprot. Please note that dbxref.i needs to be installed in SRSSITE
icarus/db/dbxref.i
icarus/db/swissprot.is
2007/01/04: srscheck fix for srscheck/srsdo/srscheck reporting that virtual libs need rebuilding
icarus/workflows/moveIndicesPhase.i
2006/12/22: genecards Minor fix for araay element out of bounds problem
icarus/db/genecards.is
2006/12/21: system Added href for DIP and changed HREF for Gene3D
icarus/db/href.i
2006/12/21: uniprot ipi Added link production for DIP, changed link production for Gene3D
icarus/db/swissprot.is
2006/12/21: go_xml Increased the limit on number of associations displayed,and fixed a layout problem with associations
icarus/db/go.is
2006/12/21: genecards Some fixes to prevent parsing errors in the bioalma section
icarus/db/genecards.is
2006/12/19: go_xml Changes needed for the disappeaance of the "Number of associtaions" field, which caused no associations to be displayed at all
icarus/db/go.i
icarus/db/go.is
2006/12/18: system Extended id range for Sequence_Id to cope with > 1000 subentries within UNIGENE/UNIEST databases
icarus/db/srsgen.i
2006/12/15: kegg Added OMIM to list of db xrefs
icarus/db/lcommon.is
2006/12/15: ensembl_mysql Fixes/corrections of orthologs in the ensembl gene display, and corrections for link annotations which might cause ensembl to be queried when it should not
icarus/db/ensemblRDB.i
icarus/db/ensemblgene.i
icarus/db/ensemblgenemodel.i
icarus/db/ensembltranscript.i
2006/12/13: genecards Correction for a postprocessing command used for the genecards tar ball, which in some shells could result in the deletion of the tarball
icarus/db/genecardstar.it
2006/12/13: entrezgene Fix for incorrect processing of some Interactions information
icarus/db/entrezgene.is
2006/12/12: genecards system Changes to handle genecards version 2.35. The Genecards distribution file has changed, so please read the remarks at the top of genecards.i on how to install genecards
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecardstar.it
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2006/12/12: entrezgene Fix for incorrect processing of some Interactions information
icarus/db/entrezgene.is
2006/12/05: uniprot ipi Fix for GENE3d link in IPI which is different to the in UNIPROT
icarus/db/swissprot.is
2006/12/04: uniprot ipi Updated regularexpression for new version of Gene3D cross references
icarus/db/swissprot.is
2006/11/27: pdb Small change in the way we try to read the file listings fpr pdb at the rcsb frp site. This should prevent prisma from hanging in the check state fpr pdb
icarus/db/pdb.it
2006/11/24: hmmer pfam Change to allow for the change of the pfam data downloads site from ftp.genetics.wustl.edu to selab.janelia.org
icarus/db/hmmpfam.it
icarus/db/pfama.it
icarus/db/pfamb.it
icarus/db/pfamc.it
icarus/db/pfamhmm.it
icarus/db/pfamseed.it
icarus/db/swisspfam.it
2006/11/20: system Changes to allow for Drugbank, HPA and euHCVdb in the uniprot cross references section
icarus/db/dbxref.i
icarus/db/href.i
2006/11/15: uniref Added support for the uniparc ID in uniref
icarus/db/uniref.is
icarus/db/unirefcommon.i
srstags/srstags/web/views/unirefentry/uniref.jsp
2006/11/14: uniprot ipi Change to allow for a change in the format of the ID line in uniprot entries.
icarus/db/swissprot.is
2006/11/14: uniref Change to allow for the new isSeed parameter in uniref members
icarus/db/uniref.is
icarus/db/unirefcommon.i
2006/11/10: kegg Change to allow for the renaming of the OTHER_REAC tag to ALL_REAC. We keep calling this the OtherReaction field
icarus/db/lenzyme.is
2006/11/08: emboss Corrections for some errors in the application definitions for dreg and fuzzpro
icarus/lion/emboss/dreg.i
icarus/lion/emboss/fuzzpro.i
2006/11/06: medline Added code to eliminate various very common words from the medline generic text indices - this behaviour can by modified by editing the stopwords list at the top of medline.is
icarus/db/medline.is
2006/11/06: geneseq Improved display of patent assignee field
icarus/db/aageneseq.i
icarus/db/geneseq.is
2006/11/03: kegg Changes to allow for the new GLYCAN and COMPOUND lines in lreaction
icarus/db/lreaction.i
icarus/db/lreaction.is
srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp
2006/11/03: kegg latest update for the kegg species mapping file
icarus/db/kegg_species.i
2006/10/31: medline Added comments about the different databases which make up medline in SRS
icarus/db/medline.i
2006/10/31: blast Some changes for more reliable hypertext links to SRS entries for blast hits
icarus/db/blast.is
2006/10/26: kegg Change so we no longer unpack all 500000 files in the pathway distribution tarball, but only the html and gif files we need (about 80000). Also added code to remove obsolete files
icarus/db/pathwaytar.it
2006/10/26: kegg Fixed some parsing errors for map/omim entries, and enabled hypertext links to the kegg genes databases
icarus/db/pathway.is
2006/10/25: entrezgene small change to fix a problem with pebmed hypertext links in the generif section
icarus/db/entrezgene.is
2006/10/23: geneseq Changed the ID type used for priority subentries, as the one we used proviously was causing problems due to overlapping subentry reanges. Please note that after applying this change you will have to re-index nageneseq and aageneseq, and that users may encounter errors until that has been done
icarus/db/aageneseq.i
2006/10/18: ensembl_mysql Changes for ensembl release 41. Note that only the names of the mysql databases have changed, and that these changes also can be picked up from mysql if you have the most recent version of rdbaccess.i
icarus/db/ensemblRDB.i
2006/10/13: reactome Some additional changes needed to handle some entries in reactome 18
icarus/db/reactome.i
icarus/db/reactome.is
icarus/db/reactome.it
icarus/db/reactome_datamodel.i
icarus/db/reactome_schema.i
2006/10/12: system Change to make sure that prisma downloads the 2006 version of mesh
icarus/db/mesh.it
2006/10/12: emboss Updated our Emboss support to work with Emboss 4.0
icarus/lion/emboss/afEmboss.is
icarus/lion/emboss/antigenic.i
icarus/lion/emboss/antigenic.it
icarus/lion/emboss/backtranseq.i
icarus/lion/emboss/backtranseq.it
icarus/lion/emboss/biosedn.i
icarus/lion/emboss/biosedn.it
icarus/lion/emboss/biosedp.i
icarus/lion/emboss/biosedp.it
icarus/lion/emboss/btwisted.i
icarus/lion/emboss/btwisted.it
icarus/lion/emboss/cai.i
icarus/lion/emboss/cai.it
icarus/lion/emboss/chaos.i
icarus/lion/emboss/chaos.it
icarus/lion/emboss/charge.i
icarus/lion/emboss/charge.it
icarus/lion/emboss/checktrans.i
icarus/lion/emboss/checktrans.it
icarus/lion/emboss/chips.i
icarus/lion/emboss/chips.it
icarus/lion/emboss/compseqn.i
icarus/lion/emboss/compseqn.it
icarus/lion/emboss/compseqp.i
icarus/lion/emboss/compseqp.it
icarus/lion/emboss/consn.i
icarus/lion/emboss/consn.it
icarus/lion/emboss/consp.i
icarus/lion/emboss/consp.it
icarus/lion/emboss/cpgplot.i
icarus/lion/emboss/cpgplot.it
icarus/lion/emboss/cpgreport.i
icarus/lion/emboss/cpgreport.it
icarus/lion/emboss/cusp.i
icarus/lion/emboss/cusp.it
icarus/lion/emboss/cutseqn.i
icarus/lion/emboss/cutseqn.it
icarus/lion/emboss/cutseqp.i
icarus/lion/emboss/cutseqp.it
icarus/lion/emboss/dan.i
icarus/lion/emboss/dan.it
icarus/lion/emboss/degapseqn.i
icarus/lion/emboss/degapseqn.it
icarus/lion/emboss/degapseqp.i
icarus/lion/emboss/degapseqp.it
icarus/lion/emboss/descseqn.i
icarus/lion/emboss/descseqn.it
icarus/lion/emboss/descseqp.i
icarus/lion/emboss/descseqp.it
icarus/lion/emboss/diffseqn.i
icarus/lion/emboss/diffseqn.it
icarus/lion/emboss/diffseqp.i
icarus/lion/emboss/digest.i
icarus/lion/emboss/digest.it
icarus/lion/emboss/distmatn.i
icarus/lion/emboss/distmatp.i
icarus/lion/emboss/dotmatchern.i
icarus/lion/emboss/dotmatchern.it
icarus/lion/emboss/dotmatcherp.i
icarus/lion/emboss/dotmatcherp.it
icarus/lion/emboss/dotpathn.i
icarus/lion/emboss/dotpathn.it
icarus/lion/emboss/dotpathp.i
icarus/lion/emboss/dotpathp.it
icarus/lion/emboss/dottupn.i
icarus/lion/emboss/dottupn.it
icarus/lion/emboss/dottupp.i
icarus/lion/emboss/dottupp.it
icarus/lion/emboss/dreg.i
icarus/lion/emboss/dreg.it
icarus/lion/emboss/einverted.i
icarus/lion/emboss/einverted.it
icarus/lion/emboss/embossViews.i
icarus/lion/emboss/eprimer3.i
icarus/lion/emboss/eprimer3.it
icarus/lion/emboss/eprimers.i
icarus/lion/emboss/eprimers.it
icarus/lion/emboss/equicktandem.i
icarus/lion/emboss/equicktandem.it
icarus/lion/emboss/est2genome.i
icarus/lion/emboss/est2genome.it
icarus/lion/emboss/etandem.i
icarus/lion/emboss/etandem.it
icarus/lion/emboss/extractseqn.i
icarus/lion/emboss/extractseqp.i
icarus/lion/emboss/freakn.i
icarus/lion/emboss/freakn.it
icarus/lion/emboss/freakp.i
icarus/lion/emboss/freakp.it
icarus/lion/emboss/fuzznuc.i
icarus/lion/emboss/fuzzpro.i
icarus/lion/emboss/fuzztran.i
icarus/lion/emboss/garnier.i
icarus/lion/emboss/garnier.it
icarus/lion/emboss/geecee.i
icarus/lion/emboss/getorf.i
icarus/lion/emboss/getorf.it
icarus/lion/emboss/helixturnhelix.i
icarus/lion/emboss/helixturnhelix.it
icarus/lion/emboss/hmoment.i
icarus/lion/emboss/hmoment.it
icarus/lion/emboss/iep.i
icarus/lion/emboss/iep.it
icarus/lion/emboss/infoalignn.i
icarus/lion/emboss/infoalignn.it
icarus/lion/emboss/infoalignp.i
icarus/lion/emboss/infoalignp.it
icarus/lion/emboss/infoseqn.i
icarus/lion/emboss/infoseqn.it
icarus/lion/emboss/infoseqp.i
icarus/lion/emboss/infoseqp.it
icarus/lion/emboss/isochore.i
icarus/lion/emboss/isochore.it
icarus/lion/emboss/marscan.i
icarus/lion/emboss/maskseqn.i
icarus/lion/emboss/maskseqn.it
icarus/lion/emboss/maskseqp.i
icarus/lion/emboss/maskseqp.it
icarus/lion/emboss/matchern.i
icarus/lion/emboss/matchern.it
icarus/lion/emboss/matcherp.i
icarus/lion/emboss/matcherp.it
icarus/lion/emboss/megamerger.i
icarus/lion/emboss/megamerger.it
icarus/lion/emboss/merger.i
icarus/lion/emboss/merger.it
icarus/lion/emboss/msbarn.i
icarus/lion/emboss/msbarn.it
icarus/lion/emboss/msbarp.i
icarus/lion/emboss/msbarp.it
icarus/lion/emboss/needlen.i
icarus/lion/emboss/needlen.it
icarus/lion/emboss/needlep.i
icarus/lion/emboss/needlep.it
icarus/lion/emboss/newcpgreport.i
icarus/lion/emboss/newcpgreport.it
icarus/lion/emboss/newcpgseek.i
icarus/lion/emboss/newcpgseek.it
icarus/lion/emboss/octanol.i
icarus/lion/emboss/octanol.it
icarus/lion/emboss/palindrome.i
icarus/lion/emboss/palindrome.it
icarus/lion/emboss/pasteseqn.i
icarus/lion/emboss/pasteseqp.i
icarus/lion/emboss/patmatdb.i
icarus/lion/emboss/patmatdb.it
icarus/lion/emboss/patmatmotifs.i
icarus/lion/emboss/patmatmotifs.it
icarus/lion/emboss/pepcoil.i
icarus/lion/emboss/pepcoil.it
icarus/lion/emboss/pepinfo.i
icarus/lion/emboss/pepinfo.is
icarus/lion/emboss/pepinfo.it
icarus/lion/emboss/pepnet.i
icarus/lion/emboss/pepnet.it
icarus/lion/emboss/pepstats.i
icarus/lion/emboss/pepstats.it
icarus/lion/emboss/pepwheel.i
icarus/lion/emboss/pepwheel.it
icarus/lion/emboss/pepwindow.i
icarus/lion/emboss/pepwindow.it
icarus/lion/emboss/pepwindowall.i
icarus/lion/emboss/pepwindowall.it
icarus/lion/emboss/plotconn.i
icarus/lion/emboss/plotconp.i
icarus/lion/emboss/plotorf.i
icarus/lion/emboss/plotorf.it
icarus/lion/emboss/polydotn.i
icarus/lion/emboss/polydotn.it
icarus/lion/emboss/polydotp.i
icarus/lion/emboss/polydotp.it
icarus/lion/emboss/preg.i
icarus/lion/emboss/preg.it
icarus/lion/emboss/prettyplotn.i
icarus/lion/emboss/prettyplotn.it
icarus/lion/emboss/prettyplotp.i
icarus/lion/emboss/prettyplotp.it
icarus/lion/emboss/prettyseq.i
icarus/lion/emboss/pscan.i
icarus/lion/emboss/pscan.it
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/rfEmboss.is
icarus/lion/emboss/seqmatchalln.i
icarus/lion/emboss/seqmatchallp.i
icarus/lion/emboss/seqmatchallp.it
icarus/lion/emboss/seqretn.i
icarus/lion/emboss/seqretn.it
icarus/lion/emboss/seqretp.i
icarus/lion/emboss/seqretp.it
icarus/lion/emboss/showalignn.i
icarus/lion/emboss/showalignp.i
icarus/lion/emboss/showalignp.it
icarus/lion/emboss/showorf.i
icarus/lion/emboss/showseqn.i
icarus/lion/emboss/showseqn.it
icarus/lion/emboss/showseqp.i
icarus/lion/emboss/showseqp.it
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/sixpack.it
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/supermatchern.it
icarus/lion/emboss/supermatcherp.i
icarus/lion/emboss/supermatcherp.it
icarus/lion/emboss/syco.i
icarus/lion/emboss/tfscan.i
icarus/lion/emboss/tfscan.it
icarus/lion/emboss/tmap.i
icarus/lion/emboss/tmap.it
icarus/lion/emboss/transeq.i
icarus/lion/emboss/trimest.i
icarus/lion/emboss/trimest.it
icarus/lion/emboss/trimseqn.i
icarus/lion/emboss/trimseqn.it
icarus/lion/emboss/trimseqp.i
icarus/lion/emboss/trimseqp.it
icarus/lion/emboss/unionn.i
icarus/lion/emboss/unionn.it
icarus/lion/emboss/unionp.i
icarus/lion/emboss/unionp.it
icarus/lion/emboss/vectorstrip.i
icarus/lion/emboss/vectorstrip.it
icarus/lion/emboss/watern.i
icarus/lion/emboss/watern.it
icarus/lion/emboss/waterp.i
icarus/lion/emboss/waterp.it
icarus/lion/emboss/wobble.i
icarus/lion/emboss/wobble.it
icarus/lion/emboss/wordcount.i
icarus/lion/emboss/wordcount.it
icarus/lion/emboss/wordmatchn.i
icarus/lion/emboss/wordmatchn.it
icarus/lion/emboss/wordmatchp.i
icarus/lion/emboss/wordmatchp.it
srstags/srstags/web/views/emboss/tableOrGraphView.jsp
2006/10/12: system reactome Updates for reactome version 18. Note that by default we expect the database name in mysql to be Reactome18
icarus/db/rdbaccess.i
icarus/db/reactome.i
icarus/db/reactome.is
icarus/db/reactome.it
icarus/db/reactome_datamodel.i
icarus/db/reactome_schema.i
icarus/db/srsdb.i
srstags/srstags/web/WEB-INF/tags/reactome_displaynamefromcode.tag
srstags/srstags/web/WEB-INF/tags/reactome_nobadchars.tag
srstags/srstags/web/WEB-INF/tags/reactome_reactomecomponentsandinstances.tag
srstags/srstags/web/WEB-INF/tags/reactome_reactomedisplayrankedlist.tag
srstags/srstags/web/WEB-INF/tags/reactome_reactomehierlink.tag
srstags/srstags/web/WEB-INF/tags/reactome_reactomelistitem.tag
srstags/srstags/web/views/reactomeentry/event.jsp
srstags/srstags/web/views/reactomeentry/event_hierarchyprint.jsp
2006/10/12: kegg update kegg species mapping file
icarus/db/kegg_species.i
2006/10/10: entrezgene Change needed to handle the extra level of nesting for RefSeq data in entrezgene, announced by the ncbi earlier this year, and which has appeared in the entrezgene data on October 10. Note that the changes only affect datadisplay, and that no re-indexing is needed
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/entrezgene_dm.i
srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2006/10/09: kegg Change needed to handle the new OTHER_REAC line in the lenzyme data
icarus/db/lenzyme.i
icarus/db/lenzyme.is
srstags/srstags/web/views/lenzymeentry/lenzymeentry.jsp
2006/10/05: embl Correction for a wrong database dependency in the definition for emblwgsnew
icarus/db/emblwgsnewfiles.it
2006/10/04: chebi Updates to work with the latest release of chebi (26)
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
srstags/srstags/web/views/chebientry/chebientry.jsp
2006/10/03: geneseq fixed some problems with creating views for the geneseq databases
icarus/db/aageneseq.i
icarus/db/nageneseq.i
2006/10/02: cath Modified the download directory setting so prisma downloads the latest version of CATH
icarus/db/cath.it
2006/09/28: system Change to allow for kegg hypertext links in uniprot. Please merge the new dbxref.i file with your copy in SRSSITE
icarus/db/dbxref.i
2006/09/15: kegg Latest update of the kegg species mapping file
icarus/db/kegg_species.i
2006/09/14: blast system update so SRS works with the latest version of blast (2.2.14). Note that these changes are not backward compatible, so if you apply this update you will have to update your blast binaries as well. We also added a variable in localApplicationOptions.i (merge it with your copy in SRSSITE) which allows you to set the number of cpus used simultaneous by a blast job
icarus/db/blastcommon.i
icarus/db/blastn.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/localApplicationOptions.i
icarus/db/tblastn.i
icarus/db/tblastx.i
2006/09/13: system Change to allow for the new hypertext links to arrayexpress and peroxibase in the uniprot data. Please note that the new href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2006/09/13: prosite system moved the definition for the version field from prosite.i to the general defintions file srsgen.i, as it is now also used by homologene. Note that you will need to merge the new copy of srsgen.i with your copy of this file in SRSSITE
icarus/db/prosite.i
icarus/db/srsgen.i
2006/09/06: embl Correction for the filenames now used on the ebi ftp site for contig and tpa updates
icarus/db/emblnewfiles.it
2006/09/06: embl Correction for wrong insertion of hypertext links to the enzyme database
icarus/db/embl.is
2006/09/06: genpept updated/corrected hypertext link definitions used for dbxrefs in the comments section
icarus/db/genpept.is
2006/08/25: iprmatches homologene Added/updated images used for the display of iprmatches and homologene data
srstags/srstags/web/images/iprmat0.gif
srstags/srstags/web/images/iprmat1.gif
srstags/srstags/web/images/iprmatB.gif
srstags/srstags/web/images/iprmatD.gif
srstags/srstags/web/images/iprmatF.gif
srstags/srstags/web/images/iprmatGR.gif
srstags/srstags/web/images/iprmatH.gif
srstags/srstags/web/images/iprmatM.gif
srstags/srstags/web/images/iprmatP.gif
srstags/srstags/web/images/iprmatR.gif
srstags/srstags/web/images/iprmatS.gif
srstags/srstags/web/images/iprmatX.gif
2006/08/24: ensembl_mysql Changed Protein sequence format to fasta
icarus/db/ensemblproteinmodel.i
2006/08/24: system homologene We have added support for the homologene database from the ncbi. Pleas note that the changes in concepts.i and srsdb.i need to be merged with your copy of these files in SRSSITE
icarus/db/concepts.i
icarus/db/homologene.i
icarus/db/homologene.is
icarus/db/homologene.it
icarus/db/homologene_datamodel.i
icarus/db/srsdb.i
srstags/srstags/web/views/homologeneentry/homologeneentry.jsp
2006/08/23: kegg latest update for the kegg species mapping file. Note that if you have prisma and have enabled the kegggenome database, this file will be generated automatically
icarus/db/kegg_species.i
2006/08/22: embl system Added a new helper library (emblwgsnewfiles) to remove duplicates from the emblwgsnew datbase. The mechanism used is the same as the one used for emblnew. Note that the change in srsdb.i nedds to merged with your copy of that file on SRSSITE
icarus/db/emblnewfiles.is
icarus/db/emblwgsnewfiles.i
icarus/db/emblwgsnewfiles.it
icarus/db/srsdb.i
2006/08/22: entrezgene system Added support for the display of Protein-Protein interaction which are available in some entrezgene entries. Please note that the new copy of href.i needs to merged with your verion of that file in SRSSITE
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/entrezgene_dm.i
icarus/db/href.i
srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2006/08/22: system Made clearer how the rdb access defintions need to be changed to access mysql and oracle, and added code which uses mysql queries tofind out what the ensembl database names are (they change with each release of ensembl), so there is no need to modify SRSDB:ensemblRDB.i each time ensembl is updated.
icarus/db/rdbaccess.i
2006/08/22: ensembl_mysql Reformatted the file, and changed databases names to work with ensembl 40
icarus/db/ensemblRDB.i
2006/08/11: kegg Added Reaction field for new format pathway files
icarus/db/pathway.i
2006/08/11: blast Changed the default setting of the Filter option of blast to have sequence filtering switched on
icarus/db/blastcommon.i
2006/08/11: embl Fix for a problem which prevented the construction of contig sequences if tincaching is enabled
icarus/db/embl.is
2006/08/10: entrezgene system Update needed to handle some changes in the Additional Links section, which caused the omim field to be empty, and messed up the display of the additional links in the web interface. After applying this fix, please re-index the omim field. Note that you will have to merge the new version of href.i with your copy of that file in SRSSITE
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/href.i
2006/08/01: rhdb Correction for the link definition between RHDB and GENBANKWGS
icarus/db/rhdb.i
2006/07/28: uniprot ipi Change so we use the pubmedId rather than the no longer exisiting medlineid for medline links
icarus/db/swissprot.is
2006/07/27: embl Change to allow for the slightly different format of the sequence length on the ID line for deleted entries
icarus/db/embl.is
2006/07/24: geneseq Minor change to use correct token for patent date in table display
icarus/db/geneseqsuppcommon.i
2006/07/24: system kegg Revision of parser to reflect KEGG changes to using reaction rather than enzyme, drug rather than dr, and to allow for inconsistencies in the data
icarus/db/href.i
icarus/db/pathway.is
2006/07/20: Added cvs header
icarus/db/genKeggSpecies.i
2006/07/20: system Change to make sure the swisscommon.i file is included if IPI is enabled, but uniprot not
icarus/db/srsdb.i
2006/07/20: system Contains links to pathosign, rzpd-protexp and ensembl_havana
icarus/db/dbxref.i
2006/07/20: geneseq Correction for hypertext link to the data provider
icarus/db/aageneseq.it
icarus/db/nageneseq.it
2006/07/20: kegg added support for the TARGET line in the kegg drug dataset
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2006/07/19: ensembl_mysql Added a hypertext link to ensembl genes
srstags/srstags/web/views/ensemblaffyentry/affyentry.jsp
2006/07/19: ensembl_mysql Change in hyperlink defintion to allow for a change in the ID field
srstags/srstags/web/views/ensemblproteinentry/proteinentry.jsp
2006/07/19: ensembl_mysql Included ensembl virtual libraries in the package file used for installing ensembl
icarus/lion/packages/ensemblRDB.ip
2006/07/19: srscheck fixed incorrect message notifying user of missing files and added fix for situation where complete offline set of indices but no offline data files would ifnore a force flag
icarus/workflows/checkLocalFiles.i
2006/07/17: imgt Correction for the way read-link indices are build from imgt. After this update please rebuild the imgt read-link indices by running "srsbuild -l imgt"
icarus/db/imgt.i
2006/07/17: kegg Latest version of the kegg species mapping list used for kegggenes and lenzyme
icarus/db/kegg_species.i
2006/07/17: chebi Updated for new version of chebi (COMPOUND_CHILD_ID is changed to COMPOUND_ID).
icarus/db/chebi_schema.i
2006/07/14: uniref Change to allow for a change in the way the date is formatted in uniref
icarus/db/uniref.is
2006/07/14: kegg Changes to allow for the fact that the kegg compound and reaction databases no loner contain literature references
icarus/db/lcompound.i
icarus/db/lreaction.i
srstags/srstags/web/views/lreactionentry/lreactionentry.jsp
2006/07/12: genecards Changes for release 2.34 of genecards
icarus/db/genecardstar.it
2006/07/12: hmmer Corrected the way hmmsearch results are linked to uniprot data
icarus/db/hmmsearch.i
icarus/db/hmmsearch.is
2006/07/12: genecards Correction for for the display of hypertext links to ExpolDB in genecards entries
icarus/db/genecards.is
2006/07/11: system Correction needed as a number of previously available href definitions had disappeared with the last update of href.i
icarus/db/href.i
2006/07/11: prosite New file containing the date field to match the new prosite parser.
srstags/srstags/web/views/prositeentry/prositeentry.jsp
2006/07/11: system ProruleR has been added for use in prosite.
icarus/db/href.i
2006/07/11: system Updated with new uniprot link to rzpd-protexp
icarus/db/dbxref.i
icarus/db/href.i
2006/07/11: prosite You can now view prosite in the extended query form. Previously there was an error caused by two Reference_Id idTypes.
icarus/db/prositedoc.i
2006/07/05: system Added DF_DUPDate and DF_IUPDate srs fields for the new prosite.i file.
icarus/db/srsgen.i
2006/07/05: prosite Adjusted for new data format.
icarus/db/prosite.i
icarus/db/prosite.is
2006/06/29: ensembl_mysql Added wildcard asterisk to searches for MIM owing to data change
srstags/srstags/web/views/chromosome/chromosome.jsp
2006/06/29: ensembl_mysql Changes for ensembl 39 (change in database names) and isDistinct flag set to yes for karyotype libraries
icarus/db/ensemblRDB.i
2006/06/29: ensembl_mysql Cosmetic changes
srstags/srstags/web/views/ensemblgeneentry/geneentry.jsp
2006/06/26: srscheck Undo a mistake with CVS checkin of previous version
icarus/workflows/linkPhase.i
2006/06/23: genbank embl refseq geneseq Changes to allow for some awkward handling of world patent numbers used for linking to patents at the EPO web site
icarus/db/gbemblcommon.is
icarus/db/geneseq.is
2006/06/22: srscheck Fix for building readlinks when the chunkSize attribute is set.
icarus/workflows/linkPhase.i
2006/06/21: embl system Update to reflect changes in the way EMBL release 87 is ditributed. This involves the discontinuation of EMBLTPA and EMBLCONTIGS (these are now included in the main release, and updates are in EMBLNEW). Also changed the configuration for prisma data updates so it will pick up the various files containing deleted entries
icarus/db/embl.i
icarus/db/emblcontigs.i
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
icarus/db/emblrelease.it
icarus/db/embltpa.i
icarus/db/emblwgsnew.it
icarus/db/emblwgsrelease.it
icarus/db/srsdb.i
2006/06/19: uniprot ipi Change to make sure that RL lines containing a patent are displayed in the swissentry view
icarus/db/swissprot.is
2006/06/16: genbank refseq Change to allow for a small change in the Journal line which allows for pre-grant patents
icarus/db/genbank.is
2006/06/15: kegg Change needed for a change in the structure of the species line of the kegggenome database. This also affects the kegg species mapping file (kegg_species.i) and the icarus script which can be used to generate it (genKeggSpecies.i)
icarus/db/genKeggSpecies.i
icarus/db/kegg_species.i
icarus/db/kegggenome.i
icarus/db/kegggenome.is
2006/06/13: pdb Change so prisma will download pdb data from the rcsb site rather than from the ebi, as wgetPrisma seems to have problems retrieving the necessary information from the ebi ftp site
icarus/db/pdb.it
2006/06/12: system uniprot ipi Change to allow for the new host organism field in uniprot. Note that the change in srsgen.i needs to merged with your copy of of srsgen.i in the SRSSITE directory. After applyig the change you will have to index the new hos field
icarus/db/srsgen.i
icarus/db/swisscommon.i
icarus/db/swissprot.is
srstags/srstags/web/views/swissentry/swissentry.jsp
2006/06/12: system added links to prevent indexing errors with IPI - please merge this update with your copy of dbxref.i in the SRSSITE directory
icarus/db/dbxref.i
2006/06/09: embl Modification to handle the changes in the ID line in EMBL which will appear in release 87 (see http://www.ebi.ac.uk/embl/Documentation/changesdetails.html). The updated parser will work with both old and new format, so you can apply the update whenever you want (but before you update your data). We have kept the changes for the end-user minimal: The ID is still being indexed, the sequence version continues to be indexed as AccNo.Version (eg AB12345.1). The only change is in the division field. For each entry (in EMBL 87 or later) it will contain two values. One indicating the type of data (STD, EST, HTG etc) and one the traditional EMBL division (HUM, MUS, PLN etc). If you use SRS queries for constructing various subsets of data, you probably will have to adapt these. For example [embl-div:hum] will now have to be "[embl-div:hum] & [embl-div:std]" (unless ofcourse you would like to have all the ESTs, GSSs etc)
icarus/db/embl.is
icarus/db/emblcommon.i
2006/06/06: ensembl_mysql Updated for new ensembl schema changes
icarus/db/ExonsandIntrons.il
icarus/db/OutputExons.il
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
2006/06/06: kegg made entry view a view of type entry, prevents it being displayed as a result view
icarus/db/lglycan.i
2006/06/05: ensembl_mysql Updated for use with tfle due to the appearrance of the ensembl virtual database
icarus/db/UTRandCDS.il
2006/06/01: system Correction for some inadvertently inserted end of line characters
icarus/db/href.i
2006/05/31: uniprot ipi Fix for matching . separators in h_des_enzyme
icarus/db/swissprot.is
2006/05/25: dbsts Added optional flag to h_cc_medline to account for entries where comments section does not have MUID information
icarus/db/dbsts.is
2006/05/25: dbsts Change to make sure that prisma download the latest file from the files listed on the dbsts ftp site
icarus/db/dbsts.it
2006/05/25: blast fasta Fix to make sure we do not build duplicate links
icarus/db/blast.is
icarus/db/fasta.is
2006/05/25: medline Fixed a problem with hypertext links for mesh qualifiers which include an ampersand
srstags/srstags/web/views/medlineentry/medlineentry.jsp
2006/05/23: kegg Latest species mapping list for Kegg databases
icarus/db/kegg_species.i
2006/05/22: system Change to the loader used for descriptions so it will load relevant data for a number of databases which do not have description field - note that you will have to merge this update with your copy of this file in the SRSSITE directory
icarus/db/loader.i
2006/05/22: srscheck Fix for some problems with the removeIndices option of srscheck
icarus/workflows/removePhase.i
2006/05/18: embl genbank refseq Change so we provide correct hypertext links to espacenet for Japanese patents prior to 2000
icarus/db/embl.is
icarus/db/gbemblcommon.is
icarus/db/genbank.is
2006/05/18: system uniprot ipi Updated to create a hyperlink to PathoSign
icarus/db/href.i
icarus/db/swissprot.is
2006/05/18: genecards system Updates for release 2.34 of genecards. As the distribution files of genecards have changed, please read the comments in genecards.i prior to installation
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecardstar.it
icarus/db/href.i
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
srstags/srstags/web/views/genecardsentry/genecardsexpression.jsp
2006/05/16: geneseq Change to correct a problem were part of the patent description ended up appended to the patent number in the patent number index
icarus/db/geneseqsupp.is
2006/05/15: srscheck Fix for an unanticipated side effect of having virtual databases consisting of relational databases
icarus/workflows/coreCheckClasses.i
2006/05/11: ensembl_mysql Updated after affy_* tables and columns were renamed to oligo_* by the Ensembl group
icarus/db/ensemblRDB.i
icarus/db/ensemblaffymodel.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
2006/05/11: ensembl_mysql revert back to older copy
icarus/db/ensemblRDB.i
icarus/db/ensemblaffymodel.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
2006/05/08: kegg Another correction so prisma can handle the unpacking of the kegg images tarball despite te fact that the extracted files are read-only
icarus/db/kegg_images.i
2006/05/08: bind Change in download localtion for the bind databases. Note that you will need to obtain a username and password to be able to download the data
icarus/db/bindinteraction.it
2006/05/08: kegg Updated species mapping list for kegg
icarus/db/kegg_species.i
2006/04/28: kegg updated species mapping file for the kegg databases
icarus/db/kegg_species.i
2006/04/27: ensembl_mysql A clause was added in case alignment.colour was empty
srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp
2006/04/27: system prosite Added support for the new prosite rule field (PR). Note that there is also a new PP field, but we have not implemented support for it yet, as there is a discrepancy between its actual contents and the description of this field in the prosite manual. Also note that the new href.i needs to be merged with your copy of that file in the SRSSITE directory
icarus/db/href.i
icarus/db/prosite.i
icarus/db/prosite.is
2006/04/27: ensembl_mysql Change in schema for ensembl 38 (external_db.release -> db_release)
icarus/db/ensemblcore_schema.i
2006/04/27: ensembl_flat Correction for the correct download location of the ensembl flatfiles
icarus/db/ensembl.it
2006/04/27: transpath Correction for the download location of the transpath files
icarus/db/transpath_annotate.it
icarus/db/transpath_gene.it
icarus/db/transpath_molecule.it
icarus/db/transpath_pathway.it
icarus/db/transpath_reaction.it
icarus/db/transpath_reference.it
2006/04/27: ensembl_mysql Updated ensembl version number to 38
icarus/db/ensemblRDB.it
2006/04/25: kegg Fix to work around the fact that the kegg images tarballs unpack as readonly files, which would prevent subsequent updates
icarus/db/kegg_images.i
2006/04/25: pdbfinder Some improvements to sorting and table display for the header, source and compond fields of pdbfinder
icarus/db/pdbfinder.i
2006/04/21: system Change so we use the ncbi website for hypertext links to medline via medline IDs. This is needed as medline IDs are no longer part of the distributed medline data
icarus/db/href.i
2006/04/20: genpept Update to change to .gz file extension
icarus/db/genpeptrelease.it
icarus/db/gpnewfiles.it
2006/04/19: kegg Allow for the new BRACKET lines in the lcoompound and lglycan data
icarus/db/lcommon.is
icarus/db/lcompound.is
icarus/db/lglycan.is
2006/04/19: kegg Allow for the new BRACKET lines in the ldrug data, and a corrected a few minor sorting/display issues
icarus/db/ldrug.i
icarus/db/ldrug.is
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2006/04/19: medline Change so we do not get irrelevant error messages during indexing of medlinenewfiles
icarus/db/medline.is
icarus/db/medlinenewfiles.i
2006/04/19: genpept Change to cope with genpept update files which do not have a genbank header providing a date for the update
icarus/db/gpnewfiles.is
2006/04/13: system Added drugR and drugMapR for useGG pathwya database
icarus/db/href.i
2006/04/13: kegg ldrug hyperlinks have been added to the pathway image maps
icarus/db/pathway.is
2006/04/12: kegg Updated for the latest data files so that the images show correctly.
icarus/db/pathway.is
2006/04/11: kegg Addition of new Pathway field
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
2006/04/11: kegg Changes made due to addition of new 'pathway' field
icarus/db/ldrug.i
icarus/db/ldrug.is
2006/04/11: kegg Changes made due to addition of new 'pathway' field and changed id field
icarus/db/lcommon.is
2006/04/10: kegg A new comment about how to create a symbolic link to the images has been placed at the top of the file.
icarus/db/lcompound.i
icarus/db/ldrug.i
icarus/db/lglycan.i
icarus/db/lreaction.i
2006/04/10: srscheck Fixed so missing separator error doesn't appear.
icarus/workflows/moveIndicesPhase.i
2006/04/07: blocks Changes to create links using Uniprot Accession rather than Id
icarus/db/blocks.i
icarus/db/blocks.is
2006/04/07: unigene Fix for missing _ in seqacc production to allow proper indexing of refseq id's
icarus/db/unigene.is
2006/04/05: ensembl_mysql The ID of pufferfish transcripts has been changed to ensembl ID
icarus/db/ensemblRDB.i
2006/04/04: genbank embl refseq Change to allow for more than 210000 sequence features in embl/genbank/refseq entries. Also changed the parallizatiuon setting of refseqnew so it will do larger files in parts. Note that in order to apply this fix ju must have applied the binary patch 8.1.1.4 to your srs installation.
icarus/db/gbemblcommon.is
icarus/db/refseqnew.i
2006/04/04: ensembl_mysql Changes made due to switching of ensembl ID field from a numeric ID to the etid field. This made the entry objects change in structure.
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/ensemblproteinmodel.i
icarus/db/exondatamodel.i
2006/04/04: ensembl_mysql Changes made for change in the Ensembl37 schema
icarus/db/ensemblcore_schema.i
2006/04/04: ensembl_mysql Changes made for ensembl virtual databases
icarus/db/ensemblRDB.i
icarus/db/ensemblaffy.i
icarus/db/ensemblcommon.i
icarus/db/ensemblgene.i
icarus/db/ensemblkar.i
icarus/db/ensemblmarker.i
icarus/db/ensemblseq.i
icarus/db/ensembltranscript.i
2006/04/04: blocks Correction for the command used to unpack blocks, as the old construction could lead to a zero-sized file
icarus/db/blocks.it
2006/04/03: transpath Change needed to work around a problem where srsbuild would not build the link between tfgene and transpathgene
icarus/db/transpath_datamodel.i
icarus/db/transpath_gene.i
2006/04/03: geneticcode Fix for URL to Genetic Codes homepage
icarus/db/geneticcode.it
2006/03/31: pfam Due to a problem in the parsing process hypertext links to Medline would not be present for certain PFAM entries. This has now been fixed. After copying this file into place please run wsrefresh.
icarus/db/pfam.is
2006/03/30: kegg Updated species list for the kegg databases
icarus/db/kegg_species.i
2006/03/29: transfac Change to display the TFSITE entry correctly when called with getz. Previously the sequence field was being displayed twice, once in the record and once after the record.
icarus/db/tfsite.i
2006/03/29: pfam Fixed problem with incorrect display of references where a first page and last page are not both defined
icarus/db/pfam.is
srstags/srstags/web/views/pfamentry/refs.jsp
2006/03/28: taxonomy Added indexing in parts for taxonomy
icarus/db/taxonomy.i
2006/03/28: rhdb transfac unigene Added sort tokens for various fiels to have better sort results
icarus/db/rhdb.i
icarus/db/rhexp.i
icarus/db/rhmap.i
icarus/db/rhpanel.i
icarus/db/tfcell.i
icarus/db/tffragment.i
icarus/db/tfgene.i
icarus/db/tfsite.i
icarus/db/unigene.i
2006/03/28: system kegg Added the kegg drug database (ldrug), and added support for displaying the images which come with lcompound and lreaction. Added the keggimages database as a dummy database which can be used with SRS PRISMA to handle the download of the images. Note that the change in srsdb.i need to be merged with your copy of srsdb.i in the SRSSITE directory
icarus/db/concepts.i
icarus/db/kegg_images.i
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/ldrug.i
icarus/db/ldrug.is
icarus/db/ldrug.it
icarus/db/lglycan.i
icarus/db/lglycan.is
icarus/db/localApplicationOptions.i
icarus/db/lreaction.i
icarus/db/lreaction.is
icarus/db/srsdb.i
icarus/db/srsgen.i
srstags/srstags/web/views/lcompoundentry/lcompgeneral.jsp
srstags/srstags/web/views/ldrugentry/ldrugentry.jsp
srstags/srstags/web/views/lglycanentry/lglycangeneral.jsp
srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp
2006/03/28: uniprot Change so SRS PRISMA will not omit downloading the release info text file which it needs to correctly set the version of the uniprot databases
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
2006/03/28: blast fasta system Changed IDs in fasta/blast results so they no longer contain the database name and hit ID, as the blast/fasta result IDs was perceived as being too long to be displayed in tables. Change to use the accession number rather than the ID as field to link to from blast/fasta results. Changed the default result view for blast and fasta results to be the homology view (wich is identical to the blast graphical viewer - but the name was perceived as misleading as it was also applicable to fasta results)
icarus/db/blast.is
icarus/db/blastcommon.i
icarus/db/blastn.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/fasta.i
icarus/db/fasta.is
icarus/db/fastaft.il
icarus/db/fastx.i
icarus/db/fasty.i
icarus/db/nfasta.i
icarus/db/ssearch.i
icarus/db/tblastn.i
icarus/db/tblastx.i
icarus/db/tfasta.i
icarus/db/tfastx.i
icarus/db/tfasty.i
2006/03/28: embl genbank Correction for new link definitions to taxonomy. There is no need to rebuild links after applying this patch
icarus/db/emblwgsrelease.i
icarus/db/genbank.i
2006/03/28: transpath Correction in database description
icarus/db/transpath_annotate.it
icarus/db/transpath_gene.it
icarus/db/transpath_molecule.it
icarus/db/transpath_pathway.it
icarus/db/transpath_reaction.it
icarus/db/transpath_reference.it
2006/03/28: system Correction needed to prevent the web services server from crashing
icarus/db/readseq.i
2006/03/28: chebi ensembl_mysql entrezgene geneseq go_xml go_mysql hmmer pfam reactome taxonomy Non essentail changes like addition of CVS headers, corrections of comments etc
icarus/db/chebi_schema.i
icarus/db/chromosomegraphic.i
icarus/db/ensemblRDB.it
icarus/db/ensembl_compara_schema.i
icarus/db/entrezgene_dm.i
icarus/db/geneseqsuppcommon.i
icarus/db/go.i
icarus/db/gogeneproducts.i
icarus/db/gogeneproducts_schema.i
icarus/db/gogenproddatam.i
icarus/db/goparse.is
icarus/db/gotermdatamodel.i
icarus/db/goterms_schema.i
icarus/db/hmmbuild.is
icarus/db/pfamseed.it
icarus/db/reactome.i
icarus/db/reactome_schema.i
icarus/db/treemodel.i
2006/03/28: ensembl_mysql Updated for ensembl37
icarus/db/ensemblRDB.i
icarus/db/ensemblcore_schema.i
icarus/db/ensemblproteinmodel.i
2006/03/28: kegg latest update for kegg species mapping file
icarus/db/kegg_species.i
2006/03/27: srscheck Various fixes, including better recognition of complete offline data/index sets, removal of obsolete on-line data files, crashes of srscheck when encountering readlinks from a chunksized library, situations where prisma entered into a loop. If you have srs PRISMA, please ensure that you also update your prisma files from http://downloads.lionbio.co.uk/downloads/prisma4_dist/Changes_since_8.1.html
icarus/workflows/buildPhase.i
icarus/workflows/checkLocalFiles.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
icarus/workflows/moveIndicesPhase.i
icarus/workflows/srsCheckMain.i
icarus/workflows/virtualQueryPhase.i
2006/03/22: system Added support for the new link introduced into the UniProt database to link to the protein phosphorylation database. Copy href.i and dbxref.i to your $SRSSITE directory and run srssection to apply the changes.
icarus/db/dbxref.i
icarus/db/href.i
2006/03/22: unigene New field added GENE_ID with links to the Entrez Gene database
icarus/db/unigene.i
icarus/db/unigene.is
2006/03/22: genecards The BioAlma genes have been coded in. Additionally a link to Entrezgene has been added.
icarus/db/genecards.i
icarus/db/genecards.is
2006/03/22: genecards The BioAlma genes now have a new section to display them.
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2006/03/22: system The link to the NCBI SNP database has been corrected. The link now goes to the reference SNP record as opposed to the submitted SNP record. Copy dbxref.i to your $SRSSITE directory and run srssection to implement this patch.
icarus/db/dbxref.i
2006/03/17: entrezgene Added a TaxId field in order to query/retrieve the ncbi taxonomy id, and added a link to the taxonomy database
icarus/db/entrezgene.i
icarus/db/entrezgene.is
2006/03/17: unilib Correction to the way the link between unilib and taxonomy is build
icarus/db/unilib.i
2006/03/15: geneticcode updated url for NCBI genetic codes homepage
icarus/db/geneticcode.it
2006/03/15: embl genbank refseq Change to the way we link EMBL/GenBank/RefSeq and the taxonomy database. We were using the Organism field to link to taxonomy, but with the latest version of Genbank this proved to be impossible. We now have added a new field (TaxID) to all databases in EMBL and GenBank format (which also include refseq and imgt) which holds the taxonomy id, and we use this for linking. The added bonus is that you now also can query these databases directly by TaxID. Applying this update requires some planning: If you apply the changes inmediately, then your users will get error messages about missing txi indices, so it would be best either to schedule some downtime to build the new indices, or use a separate SRS instance to build the new indices prior to updating you production SRS installation. Note that with this fix building the link index between genbankrelease and taxonomy still may require more than 2Gb of memory.
icarus/db/emblcommon.i
icarus/db/emblcontigs.i
icarus/db/emblnew.i
icarus/db/emblrelease.i
icarus/db/embltpa.i
icarus/db/emblwgsnew.i
icarus/db/gbemblcommon.is
icarus/db/genbankcommon.i
icarus/db/genbanknew.i
icarus/db/genbankrelease.i
icarus/db/genbankwgs.i
icarus/db/refseqnew.i
icarus/db/refseqpnew.i
icarus/db/refseqprelease.i
icarus/db/refseqrelease.i
2006/03/15: geneseq Changed unpackCommand to reformatCommand to ensure that all geneseq distribution files are unpacked even if not all the files are updated
icarus/db/nageneseqtar.it
2006/03/14: uniprot Added check so Last Annotation Update date field is not shown in IPI database
srstags/srstags/web/views/swissentry/swissentry.jsp
2006/03/13: system A link to GenomeReviews has been added (for use in uniprot links)
icarus/db/dbxref.i
icarus/db/href.i
2006/03/13: uniprot Change so we build the uniprot_trembl - taxonomy link in 16 parts. This is needed as it becomes difficult to build the link in one part
icarus/db/uniprot_trembl.i
2006/03/13: uniprot Change to the way we link uniprot to taxonomy. By using the contents of the TaxID field in uniprot, we achieve better and more efficient linking
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2006/03/13: pdb Correction for the pdbmodel download settings. An additional "subDirectories:yes" was needed to collect all pdbmodel files into the same directory for us in SRS
icarus/db/pdbmodel.it
2006/03/13: uniprot ipi The h_link production has been altered to contain the GenomeReviews link
icarus/db/swissprot.is
2006/03/10: entrezgene Added a direct link from entrezgene to uniprot. After applying this update you will have to build the link indices between entrezgene and uniprot_swissprot, uniprot_trembl
icarus/db/entrezgene.i
2006/03/10: genbank embl refseq Change to the temporary workaround needed to prevent crashes on entries with more than 200000 sequence features. Rather than skipping specific entries completely, we now stop processing the feature table after 200000. Note that it will still be possible to view the complete entry in text mode
icarus/db/gbemblcommon.is
icarus/db/genbank.is
2006/03/10: geneseq Correction for a wrong name for a tabletoken in 2 field defintions
icarus/db/geneseqsuppcommon.i
2006/03/10: geneseq The 'description' and 'patent filing date' fields have been added to the aageneseq entry view
srstags/srstags/web/views/aageneseqentry/general.jsp
srstags/srstags/web/views/aageneseqentry/patent.jsp
2006/03/10: geneseq The 'description' and 'patent filing date' fields have been added to the nanegeneseq entry view
srstags/srstags/web/views/nageneseqentry/general.jsp
srstags/srstags/web/views/nageneseqentry/patent.jsp
2006/03/07: system Change which prevents a potential crash of the srs web services server when launching an application
icarus/db/readseq.i
2006/03/07: srscheck Workaround for a problem which under some circumstances would cause a crash of prisma in the chack phase priot to moving indices/data on line
icarus/workflows/moveIndicesPhase.i
2006/03/06: srscheck Change so srscheck/prisma wil flush the buffer after each debug/log print statement - this will make it easier to locate problems during srscheck and prisma runs
icarus/workflows/coreCheckClasses.i
2006/03/06: genbank refseq Temporary solution for a problem with refseq entry NT_022517. This entry now contains so many sequence features (217089) that srsbuild will crash on it. For the moment we have modified the parser so the indexing process will skip this entry. We will change this behaviour once we have fixed binaries available
icarus/db/genbank.is
2006/03/06: genbank embl refseq This patch strips out double quotes surrounding URLs within certain parts of the features section. Previously single quotes were used but some installations could not display the entry correctly due to this. To install, replace the existing gbemblcommon.is and run wsrefresh to propagate the changes to your web interface.
icarus/db/gbemblcommon.is
2006/03/03: system Corrected ncbigiR link to include GENPEPT databank
icarus/db/href.i
2006/03/02: blast fasta Change for a more robust way of linking blast/fasta results to the query databases used
icarus/db/blast.is
icarus/db/fasta.is
2006/03/02: embl Update to allow display of EMBL entries. This corrects a problem caused by the 28/2 update regarding the genome project field. Replace your existing embl.is with this file and run wsrefresh to refresh web services.
icarus/db/embl.is
2006/03/01: ensembl_mysql iprmatches transfac Update to force some dynamically generated images to be written into the correct directory
srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp
srstags/srstags/web/views/iprmatchesentry/iprmatchesentry.jsp
srstags/srstags/web/views/tffactorentry/features.jsp
2006/02/28: system Added new lookups to provide links to RefSeq from IPI records. To install this patch replace the existing dbxref.i in $SRSDB with this one and copy it to your $SRSSITE directory. If you have made changes in your site copy of this file be sure to merge them with this new version.
icarus/db/dbxref.i
2006/02/28: kegg system Added the genKeggSpecies.i script which can create the kegg_species.i mapping file. For datails, see the comments at the top of genKeggSpecies.i. Also added helper libraries lenzymedata, kegggenesdata and keggorthologydata which are needed so prisma will schedule the generation of the kegg_species.i file appropriately. We also added the gene-is (entrezgene) as a searchable field to kegggenes, and added a link from the kegggenes databases to entrezgene. Note that you will have to merge the changes in srsdb.i with your srsdb.i file in the SRSSITE directory. Also note that if you use the configuration update feature of prisma, this will not automatically add the new helper libraries - you will have to do that manually
icarus/db/genKeggSpecies.i
icarus/db/kegg_species.i
icarus/db/kegggenes.i
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
icarus/db/kegggenes_na.it
icarus/db/kegggenome.is
icarus/db/kegggenome.it
icarus/db/keggorthology.i
icarus/db/keggorthology.it
icarus/db/lenzyme.i
icarus/db/lenzyme.it
icarus/db/srsdb.i
2006/02/28: genbank embl refseq system Change to support the new Genome Project field in GenBank/RefSeq/EMBL records. The following files are all required: genbank.is gbemblcommon.i, href.i (copy it to your $SRSSITE directory) and dnadbentry.jsp. Once you have downloaded and put in place these files run srssection and restart your browser instances.
icarus/db/gbemblcommon.i
icarus/db/genbank.is
icarus/db/href.i
srstags/srstags/web/views/dnadbentry/dnadbentry.jsp
2006/02/28: dbest genpept Changed setup so the links to taxonomy from dbest and genpeptprelease will be build in 16 parts
icarus/db/dbest.i
icarus/db/genpeptrelease.i
2006/02/28: fasta Small changes for slightly more robust performance
icarus/db/fasta.is
2006/02/27: kegg Update kegg species mapping file - this file is used for lenzyme, kegggenes_na and kegggenes_aa
icarus/db/kegg_species.i
2006/02/17: srscheck Corrected an error in a print command which caused srscheck to crash
icarus/workflows/srsCheckMain.i
2006/02/17: interpro Correction for the hypertextlinks to the prints database which are displayed in interpro entries
icarus/db/interpro.is
2006/02/17: system add definition for links to BioCyc database for UNIPROT entries
icarus/db/dbxref.i
icarus/db/href.i
2006/02/16: interpro Correction for the hypertext link to prodom data
icarus/db/interpro.is
2006/02/16: prodom Modification so we don't try to insert hypertext links to protein entries for entry number 1. There are simply too many of them, which breaks the web front-end
icarus/db/prodom.is
2006/02/14: blast Correction for a tokenname involved in displaying blast results - a wrong name was used in the previous update, which was needed to handle blast 2.2.13 results
icarus/db/blast.is
2006/02/13: embl genbank refseq Change to make sure we display a "//" at the end of embl and genbank entries if they do not contain a sequence
icarus/db/embl.is
icarus/db/genbank.is
2006/02/13: system Change which allows users to provide "dbname:accno" style input for tools which require a sequence as input. Please also apply the SRS8.1.1.3 patch release, and copy the new copy of SRSICA/quickSearch.i which comes with the patch release to the SRSSITE directory
icarus/db/readseq.i
2006/02/10: blast Change needed to cope with the output generated by blast version 2.2.13, which has an extra column, listing the number of HSPs in the list of hits
icarus/db/blast.is
2006/02/10: srscheck added fix for args missing - and added diff from 81 branch
icarus/workflows/srsCheckMain.i
2006/02/10: kegg fix for nested html tags in pathway field
icarus/db/kegggenes.is
2006/02/09: uniprot ipi Correction for the parsing of the entry update date. After applying this fix, please re-index the annotation update fields (lau)
icarus/db/swissprot.is
srstags/srstags/web/views/swissentry/swissentry.jsp
2006/02/09: rebase Replaced the old "files" type datafile specfication with a searchName. This was the last library which was still using this old specification, which dates back to SRS4
icarus/db/rebase.i
2006/02/09: system added GENPEPT to list of libs in hypertext links to GI numbers
icarus/db/href.i
2006/02/08: kegg Updated the kegg species mapping file for the latest species available in kegg
icarus/db/kegg_species.i
2006/02/07: genpept Change to ensure we only download the gpdat.seq file - which is a symlink to the gpdatNNN.seq
icarus/db/genpeptrelease.it
2006/02/07: kegg fix for ]+-e case # 9366
icarus/db/lcommon.is
icarus/db/lreaction.is
2006/02/06: go_xml A corection for the link to child-entries of a go entry
srstags/srstags/web/views/goentry/gorelatives.jsp
2006/02/02: uniprot ipi Modifications to cope with a change in the format of the date fields in uniprot. These changes will appear in uniprot after 7-Feb-2006. We made changes in such a way that they should cope with both the old and the new format, but a consequence of these changes is that uniprot can no longer be searched for release numbers (creation, sequence update and annotation update).
icarus/db/swisscommon.i
icarus/db/swissprot.is
srstags/srstags/web/views/swissentry/swissentry.jsp
2006/02/01: geneseq Change so the geneseq supplementarty databases also have the generic "AllIDs" field for searching
icarus/db/geneseqsuppcommon.i
2006/02/01: system Updated pubmedIdR
icarus/db/href.i
2006/01/31: enzyme Changed maximum size for a entryname to 12 characters. After applying this change you will have to re-index the enzyme
icarus/db/enzyme.i
2006/01/31: genbank embl refseq Fix to patch of 25th of January. The patch of 25th Januwary was incomplete. This follow up addresses the remaining issues.
icarus/db/gbemblcommon.is
2006/01/30: prodom Correction for the way the keyword field is indexd
icarus/db/prodom.is
2006/01/27: genecards Change to the entry view. The links to GeneNote, GeneAnnot and GeneTide are no longer linked gifs. This is because the gifs could have different names dependent on the way genecards data was obtained. Instead they are now straight-forward hypertext links.
srstags/srstags/web/views/genecardsentry/genecardsexpression.jsp
2006/01/25: system The format of the link to the Human Gene Nomenclature database has been updated. This patch addresses that issue.
icarus/db/href.i
2006/01/25: genbank embl refseq This patch fixes a problem with an incorrect link being inserted in the plain text subentry view of a feature. To apply this patch replace the existing gbemblcommon.is file with this one and restart web services using either wsrefresh or wsstop followed by wsstart
icarus/db/gbemblcommon.is
2006/01/23: ensembl_mysql Urls have been updated after srs82 urls had inadvertently got checked in.
icarus/db/ensemblgenemodel.i
2006/01/20: bind The parallelType has been updated from filesSize to files for use in indexing.
icarus/db/bindcomplex.i
icarus/db/bindinteraction.i
icarus/db/bindpathway.i
2006/01/19: srscheck Fix for a bug wich caused some link indices not to be build under certain conditions. We would recommend to apply this update inmendiately and run "srscheck; srsdo" or "runPrisma -local" (if you have prisma) to ensure that your link indices are up to date
icarus/workflows/linkPhase.i
2006/01/17: transfac Fix for references that don't have a last page
icarus/db/transfaccommon.is
2006/01/17: reactome The ecm and cme fields have been updated for the Reactome15 schema
icarus/db/reactome.i
2006/01/13: genecards The Genecards predefined query has been changed so that searches against name search against the gene name and alias field
icarus/db/genecards.i
2006/01/10: transfac Change to correctly display sequence information for a TFFACTOR entry . In order to apply this update you need the files transfaccommon.is , tffactor.i , tffactor.is and the JSP file tffactorentry.jsp. Replace the existing files with these, run srssection and restart all your browser instances.
icarus/db/tffactor.i
icarus/db/tffactor.is
icarus/db/transfaccommon.is
srstags/srstags/web/views/tffactorentry/tffactorentry.jsp
2006/01/09: system Link to linkHub was reinstated into dbxref.i . It had accidentally been removed in the last update to this file.
icarus/db/dbxref.i
2006/01/05: nrl3d Changed the download address for nrl3d to ftp.pir.georgetown.edu, as the old address no longer seems to work. Please note that nrl3d is no longer maintained and its conntent is static since 2001
icarus/db/nrl3d.it
2006/01/05: kegg Modified the kegg species map to handle data originating from ensembl better (we were getting duplicate identifiers for ensembl/non-ensembl entries). After updating this file, please re-index kegggenes_na and kegggenes_aa
icarus/db/kegg_species.i
2006/01/05: system update mgdR link (Mouse Genome Database) to Jackson Laboratory
icarus/db/href.i
2006/01/03: genecards Added a note regarding indexing genecards using srscheck, commented out the parallel indexing for the moment as a bug in srsbuild may result in not all files being indexed, and corrected a short field name for the Subcellular location field. After applying this fix please re-index genecards
icarus/db/genecards.i
icarus/db/genecards.is
2006/01/03: kegg Updated the kegg species mapping list with the latest data from kegggenome
icarus/db/kegg_species.i
2005/12/29: pfam Link annotations have been altered
icarus/db/pfama.i
icarus/db/pfamb.i
2005/12/23: genecards Added support for the new category field, and added parallelization of indexing for genecards
icarus/db/genecards.i
icarus/db/genecards.is
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
2005/12/22: uniref As it is becomoming problematic to build some links for uniref databases in one run, we added a partN parameter to some link definitions, so the links are now build in parts, and later on merged
icarus/db/uniref100.i
icarus/db/uniref50.i
icarus/db/uniref90.i
2005/12/22: blocks Change to the download parameters for blocks, as prisma was downloading blocks every time
icarus/db/blocks.it
2005/12/22: system uniprot ipi Corrections for various hypertext links. Note that you will have to merge the new versions of dbxref.i and href.i with your copies of these file in the SRSSITE directory
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2005/12/22: domo The data for domo is now provided as a gzipped file. This correction to domo.it will allow prisma to handle this correctly
icarus/db/domo.it
2005/12/21: geneseq Change so we use a 4 byte space to store entry identifiers, which is needed for nageneseqsupp (supplement to Thomson/Derwent geneseq) as it has now more than 16.8 million entries. After applying this change you will have to reindex nageneseqsupp (and any other database you have which use the same LibFormat as nageneseqsupp)
icarus/db/geneseqsuppcommon.i
2005/12/14: ensembl_mysql Adapted for Ensembl36
icarus/db/ensemblRDB.i
2005/12/09: embl Correction for link defintion between taxonomy and emblwgsrelease, for whci a wrong definition crept in in the previous update of this file
icarus/db/emblwgsrelease.i
2005/12/08: iprmatches Improved layout, especially if using Firefox.
srstags/srstags/web/views/iprmatchesentry/iprmatchesentry.jsp
srstags/srstags/web/views/iprmatchesentry/iprmatcheslist.jsp
2005/12/07: embl Change so we build the link between genbankwgs and emblwgsrelease in parts, as doing it in a single run requires too much memory
icarus/db/emblwgsrelease.i
2005/12/07: medline Fix for a bug which made srs using update dates rather than publication dates fpr the publication date index (pdt). After applying the fix you will have to re-index the pdt fields of medlinerelease and medlinenew, and rebuild the pdt sortsets for the different medline libraries
icarus/db/medlinecommon.i
2005/12/07: genbank refseq This patch fixes a problem with PubMed hypertext links in some GenBank / RefSeq entries. Replace genbankcommon.i with this version and run srssection to implement the fix.
icarus/db/genbankcommon.i
2005/12/07: uniprot ipi This patch fixes truncation of feature descriptions in certain records (e.g FINC_HUMAN). To apply, replace swissprot.is with this version and run wsrefresh. No reindexing is required.
icarus/db/swissprot.is
2005/12/06: genecards Correction to the genecards parser to cope with changed hypertext definitions for ensembl links. You will need this update if you update your href.i file
icarus/db/genecards.is
2005/12/06: ensembl_flat system Fix for problem with accessing the sequence features. Note that we shifted from using the ID as entryname, but are using the primary accession number, which change required you to completeley re-index ensembl (flatfile). Also a fix for hypertext links to the ensembl site. Note that the changed href.i file needs to be merged with your copy of this file in the SRSSITE directory
icarus/db/ensembl.i
icarus/db/ensembl.is
icarus/db/href.i
2005/12/05: unilib Unilib now uses a JSP to display the entry view rather than unilibentry.il
icarus/db/unilib.i
srstags/srstags/web/views/unilibentry/unilib.jsp
2005/12/05: uniref Uniref now uses a JSP to display the netry view rather than uniref.il
icarus/db/unirefcommon.i
srstags/srstags/web/views/unirefentry/uniref.jsp
2005/12/05: genecards Workaround for a bug where prisma gets confused by multiple reformatcommands with %d and %s in them
icarus/db/genecardstar.it
2005/12/02: pfam Changed id production to avoid duplicate ids for PFAM-C. To implement this fix you will have to re-index the id field of the PFAM-C database. To do this run srscheck -l pfamc; srsdo
icarus/db/pfamc.is
2005/12/02: system update external link details to LinkHub at Yale Bioinformatics for UNIPROT entries
icarus/db/dbxref.i
icarus/db/href.i
2005/11/30: interpro Added missing reference do resource object. This prevented prisma from downloading interpro
icarus/db/interpro.i
2005/11/30: dbest New JSP view
srstags/srstags/web/views/dbestentry/dbest.jsp
2005/11/30: dbest Updated for new entry view JSP
icarus/db/dbest.i
icarus/db/dbest.is
2005/11/25: ensembl_mysql The link to locuslink (requiredlib attribute) has been changed to entrezgene.
icarus/lion/packages/ensemblRDB.ip
2005/11/25: kegg Updated species list for the kegg databases
icarus/db/kegg_species.i
2005/11/25: system update EMBOSS url and version no.
icarus/db/packages.i
2005/11/24: Contain reactome15 updates
srstags/srstags/web/WEB-INF/srs.tld
2005/11/24: entrezgene Correction to the entrezgene synonym finder, so it will find aliases for gene symbols
icarus/db/entrezgene.i
2005/11/24: reactome New JSPs for reactome15
srstags/srstags/web/views/reactomeentry/compartment.jsp
srstags/srstags/web/views/reactomeentry/event.jsp
srstags/srstags/web/views/reactomeentry/event_hierarchy.jsp
srstags/srstags/web/views/reactomeentry/event_litref.jsp
srstags/srstags/web/views/reactomeentry/event_regulation.jsp
srstags/srstags/web/views/reactomeentry/event_relatedevents.jsp
srstags/srstags/web/views/reactomeentry/event_summation.jsp
srstags/srstags/web/views/reactomeentry/frontpage.jsp
srstags/srstags/web/views/reactomeentry/go.jsp
srstags/srstags/web/views/reactomeentry/intercept.jsp
srstags/srstags/web/views/reactomeentry/literatureref.jsp
srstags/srstags/web/views/reactomeentry/notevent.jsp
srstags/srstags/web/views/reactomeentry/person.jsp
srstags/srstags/web/views/reactomeentry/physicalentity.jsp
srstags/srstags/web/views/reactomeentry/reactomeentry.jsp
srstags/srstags/web/views/reactomeentry/referenceentity.jsp
srstags/srstags/web/views/reactomeentry/regulation.jsp
srstags/srstags/web/views/reactomeentry/event_hierarchyprint.jsp
2005/11/24: reactome New JSPs with reactome15
srstags/srstags/web/views/reactomeentry/intercept.jsp
2005/11/24: reactome New files for use with reactome15.
icarus/db/reactome.i
icarus/db/reactome_schema.i
icarus/db/reactome.is
icarus/db/reactome.it
icarus/db/reactome_datamodel.i
2005/11/24: ensembl New images used in reactome15.
srstags/srstags/web/images/reactomeline.png
srstags/srstags/web/images/reactomepathway.png
srstags/srstags/web/images/reactomereaction.png
2005/11/22: ensembl_mysql Updated for use with ensembl35
icarus/db/ensemblRDB.i
icarus/db/ensemblcommon.i
icarus/db/ensemblgenemodel.i
icarus/db/exondatamodel.i
2005/11/22: system update to include ENTREZGENE in $IDSearchLibraryList lookup list
icarus/db/quickSearchOptions.i
2005/11/18: uniprot Correction for the unpackcomamnds for uniprot
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
2005/11/18: system some libraries were by default enabled - this has now been corrected
icarus/db/srsdb.i
2005/11/17: system Kegg Gene links using the GenBank GID number and EntrezGene cross-references now link internally if it is possible to do so. In order for this change to take effect you will have to copy href.i to your SRSSITE directory and run srssection.
icarus/db/href.i
2005/11/17: entrezgene Remove the gen fleid and geneName loadAttr, which cause the finder to malfunction
icarus/db/entrezgene.i
2005/11/17: entrezgene comment out printName attribute in Synonym Finder
icarus/db/entrezgene.i
2005/11/16: system Added some code which prevents readseq from crashing if the last line of the data is not terminated with an end of line character
icarus/db/readseq.i
2005/11/16: hssp Changed the format of multiple alignments from color to clustal. This prevents certain HSSP entries from hanging as the colourisation is applied.
icarus/db/hssp.i
2005/11/16: uniprot ipi This patch corrects links from UniProt to the HSSP database
icarus/db/swissprot.is
2005/11/15: kegg New field PATHWAY, containing links to the PATHWAY database added to KEGGGENES_NA and KEGGGENES_AA. After adding these files to your installation you will need to build the new index using srscheck / srsdo.
icarus/db/kegggenes.i
icarus/db/kegggenes.is
2005/11/15: kegg Update to display the new field PATHWAY correctly in the entry view for the kegg genes (na and aa) database
icarus/db/kegggenes.i
icarus/db/kegggenes.is
srstags/srstags/web/views/kegggenesentry/kegggenesentry.jsp
2005/11/11: system transfac BindingFactor_Id and BindingFactorLink have been moved from tf*.i into srsgen.i.
icarus/db/srsgen.i
icarus/db/tfclass.i
icarus/db/tffactor.i
icarus/db/tfgene.i
2005/11/11: uniprot Change so prisma does not try to uncompress the reldat.txt file when it downloads a new version of uniprot
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
2005/11/11: system Fix for the collapsible sections functionality. The break in functionality was introduced by the last patch.
srstags/srstags/web/WEB-INF/tags/section.tag
2005/11/11: entrezgene add in Synonym Finder for Entrez Gene
icarus/db/entrezgene.i
2005/11/11: iprmatches javascript used by the iprmatches entry view
srstags/srstags/web/javascript/iprmatches.js
2005/11/09: system Temporary images created by entry views for UniProt, Entrez Gene and SWISSPFAM are written to SRSWWW/images/tmp by this fix. Previously they were being generated in SRSWWW/images.
srstags/srstags/web/WEB-INF/tags/alignmentImage.tag
srstags/srstags/web/WEB-INF/tags/featuretable.tag
srstags/srstags/web/WEB-INF/tags/geneproductimage.tag
2005/11/08: pdb Added Heterogen data table to parser and view
icarus/db/pdb.i
icarus/db/pdb.is
srstags/srstags/web/views/pdbentry/pdbentry.jsp
srstags/srstags/web/views/pdbentry/pdbhetatoms.jsp
2005/11/08: geneseq Correction for hypertext link insertion where in some cases a part of the patent description was included in the hypertext link
icarus/db/geneseqsupp.is
2005/11/07: iprmatches Added a missing link definition for the link between teh signature subentry and the parent
icarus/db/iprmatches.i
2005/11/04: transfac A debug statement has been removed.
icarus/db/tffactor.is
2005/11/04: ensembl_mysql Added LibLocs for the new species we support with ensembl 34: Pufferfish, chimp, fruitfly and mosquito
icarus/lion/packages/ensemblRDB.ip
2005/11/04: ensembl_mysql Change needed to work with the Mosquito data
icarus/db/exondatamodel.i
2005/11/04: kegg Change to allow for the new Orthlogy field in the lreaction data
icarus/db/lreaction.i
icarus/db/lreaction.is
srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp
2005/11/04: kegg Change to allow for the new pathway field in the kegg genes data
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
srstags/srstags/web/views/kegggenesentry/kegggenesentry.jsp
2005/11/04: uniprot ipi Correction for indexing the moleculetype field
icarus/db/swissprot.is
2005/11/04: emboss Fix for a problem where the web interface erroneously reported that garnier had failed
icarus/lion/emboss/garnier.i
icarus/lion/emboss/garnier.is
2005/11/04: ensembl_mysql Improved sequence display for ensembl exon sequences
srstags/srstags/web/views/exonsequences/seqs.jsp
2005/11/04: srscheck Removed setting of size attribute of FileDes object as this could incorrectly lead to reporting an absence of files in the online data directory in some circumstances.
icarus/workflows/coreCheckClasses.i
2005/11/04: transfac The seqlen production has been added for use in building tffactor feature images.
icarus/db/transfaccommon.is
2005/11/04: transfac The sequence length field (sl) has been added for use in building tffactor feature images.
icarus/db/tffactor.i
2005/11/04: transfac The sequence length field (sl) has been added.
icarus/db/tffragment.i
icarus/db/tfsite.i
2005/11/04: transfac The sequence length field has been added.
srstags/srstags/web/views/tffragmententry/tffragmententry.jsp
srstags/srstags/web/views/tfsiteentry/tfsiteentry.jsp
2005/11/04: transfac This file has been altered to reference the new features.jsp file which draws images of the features.
srstags/srstags/web/views/tffactorentry/tffactorentry.jsp
2005/11/04: transfac This new file draws images of the factor features.
srstags/srstags/web/views/tffactorentry/features.jsp
2005/11/04: ensembl_mysql Updated link definitions for Ensembl 34
icarus/db/ensemblRDB.i
icarus/db/ensemblcommon.i
2005/11/03: genecards Added instructions for updating genecards using prisma
icarus/db/genecards.i
2005/11/03: geneseq system Added support for the geneseq supplementary data. These were already available dor SRS7.1 but where omitted in the SRS8.1 distribution.
icarus/db/aageneseqsupp.i
icarus/db/aageneseqsupp.it
icarus/db/geneseqsupp.is
icarus/db/geneseqsuppcommon.i
icarus/db/nageneseqsupp.i
icarus/db/nageneseqsupp.it
icarus/db/srsdb.i
2005/11/03: system Addition of titleVar variable to allow passing of titles for sections as a variable.
srstags/srstags/web/WEB-INF/tags/section.tag
2005/11/03: kegg Modified download details so prisma will download the kegg databases from ftp.pathway.jp (if you are an academic, and use prisma, you will have to modify these in order to access the academic download site
icarus/db/kegggenes_na.it
icarus/db/kegggenome.it
icarus/db/keggorthology.it
icarus/db/lcompound.it
icarus/db/lenzyme.it
icarus/db/lglycan.it
icarus/db/lreaction.it
icarus/db/pathway.it
icarus/db/pathwaytar.it
2005/11/03: kegg Updated species lookup list for use with the kegg databases
icarus/db/kegg_species.i
2005/11/02: transfac A new link to tfsite has been added.
icarus/db/tfmatrix.i
2005/11/02: transfac A new production called bsitelink has been addded which grabs the tfsite IDs for the tfmatrix>tfsite link
icarus/db/transfaccommon.is
2005/11/01: interpro iprmatches A long overdue rewrite of the interpro parser, with improved indexing/accessibilty of various fields and better linking to other databases
icarus/db/interpro.i
icarus/db/interpro.is
icarus/db/interpro.it
icarus/db/iprmatches.i
srstags/srstags/web/views/interproentry/children.jsp
srstags/srstags/web/views/interproentry/class.jsp
srstags/srstags/web/views/interproentry/contains.jsp
srstags/srstags/web/views/interproentry/extdoc.jsp
srstags/srstags/web/views/interproentry/foundin.jsp
srstags/srstags/web/views/interproentry/interproentry.jsp
srstags/srstags/web/views/interproentry/members.jsp
srstags/srstags/web/views/interproentry/pubs.jsp
srstags/srstags/web/views/interproentry/strucdb.jsp
srstags/srstags/web/views/interproentry/taxdist.jsp
2005/11/01: system Added LibLoc structures for genecards, transpath and chebi - you will have to merge these changes with yor copy of srsdb.i in the SRSSITE directory
icarus/db/srsdb.i
2005/11/01: pfam Added a default entry view to the pfamseed database
icarus/db/pfamseed.i
2005/11/01: pfam Added a jsp based entryview to pfamhmm
icarus/db/pfamhmm.i
icarus/db/pfamhmm.is
2005/11/01: system Added anew field and a datatype - you will have to merge these changes with your copy of srsgen.i in the SRSSITE directory
icarus/db/srsgen.i
2005/11/01: go_xml Added commands so prisma will update the go (xml version) database
icarus/db/go.it
2005/11/01: medline Added comments to the medline database definitions for use in the web interface
icarus/db/medline.i
icarus/db/medlinecommon.i
icarus/db/medlinenewfiles.i
icarus/db/medlinerelease.i
icarus/db/medlineupdates.i
2005/11/01: pdb Added comments to the pdbmodel database definition for use in the web interface
icarus/db/pdbmodel.i
2005/11/01: genecards Added support for the genecards database. Please make sure that you also update srsdb.i, srsgen.i and href.i
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecards.it
icarus/db/genecards_datamodel.i
icarus/db/genecardstar.it
srstags/srstags/web/views/genecardsentry/genecardsentry.jsp
srstags/srstags/web/views/genecardsentry/genecardsexpression.jsp
srstags/srstags/web/views/genecardsentry/genecardsproteins.jsp
2005/11/01: transpath Added support for the transpath databases. Please make sure that you also update srsdb.i, srsgen.i and href.i
icarus/db/transpath_annotate.i
icarus/db/transpath_annotate.it
icarus/db/transpath_common.i
icarus/db/transpath_common.is
icarus/db/transpath_datamodel.i
icarus/db/transpath_gene.i
icarus/db/transpath_gene.it
icarus/db/transpath_molecule.i
icarus/db/transpath_molecule.it
icarus/db/transpath_pathway.i
icarus/db/transpath_pathway.it
icarus/db/transpath_reaction.i
icarus/db/transpath_reaction.it
icarus/db/transpath_reference.i
icarus/db/transpath_reference.it
srstags/srstags/web/views/transpathentry/transpathannotateentry.jsp
srstags/srstags/web/views/transpathentry/transpathgeneentry.jsp
srstags/srstags/web/views/transpathentry/transpathmoleculeentry.jsp
srstags/srstags/web/views/transpathentry/transpathpathwayentry.jsp
srstags/srstags/web/views/transpathentry/transpathreactionentry.jsp
srstags/srstags/web/views/transpathentry/transpathreferenceentry.jsp
2005/11/01: ensembl_mysql Change needed for ENsembl 34
srstags/srstags/web/views/chromosome/chromosome.jsp
srstags/srstags/web/views/transcriptentry/xrefs.jsp
2005/11/01: ensembl_mysql Change needed to support Ensembl Pufferfish data
icarus/db/ExonsandIntrons.il
2005/11/01: uniprot Change so prisma can extract the release number from the reldate.txt file which comes with the uniprot data
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
2005/11/01: geneseq Change so the nageneseqtar and aageneseqtar helper databases are no longer part of the sequence library group
icarus/db/aageneseq.i
icarus/db/nageneseq.i
2005/11/01: entrezgene Change so we no longer display multiple identical medline IDs. Note that this change uses functionality which is only available in SRS8.1.1 or later, so you may need to upgrade.
icarus/db/entrezgene.i
2005/11/01: prints Change to make sure that prisma does not download the new .kdat file from the download site
icarus/db/prints.it
2005/11/01: go_mysql Changes needed to handle the retrieval of interpro data, as this has changed with the new interpro parser
icarus/db/gotermdatamodel.i
icarus/db/goterms.i
2005/11/01: system Correction for misspelled concept defintion for Ensembl. Note that you hav to merge this change with your copy of this file in the SRSSITE directory
icarus/db/concepts.i
2005/11/01: ensembl_mysql Correction needed where we display interpro data with ensembl results, as we modified the interpro parser
icarus/db/ensemblproteinmodel.i
2005/11/01: genpept Correction to the command by prisma to obtain the release number
icarus/db/genpeptnew.it
2005/11/01: medline Corrections for the download details for medline
icarus/db/medlinenewfiles.it
icarus/db/medlinerelease.it
2005/11/01: blast Description field added to blast results databases. This contains the contents of the fasta header line allowing you to search this information
icarus/db/blastcommon.i
2005/11/01: embl Document object id links can contain angle brackets which break the export to PDF functionality. This parser fix addresses that issue.
icarus/db/embl.is
2005/11/01: blast Modification so patterns such as gnl|gn_rem_geno|AR689807 are recognised as genbank record
icarus/db/blast.is
2005/11/01: system Modification to our internal sequence format conversion tool so it can take lists of databases identiffiers (DB:ACCNO) as input
icarus/db/readseq.i
2005/11/01: dbsts Some time ago we disabled a number of fields in dbsts, as its irregular contents caused crashes when displaying the data. We have now re-enabled these fields, as the latest patch release of SRS8.1 (8.1.1.2) conatains a fixe, preventing these crashes. Ofcourse you will have to upgrade to SRS8.1.1.2 to use this
icarus/db/dbsts.i
icarus/db/dbsts.is
icarus/db/dbsts.it
srstags/srstags/web/views/dbstsentry/references.jsp
2005/11/01: fasta fixes to support FASTA header lines of form gi|xxx|gnl|xxx|xxx
icarus/db/fasta.is
2005/11/01: prosite increased stability for the commands used to update the prosite data for emboss
icarus/db/prosite.it
2005/11/01: rebase increased stability for the commands used to update the rebase data for embos and tacg
icarus/db/rebase.it
2005/11/01: train new view for the train database (a realtional database used for training)
srstags/srstags/web/views/train/trainentry.jsp
2005/11/01: ensembl_mysql update for Ensembl release 34
icarus/db/chromosomegraphic.i
2005/10/31: uniprot ipi Document object id links can contain angle brackets which break the export to PDF functionality. This parser fix addresses that issue and also corrects the link to PIR which occasionally did not work. Please note that you will also need the latest href.i copied into your SRSSITE directory for the PIR fix to work.
icarus/db/swissprot.is
2005/10/31: emboss Fix for a problem where SRS would wrongly report that an emboss application had failed
icarus/lion/emboss/afEmboss.is
icarus/lion/emboss/dan.is
icarus/lion/emboss/diffseq.is
icarus/lion/emboss/garnier.is
icarus/lion/emboss/iep.is
icarus/lion/emboss/pepinfo.is
icarus/lion/emboss/rfEmboss.is
2005/10/31: system Occasionally links to PIR would not work due a difference in the Id/Accession. This patch fixes that and should be applied in conjunction with the latest swissprot.is
icarus/db/href.i
2005/10/31: adding EnsEMBL readme
README.ensemblRDB
2005/10/31: ensembl_mysql changes for EnsEMBL version 34
srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp
srstags/srstags/web/views/exonsequences/exonentry.jsp
2005/10/31: ensembl_mysql changes for EnsEMBL version 34 support for Chimp, Fruitfly and Pufferfish has been added
icarus/db/OutputExons.il
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
icarus/db/UTRandCDS.il
icarus/db/ensemblRDB.i
icarus/db/ensemblaffymodel.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/ensemblhuman_cq.i
icarus/db/ensemblmouse_cq.i
icarus/db/ensemblrat_cq.i
icarus/db/exondatamodel.i
icarus/lion/packages/ensemblRDB.ip
2005/10/31: pdb taking out link to PROMOTIF as the URL doesnt exist anymore
srstags/srstags/web/views/pdbentry/pdblinks.jsp
2005/10/28: chebi adding chebi entry view
srstags/srstags/web/views/chebientry/chebientry.jsp
2005/10/28: chebi adding files necessary to enable the oracle version of the chebi database for SRS Relational customers
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
2005/10/28: transfac tin_bs_fields production has been modified slightly for new v9.3 data
icarus/db/tfgene.is
2005/10/27: transfac Some missing concepts from the link to EPD have been added.
icarus/db/tfsite.i
2005/10/27: transfac The tin_bf_fields and h_link productions have been altered to match transfac data version 9.3.
icarus/db/transfaccommon.is
2005/10/27: transfac h_bs and h_seqcom productions have been modified slightly and tin_ex_fields has been rearranged to work with transfac professional v9.3
icarus/db/tffactor.is
2005/10/27: transfac h_dr has been removed in favour of using h_link inside transfaccommon.is. Modified in line with changes in transfac professional v9.3
icarus/db/tfsite.is
2005/10/27: transfac tin_bs_fields production has been updated to work with transfac professional v9.3
icarus/db/tfgene.is
2005/10/24: pdb An new link to the enzyme database has been defined.
icarus/db/pdb.i
2005/10/24: pdb An new production called enzymelink has been added to grab enzyme IDs for use in linking to the enzyme database.
icarus/db/pdb.is
2005/10/24: uniprot DF_MoleculeType has been added in line with updates to data files.
icarus/db/swisscommon.i
2005/10/24: uniprot ipi The tin_ft_vals|ftid value has been changed so it no longer contains 'FTId=' in the token.
icarus/db/swissprot.is
2005/10/21: unigene Updating the ftp display information.
icarus/db/unigene.it
2005/10/19: system A Tffragment LibLoc has been added.
icarus/db/srsdb.i
2005/10/19: system Added hrefs for residR and comeR (Rea), tffragmentR (hoad) - updated from 81 branch.
icarus/db/href.i
2005/10/19: transfac Altered slightly to work with transfac professional v9.2
icarus/db/tfclass.is
icarus/db/tffactor.is
icarus/db/tffragment.i
icarus/db/tffragment.is
icarus/db/tfgene.is
icarus/db/tfmatrix.i
icarus/db/tfmatrix.is
icarus/db/tfsite.i
icarus/db/tfsite.is
2005/10/19: system BindingFactorID, SeqEnd and SeqStart SrsField objects have been added for use in transfac databases.
icarus/db/srsgen.i
2005/10/19: transfac Many productions have been removed so they can be drawn from the common transfaccommon.is file instead.
icarus/db/tfcell.is
2005/10/19: transfac This is a new file which contains productions common to the transfac group of libraries (tf*).
icarus/db/transfaccommon.is
2005/10/19: transfac Updated with 'more modern' JSP tags.
srstags/srstags/web/views/tfcellentry/tfcellentry.jsp
srstags/srstags/web/views/tfclassentry/tfclassentry.jsp
srstags/srstags/web/views/tffragmententry/tffragmententry.jsp
srstags/srstags/web/views/tfmatrixentry/tfmatrixentry.jsp
srstags/srstags/web/views/tfsiteentry/tfsiteentry.jsp
2005/10/19: transfac Updated with new binding regions and altered slightly to work with transfac professional v9.2
icarus/db/tfcell.i
icarus/db/tfclass.i
icarus/db/tffactor.i
icarus/db/tfgene.i
2005/10/19: transfac Updated with new binding regions section plus 'more modern' JSP tags.
srstags/srstags/web/views/tffactorentry/tffactorentry.jsp
srstags/srstags/web/views/tfgeneentry/tfgeneentry.jsp
2005/10/19: transfac Updated with new information from transfac professional v9.2
icarus/db/tfcell.it
icarus/db/tfclass.it
icarus/db/tffactor.it
icarus/db/tffragment.it
icarus/db/tfgene.it
icarus/db/tfmatrix.it
icarus/db/tfsite.it
2005/10/12: unigene uniseq Change to the .it files to allow for the fact the ncbi is now providing the unigene/uniseq/uniest data as .gz file, and no longer as .Z files.
icarus/db/unigene.it
icarus/db/uniseq.it
2005/10/12: uniprot Fixed display of Comments fields. To apply this patch replace the existing swissentry.jsp with this file. You may need to restart Tomcat and restart all your browser instances.
srstags/srstags/web/views/swissentry/swissentry.jsp
2005/10/12: blocks hypertext links to uniprot changed form accession to id
icarus/db/blocks.is
2005/10/07: system Added new lookup for cross-references to TAIR. To apply this patch copy dbxref.i to your SRSSITE directory and run srssection.
icarus/db/dbxref.i
2005/10/06: kegg Added 3 new fields for display: Inhibitor, Cofactor and Effector. To apply this patch you must obtain the latest lenzyme.i and lenzyme.is files.
srstags/srstags/web/views/lenzymeentry/lenzymeentry.jsp
2005/10/06: kegg Added 3 new fields: Inhibitor, Cofactor and Effector. To apply this patch obtain both lenzyme.i and lenzyme.is and the latest lenzyme JSP view file. You will need to re-index LENZYME once you have these files in your installation and have run srssection.
icarus/db/lenzyme.i
icarus/db/lenzyme.is
2005/10/06: fasta Correction for a token name specified for showing the fasta run details
icarus/db/fastacommon.i
2005/10/06: fasta Correction so we index/display the init and topscores correctly, and a change to allow for parenthesis in the description line of the fasta headers
icarus/db/fasta.is
2005/10/06: psiblast minor correction for parsing psiblast results - preventing a non-fatal parsing error
icarus/db/psiblast.is
2005/10/06: psiblast removed the -g option as it is no longer used by psiblast
icarus/db/psiblast.i
2005/10/05: system Intact and Transpath library names changed.
icarus/db/href.i
2005/10/04: emboss Change to allow for more than 9 images to be generated by emboss programs
icarus/lion/emboss/embossGraphFile.is
2005/10/04: go_xml Updated for latest data release.
srstags/srstags/web/views/goentry/goentry.jsp
2005/10/04: go_xml go_mysql Updated for new data release.
icarus/db/go.i
icarus/db/go.is
icarus/db/go.it
icarus/db/go_datamodel.i
2005/10/03: kegg Added support for display of Disease field. NOTE: You must have the latest kegggenome.i / kegggenome.is file for this patch to work. In addition to running srssection you will have to restart all your web browser instances.
srstags/srstags/web/views/kegggenomeentry/kegggenomeentry.jsp
2005/10/03: kegg Added support for indexing the Disease field and corrected indexing of the DB origin field and Source field. You will need to run srssection and reindex the kegg genome database. You will also need the latest kegggenomentry.jsp to see the changes on the web interface.
icarus/db/kegggenome.i
icarus/db/kegggenome.is
2005/10/03: system New hrefs added for updated parsers: Intact, Genecards, GO (xml), Transpath.
icarus/db/href.i
2005/10/03: kegg Update of KEGG species file. Several new species acronyms have been added
icarus/db/kegg_species.i
2005/09/23: ribRowHighlightLightGreyBgColor and ribRowHighlightDarkGreyBgColor have been added for use in iprmatches list view.
srstags/srstags/web/WEB-INF/themes/ebi/theme_ebi.jsp
srstags/srstags/web/WEB-INF/themes/srs81/theme_81.jsp
srstags/srstags/web/WEB-INF/themes/srs81v2/theme_81v2.jsp
srstags/srstags/web/WEB-INF/themes/srs81v3/theme_81v3.jsp
2005/09/22: geneseq Updated because empty country fields didn't have their cells displayed.
srstags/srstags/web/views/aageneseqentry/priority.jsp
2005/09/22: geneseq Updated in line with priority.jsp being updated.
srstags/srstags/web/views/aageneseqentry/patent.jsp
srstags/srstags/web/views/nageneseqentry/patent.jsp
srstags/srstags/web/views/nageneseqentry/priority.jsp
2005/09/20: dbgss This file has been updated due to parser changes which make use of the standard parser more.
icarus/db/dbgss.i
2005/09/20: dbgss This file has been updated in line with the updates to the parser.
srstags/srstags/web/views/dbgssentry/dbgss.jsp
2005/09/20: dbgss This parser has been updated making use of the standard parser more.
icarus/db/dbgss.is
2005/09/16: epd A new dataclass field had been added. Values are standard or preliminary.
icarus/db/epd.i
2005/09/16: epd A new token called dataclass has been added.
icarus/db/epd.is
2005/09/16: system The DF_DataClass has been added for use in epd.
icarus/db/srsgen.i
2005/09/16: epd guiInfo:$GI_CheckList has been added to the DF_DataClass field for use in the extended query form.
icarus/db/epd.i
2005/09/15: pfam The loader and view objects used for the entry view of pfam A, B and seed have been modified to provide a better range and format of data to be used with the new pfam jsps.
icarus/db/pfam.i
2005/09/15: pfam This file has been updated to provide better formatted data for the pfam A, B and seed entry views (jsps). The link production has been amended so links can be build to prodom and prositedoc.
icarus/db/pfam.is
2005/09/13: uniprot ipi Added HTML markup for cross-reference to ENSEMBL Vega. You also need the latest href.i and dbxref.i for this patch.
icarus/db/swissprot.is
2005/09/13: system Added link definitions for cross-referencing ENSEMBL Vega. Copy this file to your site directory and run srssection.
icarus/db/dbxref.i
icarus/db/href.i
2005/09/13: refseq As daily updates are now the only way of obtaining updates the settings for the previous update procedure have been removed to avoid confusion.
icarus/db/refseqpnew.it
2005/09/13: refseq As the ncbi is no longer providing the cumulative upddates file for refseq(p)new, change the prisma configuration to use the refseq(p)files helper libraries to remove duplicates (the same mechanism is ued for genbanknew and emblnew).
icarus/db/refseqnew.it
2005/09/13: pfam New entry view which displays the structure of the pfam A,B and seed entry and references the publishers which sit inside refs.jsp.
srstags/srstags/web/views/pfamentry/pfamentry.jsp
2005/09/13: pfam New jsp entry view to display the pfamhmm data.
srstags/srstags/web/views/pfamhmmentry/pfamhmmentry.jsp
2005/09/13: pir The loadAttr for the description field has been changed because it didn't work previously.
icarus/db/pir.i
2005/09/13: pfam This file displays the citations, and is referenced from within pfamentry.jsp.
srstags/srstags/web/views/pfamentry/refs.jsp
2005/09/12: pfam New links have been added to prodom and prositedoc.
icarus/db/pfamb.i
2005/09/12: blocks The description has been updated with a new description of how BLOCKS is made currently.
icarus/db/blocks.it
2005/09/12: rebase The rd production has been altered so for multiple targets, each target has its position and length saved for indexing.
icarus/db/rebase.is
2005/09/12: pfam The type field has been changed from using GI_MultiSelect (visible on extended query form) to GI_CheckList.
icarus/db/pfama.i
2005/09/09: epd FTP and WWW urls have been added to this page for display purposes.
icarus/db/epd.it
2005/09/09: uniprot The CommentType field has had its indexToken changed so now the CommentType index will contain phrases such as subcellular location rather than individual words.
icarus/db/swisscommon.i
2005/09/09: blocks The getReleaseCommand has been changed so the Version, rather than the Release is extracted in the command.
icarus/db/blocks.it
2005/09/09: pir The pir parser was saving the description line twice. This meant it was doubling up in the pir text entry view. The fields|des field has been removed from the parser because it was not being used.
icarus/db/pir.is
2005/09/08: blocks The ignore attribute has been removed from the syntax object.
icarus/db/blocks.i
2005/09/08: blocks The motif production tag has been modified so it matches hyperlinked motifs and also the h_motif production has been modified so it actually matches prosite IDs.
icarus/db/blocks.is
2005/09/07: prosite A checkbox has been added to the skipflag field for use in the extended query form, since this field only has one value.
icarus/db/prosite.i
2005/09/07: embl A hyphen has been added to the reg expression defining the crerel token so it can grab the right version number for imgt.
icarus/db/embl.is
2005/09/07: uniprot A www link to www.uniprot.org had a double quotes character in the wrong place so the link was not visible.
icarus/db/uniprot_swissprot.it
2005/09/07: uniprot A www link to www.uniprpt.org had a double quotes character in the wrong place so the link was not visible.
icarus/db/uniprot_trembl.it
2005/09/07: rebase In the TargetPosition field definition, the field index has been changed from integer to string. This means ? characters now appear in the index.
icarus/db/rebase.i
2005/09/07: embl The date production has been modified for imgt since the create date in imgt is specified by the word 'arrived' rather than 'Created'.
icarus/db/embl.is
2005/08/26: system Added \r to the exclusion list in the tag production to make it compatible with parsing the ENZYME database.
icarus/db/standard.is
2005/08/26: refseq As the ncbi has stopped providing the cumulative update files for refseqnew and refseqpnew, we now need to use the daily updates. This requires the enabling of the refseqfiles and refseqpfiles helper libraries (to handle the download, and provide the helper library which is used to remove duplicates (ie previous updates of updates)). The change in the refseq(p)new.it files make sure that prisma will not download files for refseq(p)new, but relies on refseq(p)files for this
icarus/db/refseqnew.it
icarus/db/refseqpnew.it
2005/08/25: bind Commented out a number of Link definitions as the Cross-References no longer appear in the underlying XML data file.
icarus/db/bindinteraction.i
2005/08/24: dbest Changed order of characters in regular expression so that '-' appears last. This prevents interpreting the '-' character as a range search operator.
icarus/db/dbest.is
2005/08/24: genbank refseq This fix applies if you are using refseqfiles and refseqpfiles to obtain daily updates for RefSeq and RefSeq proteins respectively. Without this fix the filtering out of duplicate entries may not work. To apply, replace the files genbank.is and gbnewfiles.is with the patched versions and reindex refseq(p)files, refseq(p)new and refseq(p).
icarus/db/gbnewfiles.is
icarus/db/genbank.is
2005/08/22: dbest This patch fixes the problem where some EST names are not indexed due to brackets in their name.
icarus/db/dbest.is
2005/08/18: system Change to the short name in use for the Omim field in entrezgene, (was omim, is now mim) as it was causing a clash in indexnames between the index of the omim field, and the link index between entrezgene and omim. Note that you will have to merge the change with your copy of srsgen.i in SRSSITE, and that you will have to rebuild the mim index of entrezgene and the link indx between omim and entrezgene
icarus/db/srsgen.i
2005/08/15: system Parses searches noew which contain multiple databases and also databases containing numbers (uniref family).
logs/logcount.is
2005/08/12: embl genbank refseq Changes neede to handle embl entries with multiple organism lines
icarus/db/embl.is
icarus/db/emblcommon.i
icarus/db/gbemblcommon.i
icarus/db/genbank.is
srstags/srstags/web/views/dnadbentry/dnadbentry.jsp
2005/08/12: blast Small change for better handling of blast results where users have submitted multiple sequences
icarus/db/blast.is
2005/08/11: ensembl_mysql Updates for ensembl release 32
icarus/lion/packages/ensemblRDB.ip
2005/08/10: go_mysql Added download instructions for the goterm (mysql) data for use with prisma
icarus/db/goterms.it
2005/08/10: epd genbank genpept go_xml kegg prosite rhdb uniprot uniref Added getreleasecommands so the release version will be set within SRS whenever these databases are updated
icarus/db/epd.it
icarus/db/genbankrelease.it
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.it
icarus/db/go.it
icarus/db/pathway.it
icarus/db/prosite.it
icarus/db/prositedoc.it
icarus/db/rhdb.it
icarus/db/rhexp.it
icarus/db/rhmap.it
icarus/db/rhpanel.it
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
icarus/db/uniref100.it
icarus/db/uniref50.it
icarus/db/uniref90.it
2005/08/10: blocks Added reformatting commands to generate datafiles used for emboss, and added a getreleasecommand to set the release version in SRS whenever blocks is updated
icarus/db/blocks.it
2005/08/10: prints Added reformatting commands to generate datafiles used for emboss, and added a getreleasecommand to set the release version in SRS whenever rebase is updated
icarus/db/prints.it
2005/08/10: prosite Added reformatting commands to generate datafiles used for prositesearch and emboss, and added a getreleasecommand to set the release whenever prosite is updated
icarus/db/prosite.it
2005/08/10: rebase Added reformatting commands to generate datafiles used for tacg (restrictionmap) and emboss, and added a getreleasecommand to set the release version in SRS whenever rebase is updated
icarus/db/rebase.it
2005/08/10: system Added support for links to hugo (hgnc) which have started to appear in uniprot and ipi. Please note that you will have to merge dbxref.i with your copy of that file in the SRSSITE directory
icarus/db/dbxref.i
2005/08/10: pfam system Added support for the Clan section of pfam (pfamc). Please not that you will have to merge the changes in srsdb.i with your copy of srsdb.i in the SRSSITE directory
icarus/db/pfamc.i
icarus/db/pfamc.is
icarus/db/pfamc.it
icarus/db/srsdb.i
2005/08/10: ipi Change to use the primary accession number as identifier rather than the ID. This brings ipi in line with the uniprot databases
icarus/db/ipi.i
2005/08/10: uniprot Corrected a misspelling in the names for the links subentries
icarus/db/uniprot.i
icarus/db/uniprot_trembl.i
2005/08/10: system Modified all external hypertext links so they will open into a new window. This behaviour can be controlled by setting the variable hreftarget in the srsdb.i file. With its default setting, target=_blank each link will open into a new window. If you remove the hreftarget variable or leave it an empty string, external links will open in the SRS window (old behaviour). You can also set it to open in a specific window by specifying something like target=srsexternal. Nore that you have to merge href.i and srsdb.i with your copy of these files in the SRSSITE directory
icarus/db/href.i
icarus/db/srsdb.i
2005/08/10: iprmatches system Replaced the layout script used to display iprmatches data with a jsp based view. Nothe that the changes in srsdb.i need to be merged with your copy of this file in the SRSSITE directory
icarus/db/iprmatches.i
icarus/db/iprmatches.is
icarus/db/srsdb.i
srstags/srstags/web/views/iprmatchesentry/iprmatchesentry.jsp
srstags/srstags/web/views/iprmatchesentry/iprmatcheslist.jsp
2005/08/10: ensembl_mysql Updates for ensembl release 32
icarus/db/ExonsandIntrons.il
icarus/db/OutputExons.il
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
icarus/db/UTRandCDS.il
icarus/db/ensemblRDB.i
icarus/db/ensemblRDB.it
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/ensemblhuman_cq.i
icarus/db/ensemblmouse_cq.i
icarus/db/ensemblproteinmodel.i
icarus/db/ensemblrat_cq.i
icarus/db/exondatamodel.i
srstags/srstags/web/views/ensemblproteinentry/proteinentry.jsp
srstags/srstags/web/views/exonsequences/seqs.jsp
srstags/srstags/web/views/transcriptentry/xrefs.jsp
2005/08/10: kegg added support for the new database source and origin fields
icarus/db/kegggenome.i
icarus/db/kegggenome.is
srstags/srstags/web/views/kegggenomeentry/kegggenomeentry.jsp
2005/08/10: go_mysql small modification in the gegenproducts database description
icarus/db/gogeneproducts.it
2005/08/09: uniprot ipi Change to make sure that the entry description is included in sequence objects generated for uniprot
icarus/db/swissprot.is
2005/08/09: system Correction needed to handle gcg formatted uniprot_swissprot entries correctly. Please note that you will have to merge/copy this new version of standard.is with your copy of this file in the SRSSITE directory
icarus/db/standard.is
2005/08/09: genbank embl refseq genpept Cosmetic change to the way descriprions are included in sequence objects generated for embl, genbank, refseq and genpept
icarus/db/gbemblcommon.is
icarus/db/genpept.is
2005/08/09: go_mysql DatabaseName short name was incorrect
srstags/srstags/web/views/GOTERM/geneproducts.jsp
2005/08/05: interpro Change in the microparser to ensure that the abstract is being displayed in the web interface
icarus/db/interpro.is
2005/08/05: entrezgene Change to allow for the fact that in some entrezgene entries the protein description field can be empty despite the presence of the relevant XML tags
icarus/db/entrezgene.is
2005/08/05: ensembl_mysql Changed query form to use correct field name and to search entrezgene instead of locuslink
srstags/srstags/web/views/chromosome/chromosome.jsp
2005/08/04: pfam Improved information displayed in the defaultview for pfamb, and added hypertext link to pfama from pfamb
icarus/db/pfam.is
icarus/db/pfamb.i
2005/08/02: pdbfinder Change to allwo for the new "T-Alternates" line in the data
icarus/db/pdbfinder.is
2005/08/02: ensembl_mysql Fix for incorrect display of some UTR5 regions and fix for incomplete display of exons/introns that fall over contig joins
icarus/db/exondatamodel.i
2005/08/02: ensembl_mysql The compara schema file is necessary to enable orthologue comparisons in ensembl
icarus/db/ensembl_compara_schema.i
2005/07/29: genbank embl refseq Correction for the handling of long feature key words (20 characters) which occur in imgt
icarus/db/gbemblcommon.is
2005/07/27: fasta Modified so ssearch now correctly displays the linked description and seqlength fields in the ssearch view.
icarus/db/fasta.is
2005/07/27: system uniprot ipi added missing hrefs needed for IPI database - the original url given for gene3dR is broken on external web site
icarus/db/href.i
icarus/db/swissprot.is
2005/07/26: genbank embl refseq Updated feature length (ftl) productions to match all formats.
icarus/db/gbemblcommon.is
2005/07/21: bind Change to the name of the pubmedid field, as the defintion was clashing with with another definition in srsgen.i, which caused problems when merging partial indices
icarus/db/bindcommon.i
2005/07/21: go_mysql fix for incorrect database short name in query form
srstags/srstags/web/views/GOTERM/geneproducts.jsp
2005/07/20: system Added missing (dummy) href definition for maize2dpage. Please not that you will have to merge the updated href.i file with your copy of href.i in the SRSSITE directory
icarus/db/href.i
2005/07/19: go_xml Added an internal link for navigating within the go-tree structure, and updated the go.it file as the go download site now again allows for downloads by ftp
icarus/db/go.i
icarus/db/go.it
2005/07/19: bind Added indexing parallellization for bind, so it will not try to index bind in one index command, and add/corrected download instructions for SRS prisma
icarus/db/bindcommon_datamodel.i
icarus/db/bindcomplex.i
icarus/db/bindcomplex.it
icarus/db/bindinteraction.i
icarus/db/bindpathway.i
icarus/db/bindpathway.it
2005/07/19: geneseq Added support for Indian patents and added a subentry for priorities
icarus/db/aageneseq.i
icarus/db/geneseq.is
icarus/db/nageneseq.i
srstags/srstags/web/views/aageneseqentry/patent.jsp
srstags/srstags/web/views/aageneseqentry/priority.jsp
srstags/srstags/web/views/nageneseqentry/patent.jsp
srstags/srstags/web/views/nageneseqentry/priority.jsp
2005/07/19: kegg Added support for the new motif field in the kegg genes databases
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
icarus/db/lcommon.is
srstags/srstags/web/views/kegggenesentry/kegggenesentry.jsp
2005/07/19: uniest unigene uniseq As you may have noticed, the unigene data files are now distributed on the ncbi ftp site from different subdirectories for each species. We have modified the searchnames of unigene/uniest/uniseq to handle this, and have also changed the parser to derive the organism name from the subdirectory name. The old mechanism for deriving the organism name from the filename using the lookup table defined in unigenespecies.i still works, and the use of this mechanism is triggered by putting the unigenespecies.i file in the SRSSITE directory (note that we will stop maintaining this file). Also modified the .it files so prisma handles the download from subdirectories properly. Note that you will have to update SRSLION/prisma/remoteConnection.i from http://downloads.lionbio.co.uk/downloads/prisma4_dist/prisma_latest/icarus/lion/prisma for this to work, and that this update for prisma requires you to have upgraded to SRS8.1.1
icarus/db/uniest.i
icarus/db/uniest.is
icarus/db/uniest.it
icarus/db/unigene.i
icarus/db/unigene.is
icarus/db/unigene.it
icarus/db/uniseq.i
icarus/db/uniseq.is
icarus/db/uniseq.it
2005/07/19: uniprot ipi Change so we don't include the terminating . on the organism line with the organism name
icarus/db/swissprot.is
2005/07/19: taxonomy Change to the trimming of trailing spaces
srstags/srstags/web/views/taxonomyentry/taxonomyentry.jsp
2005/07/19: medline Changed the medlinenewfiles helper library to type:hidden, so end-users don't see it
icarus/db/medlinenewfiles.i
2005/07/19: uniref Changed the species field of the uniref datasets to an organism field to bring it more in line with the other databases
icarus/db/uniref.is
icarus/db/unirefcommon.i
2005/07/19: go_xml Changes to allow for the fact the go associatin data may ort may not be present and changes in the jsp files layou (non-fuctional)
srstags/srstags/web/views/goentry/goentry.jsp
srstags/srstags/web/views/goentry/gorelatives.jsp
2005/07/19: system Correction for the name of the paracel blast package
icarus/db/packages.i
2005/07/19: unilib Correction for the subentry id structure used for unilib to reflect that it no longer contains the Library Id. Without this fix it is not possible to retrieve subentries
icarus/db/unilib.i
2005/07/19: embl Correction to the remote name translation pattern used by prisma, so it will not try to rename a "gz" ovvuring in the middle of a filename
icarus/db/emblwgsnew.it
icarus/db/emblwgsrelease.it
2005/07/19: geneseq system bind blast blocks dbest dbgss dbsts domo embl ensembl_flat ensembl_mysql entrezgene enzyme epd fasta fssp genbank geneticcode genpept go_xml go_mysql hmmer interpro iprmatches kegg nrl3d pdb pdbfinder pfam prints prosite psiblast rebase refseq rhdb transfac uniest unigene uniprot uniref uniseq userdna userprotein emboss dssp hssp imgt ipi locuslink omim pir prodom prositesearch tacg taxonomy unilib Corrections for internal hypertext links used on the library/application information pages
icarus/db/aageneseq.it
icarus/db/aageneseqtar.it
icarus/db/appdemo.it
icarus/db/apptest.it
icarus/db/bindcomplex.it
icarus/db/bindpathway.it
icarus/db/blastn.it
icarus/db/blastp.it
icarus/db/blastx.it
icarus/db/blocks.it
icarus/db/dbest.it
icarus/db/dbgss.it
icarus/db/dbsts.it
icarus/db/domo.it
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
icarus/db/emblrelease.it
icarus/db/emblwgsnew.it
icarus/db/emblwgsrelease.it
icarus/db/ensembl.it
icarus/db/ensemblRDB.it
icarus/db/entrezgene.it
icarus/db/enzyme.it
icarus/db/epd.it
icarus/db/fasta.it
icarus/db/fastx.it
icarus/db/fasty.it
icarus/db/fssp.it
icarus/db/genbanknew.it
icarus/db/genbankrelease.it
icarus/db/genbankwgs.it
icarus/db/general.it
icarus/db/geneticcode.it
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.it
icarus/db/go.it
icarus/db/gogeneproducts.it
icarus/db/goterms.it
icarus/db/gpnewfiles.it
icarus/db/hmmbuild.it
icarus/db/hmmpfam.it
icarus/db/hmmsearch.it
icarus/db/interpro.it
icarus/db/iprmatches.it
icarus/db/lcompound.it
icarus/db/lenzyme.it
icarus/db/lglycan.it
icarus/db/lreaction.it
icarus/db/nageneseq.it
icarus/db/nageneseqtar.it
icarus/db/nfasta.it
icarus/db/nrl3d.it
icarus/db/pathway.it
icarus/db/pathwaytar.it
icarus/db/pdb.it
icarus/db/pdbfinder.it
icarus/db/pdbmodel.it
icarus/db/pfama.it
icarus/db/pfamb.it
icarus/db/pfamhmm.it
icarus/db/pfamseed.it
icarus/db/prints.it
icarus/db/prosite.it
icarus/db/prositedoc.it
icarus/db/psiblast.it
icarus/db/rebase.it
icarus/db/refseqnew.it
icarus/db/refseqpnew.it
icarus/db/refseqrelease.it
icarus/db/rhdb.it
icarus/db/rhexp.it
icarus/db/rhmap.it
icarus/db/rhpanel.it
icarus/db/ssearch.it
icarus/db/swisspfam.it
icarus/db/tblastn.it
icarus/db/tblastx.it
icarus/db/tfasta.it
icarus/db/tfastx.it
icarus/db/tfasty.it
icarus/db/tfcell.it
icarus/db/tfclass.it
icarus/db/tffactor.it
icarus/db/tfgene.it
icarus/db/tfmatrix.it
icarus/db/tfsite.it
icarus/db/uniest.it
icarus/db/unigene.it
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
icarus/db/uniref100.it
icarus/db/uniref50.it
icarus/db/uniref90.it
icarus/db/uniseq.it
icarus/db/userdna.it
icarus/db/userprotein.it
icarus/lion/emboss/antigenic.it
icarus/lion/emboss/backtranseq.it
icarus/lion/emboss/biosedn.it
icarus/lion/emboss/biosedp.it
icarus/lion/emboss/btwisted.it
icarus/lion/emboss/cai.it
icarus/lion/emboss/chaos.it
icarus/lion/emboss/charge.it
icarus/lion/emboss/checktrans.it
icarus/lion/emboss/chips.it
icarus/lion/emboss/compseqn.it
icarus/lion/emboss/compseqp.it
icarus/lion/emboss/consn.it
icarus/lion/emboss/consp.it
icarus/lion/emboss/cpgplot.it
icarus/lion/emboss/cpgreport.it
icarus/lion/emboss/cusp.it
icarus/lion/emboss/cutseqn.it
icarus/lion/emboss/cutseqp.it
icarus/lion/emboss/dan.it
icarus/lion/emboss/degapseqn.it
icarus/lion/emboss/degapseqp.it
icarus/lion/emboss/descseqn.it
icarus/lion/emboss/descseqp.it
icarus/lion/emboss/diffseqn.it
icarus/lion/emboss/diffseqp.it
icarus/lion/emboss/digest.it
icarus/lion/emboss/distmatn.it
icarus/lion/emboss/distmatp.it
icarus/lion/emboss/dotmatchern.it
icarus/lion/emboss/dotmatcherp.it
icarus/lion/emboss/dotpathn.it
icarus/lion/emboss/dotpathp.it
icarus/lion/emboss/dottupn.it
icarus/lion/emboss/dottupp.it
icarus/lion/emboss/dreg.it
icarus/lion/emboss/einverted.it
icarus/lion/emboss/eprimer3.it
icarus/lion/emboss/eprimers.it
icarus/lion/emboss/equicktandem.it
icarus/lion/emboss/est2genome.it
icarus/lion/emboss/etandem.it
icarus/lion/emboss/extractseqn.it
icarus/lion/emboss/extractseqp.it
icarus/lion/emboss/freakn.it
icarus/lion/emboss/freakp.it
icarus/lion/emboss/fuzznuc.it
icarus/lion/emboss/fuzzpro.it
icarus/lion/emboss/fuzztran.it
icarus/lion/emboss/garnier.it
icarus/lion/emboss/geecee.it
icarus/lion/emboss/getorf.it
icarus/lion/emboss/helixturnhelix.it
icarus/lion/emboss/hmoment.it
icarus/lion/emboss/iep.it
icarus/lion/emboss/infoalignn.it
icarus/lion/emboss/infoalignp.it
icarus/lion/emboss/infoseqn.it
icarus/lion/emboss/infoseqp.it
icarus/lion/emboss/isochore.it
icarus/lion/emboss/marscan.it
icarus/lion/emboss/maskseqn.it
icarus/lion/emboss/maskseqp.it
icarus/lion/emboss/matchern.it
icarus/lion/emboss/matcherp.it
icarus/lion/emboss/megamerger.it
icarus/lion/emboss/merger.it
icarus/lion/emboss/msbarn.it
icarus/lion/emboss/msbarp.it
icarus/lion/emboss/needlen.it
icarus/lion/emboss/needlep.it
icarus/lion/emboss/newcpgreport.it
icarus/lion/emboss/newcpgseek.it
icarus/lion/emboss/octanol.i
icarus/lion/emboss/octanol.it
icarus/lion/emboss/palindrome.it
icarus/lion/emboss/pasteseqn.it
icarus/lion/emboss/pasteseqp.it
icarus/lion/emboss/patmatdb.it
icarus/lion/emboss/patmatmotifs.it
icarus/lion/emboss/pepcoil.it
icarus/lion/emboss/pepinfo.it
icarus/lion/emboss/pepnet.it
icarus/lion/emboss/pepstats.it
icarus/lion/emboss/pepwheel.it
icarus/lion/emboss/pepwindow.i
icarus/lion/emboss/pepwindow.it
icarus/lion/emboss/pepwindowall.i
icarus/lion/emboss/pepwindowall.it
icarus/lion/emboss/plotconn.it
icarus/lion/emboss/plotconp.it
icarus/lion/emboss/plotorf.i
icarus/lion/emboss/plotorf.it
icarus/lion/emboss/polydotn.it
icarus/lion/emboss/polydotp.it
icarus/lion/emboss/preg.it
icarus/lion/emboss/prettyplotn.it
icarus/lion/emboss/prettyplotp.it
icarus/lion/emboss/prettyseq.it
icarus/lion/emboss/pscan.it
icarus/lion/emboss/recoder.it
icarus/lion/emboss/remap.it
icarus/lion/emboss/restover.it
icarus/lion/emboss/restrict.it
icarus/lion/emboss/revseq.it
icarus/lion/emboss/seqmatchalln.it
icarus/lion/emboss/seqmatchallp.it
icarus/lion/emboss/seqretn.it
icarus/lion/emboss/seqretp.it
icarus/lion/emboss/showalignn.it
icarus/lion/emboss/showalignp.it
icarus/lion/emboss/showorf.it
icarus/lion/emboss/showseqn.it
icarus/lion/emboss/showseqp.it
icarus/lion/emboss/shuffleseqn.it
icarus/lion/emboss/shuffleseqp.it
icarus/lion/emboss/sigcleave.it
icarus/lion/emboss/silent.it
icarus/lion/emboss/sixpack.it
icarus/lion/emboss/splittern.it
icarus/lion/emboss/splitterp.it
icarus/lion/emboss/stretchern.it
icarus/lion/emboss/stretcherp.it
icarus/lion/emboss/supermatchern.it
icarus/lion/emboss/supermatcherp.it
icarus/lion/emboss/syco.it
icarus/lion/emboss/tfscan.it
icarus/lion/emboss/tmap.it
icarus/lion/emboss/transeq.it
icarus/lion/emboss/trimest.it
icarus/lion/emboss/trimseqn.it
icarus/lion/emboss/trimseqp.it
icarus/lion/emboss/unionn.it
icarus/lion/emboss/unionp.it
icarus/lion/emboss/vectorstrip.it
icarus/lion/emboss/watern.it
icarus/lion/emboss/waterp.it
icarus/lion/emboss/wobble.it
icarus/lion/emboss/wordcount.it
icarus/lion/emboss/wordmatchn.it
icarus/lion/emboss/wordmatchp.it
icarus/db/dssp.it
icarus/db/embl.it
icarus/db/emblcontigs.it
icarus/db/embltpa.it
icarus/db/emblwgs.it
icarus/db/gbnewfiles.it
icarus/db/genbank.it
icarus/db/genpept.it
icarus/db/hssp.it
icarus/db/imgt.it
icarus/db/ipi.it
icarus/db/locuslink.it
icarus/db/omim.it
icarus/db/pir.it
icarus/db/prodom.it
icarus/db/prositesearch.it
icarus/db/rebcomm.it
icarus/db/refseq.it
icarus/db/refseqfiles.it
icarus/db/refseqp.it
icarus/db/refseqpfiles.it
icarus/db/refseqprelease.it
icarus/db/restrictionmap.it
icarus/db/taxonomy.it
icarus/db/template.it
icarus/db/unilib.it
icarus/db/uniprot.it
2005/07/19: kegg Fix for correct display of glycan values
srstags/srstags/web/views/lcompoundentry/lcompoundlinks.jsp
2005/07/19: entrezgene Following customer feedback received after the first implementation of entrezgene, we have made a number of changes: Added fields for gene symbol, gene alias, ec-number, unigene id, omim id; restructured the values extracted from the organism field so values with a qualifier are indexed/presented that way - eg "host:homo sapiens" or "strain:P23123", Corrected misalignment of markers display in the entryview
icarus/db/entrezgene.i
icarus/db/entrezgene.is
2005/07/19: entrezgene Removed a new uniquevalues atrribute, as it is not yet supported by the kernel
icarus/db/entrezgene.i
2005/07/19: ensembl_mysql system Update for ensembl release 31. New features include the use of the ensembl compara dataset for the retrieval of ortholog information, a graphical view of protein features and the display of utr and exon regions in the transcript view.
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
icarus/db/chromosomegraphic.i
icarus/db/ensemblRDB.i
icarus/db/ensemblaffymodel.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/ensemblproteinmodel.i
icarus/db/exondatamodel.i
icarus/db/rdbaccess.i
icarus/lion/packages/ensemblRDB.ip
srstags/srstags/web/views/chromosome/chromosome.jsp
srstags/srstags/web/views/ensemblaffyentry/affyentry.jsp
srstags/srstags/web/views/ensemblgeneentry/geneentry.jsp
srstags/srstags/web/views/ensemblgeneentry/neighbours.jsp
srstags/srstags/web/views/ensemblgeneentry/orths.jsp
srstags/srstags/web/views/ensemblproteinentry/proteinentry.jsp
srstags/srstags/web/views/ensemblproteinentry/proteinrefs.jsp
srstags/srstags/web/views/exonsequences/exonentry.jsp
srstags/srstags/web/views/exonsequences/seqs.jsp
srstags/srstags/web/views/transcriptentry/transcriptentry.jsp
srstags/srstags/web/views/transcriptentry/xrefs.jsp
2005/07/19: kegg Updated the species lookup tables used for the kegg databases
icarus/db/kegg_species.i
2005/07/19: system Various updates, including new field defintions in use in other databases, and making entrezgene the default library for gene databases - these files will have to be merged with your copies of these files in the SRSSITE directory
icarus/db/concepts.i
icarus/db/href.i
icarus/db/srsgen.i
2005/07/12: system This parser now recognises log files with or without a session header.
logs/loguse.is
2005/07/11: system Updated to work properly in srs8.x
logs/loguse.i
logs/loguse.is
2005/07/08: system The BlastGraphical loader has been added to this file (and removed from blastcommon.i) so it can be accessed by fasta.i and ssearch.i
icarus/db/loader.i
2005/07/08: system The FastaGraphical view has been added to this file (and removed from fastacommon.i) and renamed as the HomologyView so it can be accessed by blast databases.
icarus/db/views.i
2005/07/08: fasta The HomologyView and loader have now been moved into views.i and loader.i respectively so they can be accessed by blast views.
icarus/db/fastacommon.i
2005/07/08: blast The blastgraphical view in this file now references a loader in loaders.i (rather than a loader within this file). This has been done so fasta views can access the same loader.
icarus/db/blastcommon.i
2005/07/08: blast This file now references the HomologyView (in views.i) rather than the BlastGraphical view so that the radio buttons for redrawing the view work properly.
icarus/db/blastgraphic.il
2005/07/08: fasta This file now references the HomologyView as its default view, which can be found in views.i
icarus/db/fasta.i
icarus/db/ssearch.i
2005/07/06: uniref DF_Species has been changed to DF_Organism in uniref so the BlastGraphical view doesn't fall over.
icarus/db/unirefcommon.i
2005/07/06: uniref Field code spc has been changed to org in uniref so the BlastGraphical view doesn't fall over.
icarus/db/uniref.is
2005/07/05: geneseq IN:India has been added to the list of countries.
icarus/db/geneseq.is
2005/07/05: fasta Updated with a new defaultView attribute (Library class) pointing to the FastaGraphical view.
icarus/db/fasta.i
icarus/db/ssearch.i
2005/07/05: fasta Updated with new FastaGraphical View and loader which are the same as the BlastGraphical view and loader, only called something else.
icarus/db/fastacommon.i
2005/07/05: fasta Updated with new productions and a tin for use with the new FastaGraphical view.
icarus/db/fasta.is
2005/07/05: blast Updated with references to FASTA format databases so the view displays with all the relevant information.
icarus/db/blastgraphic.il
2005/06/29: dbsts Commented out the submitter section for the dbsts entry view, as the current version of dbsts contains nasty control characters in that section which break the SRS web interface
icarus/db/dbsts.i
srstags/srstags/web/views/dbstsentry/references.jsp
2005/06/29: system Correction for wrong refseq database references in the definition for the FastaFtSeqs loader. Note that you will have to merge thisupdated loader.i file with your copy of this file in the SRSSITE directory
icarus/db/loader.i
2005/06/17: affymetrix Added for NetAffx databases.
srstags/srstags/web/views/affymetrix/affyentry.jsp
srstags/srstags/web/views/affymetrix/affyfunc.jsp
srstags/srstags/web/views/affymetrix/affyref.jsp
srstags/srstags/web/views/affymetrix/affyseq.jsp
2005/06/17: system Added uniprotkb/swiss-prot and uniprotkb/trembl for IPI.
icarus/db/dbxref.i
2005/06/09: entrezgene go accession is now padded instead of being turned into a regular expression
icarus/db/entrezgene.is
2005/06/08: genbank embl refseq Modification to the acc production to handle entries which have text in the line of accession numbers.
icarus/db/gbemblcommon.is
2005/06/08: ensembl_mysql fix for change in field name from DB_Name to TranslationDB_Name
srstags/srstags/web/views/chromosome/chromosome.jsp
2005/06/08: ensembl_mysql fix for zebrafish sequences
icarus/db/exondatamodel.i
Cutoff for inclusion in the srs8.1.1 release - updates listed below are included in SRS 8.1.1 tarballs
2005/06/02: srscheck 1 fixed problem where a field-level access restriction was not dealt with gracefully. The current behaviour is to warn that a field is not accessible, and to ignore that field during the rest of the check and build process. 2. fixed error message where missing directory was not named 3. added further checking for whether searchName/fileType combination retrieves a correct list of files
icarus/workflows/coreCheckClasses.i
2005/06/02: srscheck 1. added further checking for whether searchName/fileType combination retrieves a correct list of files
icarus/workflows/getSystemLibs.i
2005/06/02: srscheck 1. dded further checking for whether searchName/fileType combination retrieves a correct list of files, 2. fixed problem where a field-level access restriction was not dealt with gracefully. The current behaviour is to warn that a field is not accessible, and to ignore that field during the rest of the check and build process.
icarus/workflows/checkLocalFiles.i
2005/06/02: system Added hypertext links to the feature keys.
srstags/srstags/web/WEB-INF/tags/featuretable.tag
2005/06/02: srscheck added additional rm -f to local copy commands to deal with ln command on solaris that ignores -f argument
icarus/workflows/srsCheckMain.i
2005/06/02: srscheck added further checking for whether searchName/fileType combination retrieves a correct list of files
icarus/workflows/buildPhase.i
2005/06/02: srscheck fixed problem where links were not always built from one newly built dependent library to its parent if the parent library did not have online indices
icarus/workflows/linkPhase.i
2005/05/26: interpro Added CVS headers, a check for medline so we inert the correct hypertext link and added a link to the smart database
srstags/srstags/web/views/interproentry/interproentry.jsp
2005/05/26: system Added a check so we don't attempt to use an undefined library in the queick search page
icarus/db/quickSearchOptions.i
2005/05/26: domo hssp prodom Added a loadercache for faster data retrieval for the description view
icarus/db/domo.i
icarus/db/hssp.i
icarus/db/prodom.i
2005/05/26: embl genbank refseq Added comments, describing the way sequences and features are handled, and fixed a link for the feature table in the entryview used by EMBL/GenBank/Refseq
srstags/srstags/web/views/dnadbentry/dnadbentry.jsp
srstags/srstags/web/views/dnadbentry/features.jsp
2005/05/26: ensembl_mysql system Added support for Zebrafish, Dog and C.Elegans to the ensembl dataset (MySQL version). Note that if you have already installed the ensembl package (SRSLION/packages/ensemblRDB.ip), the easiest way of adding thes new datasets is to at the relevant LibLocs manually to your SRSSITE/srsdb.i file. Note that the new version of concepts.i needs to be merged with your copy of that file in the SRSSITE directory. We also added two new views, Peptidefastaseq and Transcriptfastaseq which allow the retrieval of transcripts and peptides on the command line with getz
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
icarus/db/concepts.i
icarus/db/ensemblRDB.i
icarus/db/ensemblRDB.it
icarus/db/ensemblaffymodel.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/exondatamodel.i
srstags/srstags/web/views/ensemblaffyentry/affyentry.jsp
srstags/srstags/web/views/ensemblgeneentry/geneentry.jsp
srstags/srstags/web/views/ensemblgeneentry/orths.jsp
srstags/srstags/web/views/ensemblmarker/marker.jsp
srstags/srstags/web/views/ensemblproteinentry/proteinentry.jsp
srstags/srstags/web/views/exonsequences/exonentry.jsp
srstags/srstags/web/views/transcriptentry/transcriptentry.jsp
srstags/srstags/web/views/transcriptentry/xrefs.jsp
2005/05/26: prosite Added support for the new version field in prosite
icarus/db/prosite.i
icarus/db/prosite.is
2005/05/26: blast system Change so blast is no longer using the sequence input and database selection options from fasta, but is using its own (defined in localApplicationOptions.i). Note that you will have to merge the localApplicationOptions.i file with your copy of this file in SRSSITE, and that if you have a heavily customized blast setup, you may have to go through all these files to incorporate these changes
icarus/db/blastcommon.i
icarus/db/blastgraphic.il
icarus/db/blastn.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/localApplicationOptions.i
icarus/db/tblastn.i
icarus/db/tblastx.i
2005/05/26: kegg Change so we do not display the reference section if there are no references
srstags/srstags/web/views/lenzymeentry/lenzymeentry.jsp
2005/05/26: system Change to allow for links to NCBI CDS, Legiolist, swiss model and trome, which have started to appear in uniprot and ipi. Please note that you have to merge the new versions of href.i and dbxref.i with your copies of these files in the SRSSITE directory
icarus/db/dbxref.i
icarus/db/href.i
2005/05/26: taxonomy Changes needed for the taxonomy entry view
icarus/db/treemodel.i
2005/05/26: dbsts Correction for a wrong tag closure
srstags/srstags/web/views/dbstsentry/primer.jsp
2005/05/26: kegg Correction to the comment describing the database
icarus/db/lcompound.i
icarus/db/lenzyme.i
icarus/db/lglycan.i
icarus/db/lreaction.i
2005/05/26: entrezgene Fix so hypertext links are inserted in the entrezgene entry view. Note that this update will only work with SRS8.1.1, and will break the entrezgene entryview if used with SRS8.1
srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2005/05/26: go_mysql Improved performance for linking by using microparsing
icarus/db/goparse.is
icarus/db/goterms.i
2005/05/26: system Removed a (harmless) duplicate presence of the LibLoc for entrezgene
icarus/db/srsdb.i
2005/05/26: fasta removed an erroneous double quote from the fasta command definition
icarus/db/nfasta.i
2005/05/23: genbank embl refseq Correction for accession number indexing for databases in genbank format, as it was not recognizing accessionnumber ranges properly
icarus/db/gbemblcommon.is
2005/05/20: uniest unigene uniseq Added support for Macaca mulatta for the unigene/uniseq/uniest datasets
icarus/db/unigenespecies.i
2005/05/20: unigene Added support for the new poly A field
icarus/db/unigene.i
icarus/db/unigene.is
2005/05/20: kegg Allow for a large nober of new/modified species in the kegg databases
icarus/db/kegg_species.i
2005/05/20: uniref Allow for the fact that uniref now labels UniProt references as UniProtKB
icarus/db/uniref.is
2005/05/20: geneseq Change to make sure we display the entire content of the patent section line
icarus/db/aageneseq.i
icarus/db/nageneseq.i
2005/05/19: system Added a new package describing the Paracel BLAST suite of tools.
icarus/db/packages.i
2005/05/13: kegg Added over 30 species to the lookup list of species used when indexing / retrieving data from the KEGG family of databases
icarus/db/kegg_species.i
2005/05/05: genbank refseq Altered the tin_ref_aut production so that where a full stop character is given instead of a list of authors it is not displayed or indexed.
icarus/db/genbank.is
2005/05/05: system Change to handle the case where there are no reference authors for a citation - this change displays the citation in the correct format
srstags/srstags/web/WEB-INF/tags/referencetable.tag
2005/05/05: embl Cross-Reference links to GDB were not being constructed correctly. This patch fixes that issue
icarus/db/embl.is
2005/05/05: medline Fix to address spaces in author names breaking hypertext links.
icarus/db/medline.is
2005/05/05: uniprot Fixed a problem where UniProt subentries were not being displayed due to an incorrect token name in the field definition
icarus/db/swisscommon.i
2005/05/03: genbank embl refseq Modified the acc production to fix a parsing bug.
icarus/db/gbemblcommon.is
2005/05/03: bind fix for bind pathway entry 13056 which contains an interaction id that doesn't exist
icarus/db/bindcommon_datamodel.i
2005/04/29: ensembl_mysql Added a test to remove the dependency on having the GOGENPROD library enabled
icarus/db/ensemblgenemodel.i
2005/04/29: kegg Corrected instructions in the pathway.i file for enabling pathway to work under Tomcat.
icarus/db/pathway.i
2005/04/29: kegg Link to DBlink corrected. Correct URL now used.
icarus/db/pathway.is
2005/04/29: kegg changed entry view to be type:entry so that it cannot be selected in the results view menu which could result in a loader error in a session
icarus/db/keggorthology.i
2005/04/29: kegg changed entry view to be type:entry so that it cannot be selected in the results view menu which resulted in a loader error
icarus/db/kegggenes.i
2005/04/29: enzyme removed unwanted text from cofactor display
srstags/srstags/web/views/enzymeentry/enzymeentry.jsp
2005/04/28: ensembl_mysql added hypertextlinks for gene neighbours
srstags/srstags/web/views/ensemblgeneentry/neighbours.jsp
2005/04/28: kegg Added several new Kegg species to the list of abbreviations
icarus/db/kegg_species.i
2005/04/28: entrezgene Fixed the GO links so that a variable number of zeros at the start of the GO accession is catered for
icarus/db/entrezgene.is
2005/04/28: genbank embl refseq Removed debugging output from the acc production.
icarus/db/gbemblcommon.is
2005/04/28: kegg added a spacer in Enzyme
srstags/srstags/web/views/lglycanentry/lglycanlinks.jsp
2005/04/28: system added geneID field
icarus/db/srsgen.i
2005/04/28: ensembl adding rat and mouse images for ensembl canned query pages
srstags/srstags/web/images/mouse_chromosomes.gif
srstags/srstags/web/images/rat_chromosomes.gif
2005/04/28: kegg fix for enzyme loader and also name box
srstags/srstags/web/views/lreactionentry/lreactgeneral.jsp
2005/04/28: kegg fixes for loader change and also a test to display references if they exist
srstags/srstags/web/views/lglycanentry/lglycanentry.jsp
srstags/srstags/web/views/lglycanentry/lglycangeneral.jsp
srstags/srstags/web/views/lglycanentry/lglycanlinks.jsp
2005/04/28: ensembl_mysql version in notes changed and canned query forms uncommented
icarus/lion/packages/ensemblRDB.ip
2005/04/28: kegg view fix for reaction/enzyme loader change
srstags/srstags/web/views/lcompoundentry/lcompoundlinks.jsp
2005/04/21: bind cath embl genbank refseq go_xml interpro locuslink medline omim rhdb uniprot pfam Added CVS headers to the files, and added some comments - al to make maintenance easier. There are no functional changes
srstags/srstags/web/views/bindentry/bindcomplexentry.jsp
srstags/srstags/web/views/bindentry/bindinteractionentry.jsp
srstags/srstags/web/views/bindentry/bindpathwayentry.jsp
srstags/srstags/web/views/cathentry/cathdomainseq.jsp
srstags/srstags/web/views/cathentry/cathentry.jsp
srstags/srstags/web/views/dnadbentry/dnadbentry.jsp
srstags/srstags/web/views/dnadbentry/features.jsp
srstags/srstags/web/views/dnadbentry/sequence.jsp
srstags/srstags/web/views/goentry/goentry.jsp
srstags/srstags/web/views/goentry/gogeneral.jsp
srstags/srstags/web/views/goentry/gorelatives.jsp
srstags/srstags/web/views/interproentry/interproentry.jsp
srstags/srstags/web/views/locuslinkentry/genbank.jsp
srstags/srstags/web/views/locuslinkentry/general.jsp
srstags/srstags/web/views/locuslinkentry/locuslinkentry.jsp
srstags/srstags/web/views/locuslinkentry/map.jsp
srstags/srstags/web/views/locuslinkentry/ontology.jsp
srstags/srstags/web/views/locuslinkentry/sequence.jsp
srstags/srstags/web/views/locuslinkentry/www.jsp
srstags/srstags/web/views/medlineentry/medlineresults.jsp
srstags/srstags/web/views/omimentry/omimentry.jsp
srstags/srstags/web/views/rhmapentry/references.jsp
srstags/srstags/web/views/swissentry/swissentry.jsp
srstags/srstags/web/views/swisspfamentry/swisspfamentry.jsp
srstags/srstags/web/views/medlineentry/medlineentry.jsp
2005/04/21: system Added a REQUIRED_OPTS option group for use with emboss applications. Please note that you will have to merge this change with your version of srsgen.i in the SRSSITE directory
icarus/db/srsgen.i
2005/04/21: bind Added additional fields (GenInfo Id, Molecule Type and Molecule Id) for the bind subunits
icarus/db/bindcomplex.i
srstags/srstags/web/views/bindentry/bindcomplexentry.jsp
2005/04/21: pir Condensed the pir entry view into a single file for ease of maintainability. The files sequence.jsp, references.jsp, genetics.jsp, features.jsp, function.jsp, index.jsp and general.jsp in the SRSTAGS/web/views/pirentry are no longer needed
srstags/srstags/web/views/pirentry/pirentry.jsp
2005/04/21: prints Condensed the prints entry view into 3 files for eas of maintainability. The files references.jsp, index.jsp and general.jsp in the SRSTAGS/web/views/printsentry are no longer needed
srstags/srstags/web/views/printsentry/fingerdetails.jsp
srstags/srstags/web/views/printsentry/printsentry.jsp
srstags/srstags/web/views/printsentry/sequences.jsp
2005/04/21: uniseq Condensed the uniseq entry view into a single file for ease of maintainability. The files unissequence.jsp, index.jsp and unisgeneral.jsp in the SRSTAGS/web/views/uniseqsentry are no longer needed
srstags/srstags/web/views/uniseqentry/uniseqentry.jsp
2005/04/21: entrezgene Removed code which used functionality not yet available in srs8.1 (It will be available in SRS8.1.1, which is due within a few weeks. The consequence of this is that there are very few hypertext links available in the entrezgene entry view
srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2005/04/20: taxonomy A completely new entryview for the taxonomy database
icarus/db/taxonomy.i
icarus/db/treemodel.i
srstags/srstags/web/images/tree.gif
srstags/srstags/web/views/taxonomyentry/taxonomyentry.jsp
2005/04/20: kegg Added Support for LIGAND images and more provide a more descriptive text for cross-references
icarus/db/lcommon.is
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/lenzyme.i
icarus/db/lglycan.i
icarus/db/lglycan.is
icarus/db/lreaction.i
icarus/db/lreaction.is
2005/04/20: medline Added a new publication date field, corrected table display of dates so they are displayed as DD-MMM-YYYY and made query result sortable by dates and journal title
icarus/db/medline.is
icarus/db/medlinecommon.i
2005/04/20: clustalw Added an extra loader to use with clustalw, and added group links for easy linking to search database
icarus/db/clustalw.i
icarus/db/clustalwcommon.i
icarus/db/nclustalw.i
2005/04/20: entrezgene system Added support for the entrezgene database. Please read the notes at the top of the entrezgene.i file for more information about this inplementation. Note that the updated href.i and srsdb.i files need to be merged with your copies of these files in the SRSSITE directory
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/entrezgene.it
icarus/db/entrezgene_dm.i
icarus/db/href.i
icarus/db/srsdb.i
srstags/srstags/web/WEB-INF/srs.tld
srstags/srstags/web/WEB-INF/tags/geneproductimage.tag
srstags/srstags/web/WEB-INF/tags/nestedDataDisplay.tag
srstags/srstags/web/views/entrezgeneentry/entrezgeneentry.jsp
2005/04/20: fssp Complete rewrite using the standard parser and using more efficient html insertion. Also added a jsp based entryview
icarus/db/fssp.i
icarus/db/fssp.is
icarus/db/fssp.it
srstags/srstags/web/views/fsspentry/fsspentry.jsp
2005/04/20: blast Fix for an out of range bug when viewing multiple blast runs, fix for a bug where blastn was ignoring a -S option, added a queryDes production for pulling out description information, and added a few lightweight loaders for use with the WsObjects API
icarus/db/blast.is
icarus/db/blastcommon.i
icarus/db/blastgraphic.il
icarus/db/blastn.i
2005/04/20: prosite Fix for indexing of the title and reference fields, and consolidated the entry view in a single jsp file. The urls.jsp, references.jsp, index.jsp, general.jsp and copyright.jsp files in SRSTAGS/web/views/prositedocentry are now obsolete
icarus/db/prositedoc.i
icarus/db/prositedoc.is
srstags/srstags/web/views/prositedocentry/prositedocentry.jsp
2005/04/20: go_mysql Fixes for the GOTERM database (relational version): Change in the entry view so we don't insert hypertext links to libraries we don't have. Improvements to the way the schema is displayed in visad, and changed the Definition field into Description field for display in the SRS description view
icarus/db/goterms.i
icarus/db/goterms_schema.i
srstags/srstags/web/views/GOTERM/geneproducts.jsp
srstags/srstags/web/views/GOTERM/gotermentry.jsp
srstags/srstags/web/views/GOTERM/references.jsp
2005/04/20: embl system Following various requests, we have extended the embl parser so it can work with the daily embl update files without getting duplicates originating from updates of updates. The mechanism is identical to the one used for the genbank daily updates, requiring the use of a emblnewfiles helper library. A full explanation can be found in the comments in the emblnewfiles.i file. If you would like to continue to use the cumulative update file you do not have to change anything. If you would like to start to use the daily update files, enable the emblnewfiles library (and read the instructions in emblnewfiles.i). If you use prisma, and you would like to use the daily update files, you need to modify the emblnew.it file (see comments in that file). Note that the new version of srsdb.i needs to be merged with your copy of srsdb.i in the SRSSITE directory
icarus/db/embl.is
icarus/db/emblnew.it
icarus/db/emblnewfiles.i
icarus/db/emblnewfiles.is
icarus/db/emblnewfiles.it
icarus/db/srsdb.i
2005/04/20: system Miscellenous data display improvements
srstags/srstags/web/WEB-INF/tags/citation.tag
srstags/srstags/web/WEB-INF/tags/citationFormat.tag
srstags/srstags/web/WEB-INF/tags/customResultFormat.tag
2005/04/20: embl genbank refseq Modification to allow for accession number ranges which have started to appear in the main sequence databases. We now take strings like A00001-A00003 and index it as A00001 A00002 A00003
icarus/db/emblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbankcommon.i
2005/04/20: dssp Modified dssp entry view so a link to PDB is only displayed if the PDB database is enabled. Also consolidated the view into a single JSP file. The details.jsp, general.jsp, index.jsp and residueDetails.jsp files are now obsolete, and can be removed from the SRSTAGS/web/views/dsspentry directory
srstags/srstags/web/views/dsspentry/dsspentry.jsp
2005/04/20: emboss Removed a "echo -n" commands as it is not supported on solaris 8
icarus/lion/emboss/tmap.i
2005/04/20: ensembl_mysql Updates for ENSEMBL (mysql version) release 30. We also added canned queries for the rat and mouse section. If you have already enabled the RDB version of ENSEMBL in SRS, you need to edit the visadfiles.i file in SRSSITE, adding SRSDB:ensemblmouse_cq.i and SRSDB:ensembl_rat.i, in order to use the new canned queries
icarus/db/chromosomegraphic.i
icarus/db/ensemblRDB.i
icarus/db/ensemblcommon.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblhuman_cq.i
icarus/db/ensemblmouse_cq.i
icarus/db/ensemblrat_cq.i
icarus/lion/packages/ensemblRDB.ip
srstags/srstags/web/views/chromosome/chromosome.jsp
srstags/srstags/web/views/transcriptentry/transcriptentry.jsp
srstags/srstags/web/views/transcriptentry/xrefs.jsp
2005/04/20: srscheck fixed problem for srscheck and prisma where links were not always built rom one newly built dependent library to its parent if the parent library did not have online indices
icarus/workflows/linkPhase.i
2005/04/14: kegg Update to address duplicate IDs in PATHWAY. This update introduces an accession field to PATHWAY which holds the name of the file from which the entry came, this new field is now set as the id field for the library. This update requires the PATHWAY library to be re-indexed.
icarus/db/pathway.i
icarus/db/pathway.is
2005/04/11: pdb Modified site production to handle SITE IDs with 4 characters.
icarus/db/pdb.is
2005/04/08: psiblast add in test entries for quality report tool test
icarus/db/psiblast.it
2005/04/07: uniest unigene uniseq Added support for Schistoma japonicum and Phytophtora infestans for the unigene/uniseq/uniest databases
icarus/db/unigenespecies.i
2005/04/05: psiblast Correction for wrong command definition
icarus/db/psiblast.i
2005/03/29: locuslink Change to allow for "https" occuring in some urls in the locuslink data
icarus/db/locuslink.is
2005/03/29: prodom Corrected the complete omission of hypertext links in the links section
icarus/db/prodom.is
2005/03/23: geneseq Changed the userName and passWord attributes to specify $derwentUserName and $derwentPassWord, so that they may be specified elsewhere.
icarus/db/aageneseqtar.it
icarus/db/nageneseqtar.it
2005/03/17: clustalw Fixed a bug where the use of sub-lists in the $blastList name mapping table caused a type missmatch error.
icarus/db/clustalw.is
2005/03/16: kegg Modification to the regular expression used to extract the title from the references section to cope with new references in LCompound where the title does not end with a "." but instead ends with either a "?" or a "]"
icarus/db/lcommon.is
2005/03/07: embl Added missing parser for the emblnewfiles helper database, needed for working with the daily embl updates files
icarus/db/emblnewfiles.is
2005/03/04: fssp Hyperlinks from FSSP to FSSPmatches are generated if the FSSPmatches is enabled in SRS3D.
icarus/db/fssp.is